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Kuznetsova KG, Vašíček J, Skiadopoulou D, Molnes J, Udler M, Johansson S, Njølstad PR, Manning A, Vaudel M. Bioinformatics pipeline for the systematic mining genomic and proteomic variation linked to rare diseases: The example of monogenic diabetes. PLoS One 2024; 19:e0300350. [PMID: 38635808 PMCID: PMC11025945 DOI: 10.1371/journal.pone.0300350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/23/2024] [Indexed: 04/20/2024] Open
Abstract
Monogenic diabetes is characterized as a group of diseases caused by rare variants in single genes. Like for other rare diseases, multiple genes have been linked to monogenic diabetes with different measures of pathogenicity, but the information on the genes and variants is not unified among different resources, making it challenging to process them informatically. We have developed an automated pipeline for collecting and harmonizing data on genetic variants linked to monogenic diabetes. Furthermore, we have translated variant genetic sequences into protein sequences accounting for all protein isoforms and their variants. This allows researchers to consolidate information on variant genes and proteins linked to monogenic diabetes and facilitates their study using proteomics or structural biology. Our open and flexible implementation using Jupyter notebooks enables tailoring and modifying the pipeline and its application to other rare diseases.
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Affiliation(s)
- Ksenia G. Kuznetsova
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Jakub Vašíček
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Dafni Skiadopoulou
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Miriam Udler
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Alisa Manning
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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2
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Jaitner A, Vaudel M, Tsaneva-Atanasova K, Njølstad PR, Jacobsson B, Bowden J, Johansson S, Freathy RM. Smoking during pregnancy and its effect on placental weight: a Mendelian randomization study. BMC Pregnancy Childbirth 2024; 24:238. [PMID: 38575863 PMCID: PMC10993495 DOI: 10.1186/s12884-024-06431-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/17/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND The causal relationship between maternal smoking in pregnancy and reduced offspring birth weight is well established and is likely due to impaired placental function. However, observational studies have given conflicting results on the association between smoking and placental weight. We aimed to estimate the causal effect of newly pregnant mothers quitting smoking on their placental weight at the time of delivery. METHODS We used one-sample Mendelian randomization, drawing data from the Avon Longitudinal Study of Parents and Children (ALSPAC) (N = 690 to 804) and the Norwegian Mother, Father and Child Cohort Study (MoBa) (N = 4267 to 4606). The sample size depends on the smoking definition used for different analyses. The analysis was performed in pre-pregnancy smokers only, due to the specific role of the single-nucleotide polymorphism (SNP) rs1051730 (CHRNA5 - CHRNA3 - CHRNB4) in affecting smoking cessation but not initiation. RESULTS Fixed effect meta-analysis showed a 182 g [95%CI: 29,335] higher placental weight for pre-pregnancy smoking mothers who continued smoking at the beginning of pregnancy, compared with those who stopped smoking. Using the number of cigarettes smoked per day in the first trimester as the exposure, the causal effect on placental weight was 11 g [95%CI: 1,21] per cigarette per day. Similarly, smoking at the end of pregnancy was causally associated with higher placental weight. Using the residuals of birth weight regressed on placental weight as the outcome, we showed evidence of lower offspring birth weight relative to the placental weight, both for continuing smoking at the start of pregnancy as well as continuing smoking throughout pregnancy (change in z-score birth weight adjusted for z-score placental weight: -0.8 [95%CI: -1.6,-0.1]). CONCLUSION Our results suggest that continued smoking during pregnancy causes higher placental weights.
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Affiliation(s)
- Annika Jaitner
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics and Statistics, Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK
- EPSRC Hub for Quantitative Modelling in Healthcare University of Exeter, Exeter, UK
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Bo Jacobsson
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Gothenburg, Sweden
| | - Jack Bowden
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- Novo Nordisk Genetics Centre of Excellence, Oxford, UK
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Rachel M Freathy
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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Artaza H, Eriksson D, Lavrichenko K, Aranda-Guillén M, Bratland E, Vaudel M, Knappskog P, Husebye ES, Bensing S, Wolff ASB, Kämpe O, Røyrvik EC, Johansson S. Rare copy number variation in autoimmune Addison's disease. Front Immunol 2024; 15:1374499. [PMID: 38562931 PMCID: PMC10982488 DOI: 10.3389/fimmu.2024.1374499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Autoimmune Addison's disease (AAD) is a rare but life-threatening endocrine disorder caused by an autoimmune destruction of the adrenal cortex. A previous genome-wide association study (GWAS) has shown that common variants near immune-related genes, which mostly encode proteins participating in the immune response, affect the risk of developing this condition. However, little is known about the contribution of copy number variations (CNVs) to AAD susceptibility. We used the genome-wide genotyping data from Norwegian and Swedish individuals (1,182 cases and 3,810 controls) to investigate the putative role of CNVs in the AAD aetiology. Although the frequency of rare CNVs was similar between cases and controls, we observed that larger deletions (>1,000 kb) were more common among patients (OR = 4.23, 95% CI 1.85-9.66, p = 0.0002). Despite this, none of the large case-deletions were conclusively pathogenic, and the clinical presentation and an AAD-polygenic risk score were similar between cases with and without the large CNVs. Among deletions exclusive to individuals with AAD, we highlight two ultra-rare deletions in the genes LRBA and BCL2L11, which we speculate might have contributed to the polygenic risk in these carriers. In conclusion, rare CNVs do not appear to be a major cause of AAD but further studies are needed to ascertain the potential contribution of rare deletions to the polygenic load of AAD susceptibility.
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Affiliation(s)
- Haydee Artaza
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | - Daniel Eriksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Center for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
| | - Ksenia Lavrichenko
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Maribel Aranda-Guillén
- Center for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
| | - Eirik Bratland
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Knappskog
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Eystein S. Husebye
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sophie Bensing
- Department of Endocrinology, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Anette S. B. Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Olle Kämpe
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ellen C. Røyrvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Bergen, Norway
| | - Stefan Johansson
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
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4
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Helgeland Ø, Vaudel M, Sole-Navais P, Flatley C, Juodakis J, Bacelis J, Koløen IL, Knudsen GP, Johansson BB, Magnus P, Kjennerud TR, Juliusson PB, Stoltenberg C, Holmen OL, Andreassen OA, Jacobsson B, Njølstad PR, Johansson S. Author Correction: Characterization of the genetic architecture of infant and early childhood body mass index. Nat Metab 2024; 6:378. [PMID: 38337098 DOI: 10.1038/s42255-024-01004-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Affiliation(s)
- Øyvind Helgeland
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marc Vaudel
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Pol Sole-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christopher Flatley
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Julius Juodakis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ingvild L Koløen
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | | | - Bente B Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ted Reichborn Kjennerud
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Petur B Juliusson
- Department of Health Registry Research and Development, National Institute of Public Health, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | | | - Oddgeir L Holmen
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bo Jacobsson
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Pål R Njølstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
| | - Stefan Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
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5
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Beaumont RN, Flatley C, Vaudel M, Wu X, Chen J, Moen GH, Skotte L, Helgeland Ø, Solé-Navais P, Banasik K, Albiñana C, Ronkainen J, Fadista J, Stinson SE, Trajanoska K, Wang CA, Westergaard D, Srinivasan S, Sánchez-Soriano C, Bilbao JR, Allard C, Groleau M, Kuulasmaa T, Leirer DJ, White F, Jacques PÉ, Cheng H, Hao K, Andreassen OA, Åsvold BO, Atalay M, Bhatta L, Bouchard L, Brumpton BM, Brunak S, Bybjerg-Grauholm J, Ebbing C, Elliott P, Engelbrechtsen L, Erikstrup C, Estarlich M, Franks S, Gaillard R, Geller F, Grove J, Hougaard DM, Kajantie E, Morgen CS, Nohr EA, Nyegaard M, Palmer CNA, Pedersen OB, Rivadeneira F, Sebert S, Shields BM, Stoltenberg C, Surakka I, Thørner LW, Ullum H, Vaarasmaki M, Vilhjalmsson BJ, Willer CJ, Lakka TA, Gybel-Brask D, Bustamante M, Hansen T, Pearson ER, Reynolds RM, Ostrowski SR, Pennell CE, Jaddoe VWV, Felix JF, Hattersley AT, Melbye M, Lawlor DA, Hveem K, Werge T, Nielsen HS, Magnus P, Evans DM, Jacobsson B, Järvelin MR, Zhang G, Hivert MF, Johansson S, Freathy RM, Feenstra B, Njølstad PR. Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth. Nat Genet 2023; 55:1807-1819. [PMID: 37798380 PMCID: PMC10632150 DOI: 10.1038/s41588-023-01520-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/31/2023] [Indexed: 10/07/2023]
Abstract
A well-functioning placenta is essential for fetal and maternal health throughout pregnancy. Using placental weight as a proxy for placental growth, we report genome-wide association analyses in the fetal (n = 65,405), maternal (n = 61,228) and paternal (n = 52,392) genomes, yielding 40 independent association signals. Twenty-six signals are classified as fetal, four maternal and three fetal and maternal. A maternal parent-of-origin effect is seen near KCNQ1. Genetic correlation and colocalization analyses reveal overlap with birth weight genetics, but 12 loci are classified as predominantly or only affecting placental weight, with connections to placental development and morphology, and transport of antibodies and amino acids. Mendelian randomization analyses indicate that fetal genetically mediated higher placental weight is causally associated with preeclampsia risk and shorter gestational duration. Moreover, these analyses support the role of fetal insulin in regulating placental weight, providing a key link between fetal and placental growth.
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Affiliation(s)
- Robin N Beaumont
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Christopher Flatley
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Xiaoping Wu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Øyvind Helgeland
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Pol Solé-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Clara Albiñana
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | | | - João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sara Elizabeth Stinson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Carol A Wang
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Sundararajan Srinivasan
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | | | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain
| | - Catherine Allard
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marika Groleau
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Teemu Kuulasmaa
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Daniel J Leirer
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Frédérique White
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pierre-Étienne Jacques
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Haoxiang Cheng
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ke Hao
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Mustafa Atalay
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Laxmi Bhatta
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean-Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
| | - Ben Michael Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Cathrine Ebbing
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Line Engelbrechtsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Herlev Hospital, Herlev, Denmark
| | - Christian Erikstrup
- Department Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marisa Estarlich
- Faculty of Nursing and Chiropody, Universitat de València, C/Menendez Pelayo, Valencia, Spain
- Epidemiology and Environmental Health Joint Research Unit, Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Stephen Franks
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Romy Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine-Human Genetics and the iSEQ Center, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Eero Kajantie
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Camilla S Morgen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Ellen A Nohr
- Institute of Clinical research, University of Southern Denmark, Odense, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ole Birger Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sylvain Sebert
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | - Beverley M Shields
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Camilla Stoltenberg
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Lise Wegner Thørner
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | | | - Marja Vaarasmaki
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Department of Obstetrics and Gynaecology, Oulu University Hospital, Oulu, Finland
| | - Bjarni J Vilhjalmsson
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Dorte Gybel-Brask
- Psychotherapeutic Outpatient Clinic, Mental Health Services, Capital Region, Copenhagen, Denmark
| | - Mariona Bustamante
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ewan R Pearson
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Rebecca M Reynolds
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - Sisse R Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Craig E Pennell
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andrew T Hattersley
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Mads Melbye
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Deborah A Lawlor
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- Lundbeck Center for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Svarre Nielsen
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - David M Evans
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Rachel M Freathy
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
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6
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Burger B, Vaudel M, Barsnes H. Automated splitting into batches for observational biomedical studies with sequential processing. Biostatistics 2023; 24:1031-1044. [PMID: 35536588 PMCID: PMC10583723 DOI: 10.1093/biostatistics/kxac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 10/19/2023] Open
Abstract
Experimental design usually focuses on the setting where treatments and/or other aspects of interest can be manipulated. However, in observational biomedical studies with sequential processing, the set of available samples is often fixed, and the problem is thus rather the ordering and allocation of samples to batches such that comparisons between different treatments can be made with similar precision. In certain situations, this allocation can be done by hand, but this rapidly becomes impractical with more challenging cohort setups. Here, we present a fast and intuitive algorithm to generate balanced allocations of samples to batches for any single-variable model where the treatment variable is nominal. This greatly simplifies the grouping of samples into batches, makes the process reproducible, and provides a marked improvement over completely random allocations. The general challenges of allocation and why good solutions can be hard to find are also discussed, as well as potential extensions to multivariable settings.
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Affiliation(s)
- Bram Burger
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, 5008 Bergen, Norway, Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5020 Bergen, Norway, and Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Harald Barsnes
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, 5008 Bergen, Norway and Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
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7
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Skiadopoulou D, Vašíček J, Kuznetsova K, Bouyssié D, Käll L, Vaudel M. Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides. J Proteome Res 2023; 22:3190-3199. [PMID: 37656829 PMCID: PMC10563157 DOI: 10.1021/acs.jproteome.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 09/03/2023]
Abstract
Precision medicine focuses on adapting care to the individual profile of patients, for example, accounting for their unique genetic makeup. Being able to account for the effect of genetic variation on the proteome holds great promise toward this goal. However, identifying the protein products of genetic variation using mass spectrometry has proven very challenging. Here we show that the identification of variant peptides can be improved by the integration of retention time and fragmentation predictors into a unified proteogenomic pipeline. By combining these intrinsic peptide characteristics using the search-engine post-processor Percolator, we demonstrate improved discrimination power between correct and incorrect peptide-spectrum matches. Our results demonstrate that the drop in performance that is induced when expanding a protein sequence database can be compensated, hence enabling efficient identification of genetic variation products in proteomics data. We anticipate that this enhancement of proteogenomic pipelines can provide a more refined picture of the unique proteome of patients and thereby contribute to improving patient care.
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Affiliation(s)
- Dafni Skiadopoulou
- Mohn
Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020 Bergen, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, NO-5020 Bergen, Norway
| | - Jakub Vašíček
- Mohn
Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020 Bergen, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, NO-5020 Bergen, Norway
| | - Ksenia Kuznetsova
- Mohn
Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020 Bergen, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, NO-5020 Bergen, Norway
| | - David Bouyssié
- Institut
de Pharmacologie et de Biologie Structurale (IPBS), Université
de Toulouse, CNRS, Université Toulouse III—Paul Sabatier
(UT3), 31000 Toulouse, France
| | - Lukas Käll
- Science
for Life Laboratory, School of Engineering Sciences in Chemistry,
Biotechnology and Health, KTH Royal Institute
of Technology, SE-100 44 Stockholm, Sweden
| | - Marc Vaudel
- Mohn
Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020 Bergen, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, NO-5020 Bergen, Norway
- Department
of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, N-0213 Oslo, Norway
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8
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Hernández Sánchez LF, Burger B, Castro Campos RA, Johansson S, Njølstad PR, Barsnes H, Vaudel M. Extending protein interaction networks using proteoforms and small molecules. Bioinformatics 2023; 39:btad598. [PMID: 37756698 PMCID: PMC10564616 DOI: 10.1093/bioinformatics/btad598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 08/21/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023] Open
Abstract
MOTIVATION Biological network analysis for high-throughput biomedical data interpretation relies heavily on topological characteristics. Networks are commonly composed of nodes representing genes or proteins that are connected by edges when interacting. In this study, we use the rich information available in the Reactome pathway database to build biological networks accounting for small molecules and proteoforms modeled using protein isoforms and post-translational modifications to study the topological changes induced by this refinement of the network representation. RESULTS We find that improving the interactome modeling increases the number of nodes and interactions, but that isoform and post-translational modification annotation is still limited compared to what can be expected biologically. We also note that small molecule information can distort the topology of the network due to the high connectedness of these molecules, which does not necessarily represent the reality of biology. However, by restricting the connections of small molecules to the context of biochemical reactions, we find that these improve the overall connectedness of the network and reduce the prevalence of isolated components and nodes. Overall, changing the representation of the network alters the prevalence of articulation points and bridges globally but also within and across pathways. Hence, some molecules can gain or lose in biological importance depending on the level of detail of the representation of the biological system, which might in turn impact network-based studies of diseases or druggability. AVAILABILITY AND IMPLEMENTATION Networks are constructed based on data publicly available in the Reactome Pathway knowledgebase: reactome.org.
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Affiliation(s)
- Luis Francisco Hernández Sánchez
- Department of Clinical Science, Mohn Center for Diabetes Precision Medicine, University of Bergen, Bergen 5020, Norway
- Department of Medical Genetics, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen 5020, Norway
| | - Bram Burger
- Department of Clinical Science, Mohn Center for Diabetes Precision Medicine, University of Bergen, Bergen 5020, Norway
- Department of Medical Genetics, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen 5020, Norway
- Department of Biomedicine, Proteomics Unit, University of Bergen, Bergen 5020, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, Bergen 5020, Norway
| | | | - Stefan Johansson
- Department of Clinical Science, Mohn Center for Diabetes Precision Medicine, University of Bergen, Bergen 5020, Norway
- Department of Medical Genetics, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen 5020, Norway
| | - Pål Rasmus Njølstad
- Department of Clinical Science, Mohn Center for Diabetes Precision Medicine, University of Bergen, Bergen 5020, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen 5020, Norway
| | - Harald Barsnes
- Department of Biomedicine, Proteomics Unit, University of Bergen, Bergen 5020, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, Bergen 5020, Norway
| | - Marc Vaudel
- Department of Clinical Science, Mohn Center for Diabetes Precision Medicine, University of Bergen, Bergen 5020, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, Bergen 5020, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo 0213, Norway
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9
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Jaitner A, Vaudel M, Tsaneva-Atanasova K, Njølstad PR, Jacobsson B, Bowden J, Johansson S, Freathy RM. Smoking during pregnancy and its effect on placental weight: A Mendelian randomization study. medRxiv 2023:2023.08.24.23294537. [PMID: 37662288 PMCID: PMC10473803 DOI: 10.1101/2023.08.24.23294537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background The causal relationship between maternal smoking in pregnancy and reduced offspring birth weight is well established and is likely due to impaired placental function. However, observational studies have given conflicting results on the association between smoking and placental weight. We aimed to estimate the causal effect of newly pregnant mothers quitting smoking on their placental weight at the time of delivery. Methods We used one-sample Mendelian randomization, drawing data from the Avon Longitudinal Study of Parents and Children (ALSPAC) (up to N = 805) and the Norwegian Mother, Father and Child Cohort Study (MoBa) (up to N = 4475). The analysis was performed in pre-pregnancy smokers only, due to the specific role of the genetic instrument SNP rs1051730 (CHRNA5 - CHRNA3 - CHRNB4) in affecting smoking cessation but not initiation. Results Fixed effect meta-analysis showed a 175 g [95%CI: 16, 334] higher placental weight for pre-pregnancy smoking mothers who continued smoking at the beginning of pregnancy, compared with those who stopped smoking. Using the number of cigarettes smoked per day in the first trimester as the exposure, the causal estimate was a 12 g [95%CI: 2,22] higher placental weight per cigarette per day. Results were similar when the smoking exposures were measured at the end of pregnancy. Using the residuals of birth weight regressed on placental weight as the outcome, we showed weak evidence of lower offspring birth weight relative to the placental weight for continuing smoking. Conclusion Our results suggest that continued smoking during pregnancy causes higher placental weights.
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Affiliation(s)
- Annika Jaitner
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics and Statistics, Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK
- EPSRC Hub for Quantitative Modelling in Healthcare University of Exeter, Exeter, UK
| | - Pål R. Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Bo Jacobsson
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Gothenburg, Sweden
| | - Jack Bowden
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- Novo Nordisk Genetics Centre of Excellence, Oxford, UK
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Rachel M. Freathy
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
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10
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Solé-Navais P, Flatley C, Steinthorsdottir V, Vaudel M, Juodakis J, Chen J, Laisk T, LaBella AL, Westergaard D, Bacelis J, Brumpton B, Skotte L, Borges MC, Helgeland Ø, Mahajan A, Wielscher M, Lin F, Briggs C, Wang CA, Moen GH, Beaumont RN, Bradfield JP, Abraham A, Thorleifsson G, Gabrielsen ME, Ostrowski SR, Modzelewska D, Nohr EA, Hypponen E, Srivastava A, Talbot O, Allard C, Williams SM, Menon R, Shields BM, Sveinbjornsson G, Xu H, Melbye M, Lowe W, Bouchard L, Oken E, Pedersen OB, Gudbjartsson DF, Erikstrup C, Sørensen E, Lie RT, Teramo K, Hallman M, Juliusdottir T, Hakonarson H, Ullum H, Hattersley AT, Sletner L, Merialdi M, Rifas-Shiman SL, Steingrimsdottir T, Scholtens D, Power C, West J, Nyegaard M, Capra JA, Skogholt AH, Magnus P, Andreassen OA, Thorsteinsdottir U, Grant SFA, Qvigstad E, Pennell CE, Hivert MF, Hayes GM, Jarvelin MR, McCarthy MI, Lawlor DA, Nielsen HS, Mägi R, Rokas A, Hveem K, Stefansson K, Feenstra B, Njolstad P, Muglia LJ, Freathy RM, Johansson S, Zhang G, Jacobsson B. Author Correction: Genetic effects on the timing of parturition and links to fetal birth weight. Nat Genet 2023; 55:1250. [PMID: 37165137 PMCID: PMC10335921 DOI: 10.1038/s41588-023-01412-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Pol Solé-Navais
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden.
| | - Christopher Flatley
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | | | - Marc Vaudel
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Julius Juodakis
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Jonas Bacelis
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Ben Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Maria C Borges
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Øyvind Helgeland
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Frederick Lin
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Catherine Briggs
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Carol A Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Gunn-Helen Moen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Australia
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | | | - Abin Abraham
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Dominika Modzelewska
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Ellen A Nohr
- Research Unit of Gynecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Elina Hypponen
- Australian Centre for Precision Health, Uni Clinical & Health Sciences, University of South Australia, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Amit Srivastava
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Center for the Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Octavious Talbot
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Catherine Allard
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CHUS), Sherbrooke, Québec, Canada
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ramkumar Menon
- Department of Obstetrics and Gynaecology, University of Texas Medical Branch, Galveston, TX, USA
| | - Beverley M Shields
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | | | - Huan Xu
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Center for the Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mads Melbye
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - William Lowe
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Ole B Pedersen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, University of Aarhus, Aarhus, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Rolv T Lie
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Kari Teramo
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
- University of Helsinki, Helsinki, Finland
| | - Mikko Hallman
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | | | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Line Sletner
- Department of Pediatric and Adolescents Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Mario Merialdi
- Maternal Newborn Health Innovations, PBC, Geneva, Switzerland
| | - Sheryl L Rifas-Shiman
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Thora Steingrimsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Obstetrics and Gynecology, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Denise Scholtens
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Christine Power
- Population, Policy, Practice. Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Jane West
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - John A Capra
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Statistics, University of California San Francisco, San Francisco, CA, USA
| | - Anne H Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ole A Andreassen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Struan F A Grant
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Divisions of Human Genetics and Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elisabeth Qvigstad
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Geoffrey M Hayes
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter of Oulu, University of Oulu, Linnanmaa, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Henriette S Nielsen
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals Rigshospitalet & Hvidovre Hospital, Hvidovre, Denmark
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Pål Njolstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Louis J Muglia
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Center for the Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Rachel M Freathy
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Stefan Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Center for the Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden.
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway.
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11
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Kentistou KA, Kaisinger LR, Stankovic S, Vaudel M, de Oliveira EM, Messina A, Walters RG, Liu X, Busch AS, Helgason H, Thompson DJ, Santon F, Petricek KM, Zouaghi Y, Huang-Doran I, Gudbjartsson DF, Bratland E, Lin K, Gardner EJ, Zhao Y, Jia R, Terao C, Riggan M, Bolla MK, Yazdanpanah M, Yazdanpanah N, Bradfield JP, Broer L, Campbell A, Chasman DI, Cousminer DL, Franceschini N, Franke LH, Girotto G, He C, Järvelin MR, Joshi PK, Kamatani Y, Karlsson R, Luan J, Lunetta KL, Mägi R, Mangino M, Medland SE, Meisinger C, Noordam R, Nutile T, Concas MP, Polašek O, Porcu E, Ring SM, Sala C, Smith AV, Tanaka T, van der Most PJ, Vitart V, Wang CA, Willemsen G, Zygmunt M, Ahearn TU, Andrulis IL, Anton-Culver H, Antoniou AC, Auer PL, Barnes CLK, Beckmann MW, Berrington A, Bogdanova NV, Bojesen SE, Brenner H, Buring JE, Canzian F, Chang-Claude J, Couch FJ, Cox A, Crisponi L, Czene K, Daly MB, Demerath EW, Dennis J, Devilee P, Vivo ID, Dörk T, Dunning AM, Dwek M, Eriksson JG, Fasching PA, Fernandez-Rhodes L, Ferreli L, Fletcher O, Gago-Dominguez M, García-Closas M, García-Sáenz JA, González-Neira A, Grallert H, Guénel P, Haiman CA, Hall P, Hamann U, Hakonarson H, Hart RJ, Hickey M, Hooning MJ, Hoppe R, Hopper JL, Hottenga JJ, Hu FB, Hübner H, Hunter DJ, Jernström H, John EM, Karasik D, Khusnutdinova EK, Kristensen VN, Lacey JV, Lambrechts D, Launer LJ, Lind PA, Lindblom A, Magnusson PKE, Mannermaa A, McCarthy MI, Meitinger T, Menni C, Michailidou K, Millwood IY, Milne RL, Montgomery GW, Nevanlinna H, Nolte IM, Nyholt DR, Obi N, O’Brien KM, Offit K, Oldehinkel AJ, Ostrowski SR, Palotie A, Pedersen OB, Peters A, Pianigiani G, Plaseska-Karanfilska D, Pouta A, Pozarickij A, Radice P, Rennert G, Rosendaal FR, Ruggiero D, Saloustros E, Sandler DP, Schipf S, Schmidt CO, Schmidt MK, Small K, Spedicati B, Stampfer M, Stone J, Tamimi RM, Teras LR, Tikkanen E, Turman C, Vachon CM, Wang Q, Winqvist R, Wolk A, Zemel BS, Zheng W, van Dijk KW, Alizadeh BZ, Bandinelli S, Boerwinkle E, Boomsma DI, Ciullo M, Chenevix-Trench G, Cucca F, Esko T, Gieger C, Grant SFA, Gudnason V, Hayward C, Kolčić I, Kraft P, Lawlor DA, Martin NG, Nøhr EA, Pedersen NL, Pennell CE, Ridker PM, Robino A, Snieder H, Sovio U, Spector TD, Stöckl D, Sudlow C, Timpson NJ, Toniolo D, Uitterlinden A, Ulivi S, Völzke H, Wareham NJ, Widen E, Wilson JF, Pharoah PDP, Li L, Easton DF, Njølstad P, Sulem P, Murabito JM, Murray A, Manousaki D, Juul A, Erikstrup C, Stefansson K, Horikoshi M, Chen Z, Farooqi IS, Pitteloud N, Johansson S, Day FR, Perry JRB, Ong KK. Understanding the genetic complexity of puberty timing across the allele frequency spectrum. medRxiv 2023:2023.06.14.23291322. [PMID: 37503126 PMCID: PMC10371120 DOI: 10.1101/2023.06.14.23291322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Pubertal timing varies considerably and has been associated with a range of health outcomes in later life. To elucidate the underlying biological mechanisms, we performed multi-ancestry genetic analyses in ~800,000 women, identifying 1,080 independent signals associated with age at menarche. Collectively these loci explained 11% of the trait variance in an independent sample, with women at the top and bottom 1% of polygenic risk exhibiting a ~11 and ~14-fold higher risk of delayed and precocious pubertal development, respectively. These common variant analyses were supported by exome sequence analysis of ~220,000 women, identifying several genes, including rare loss of function variants in ZNF483 which abolished the impact of polygenic risk. Next, we implicated 660 genes in pubertal development using a combination of in silico variant-to-gene mapping approaches and integration with dynamic gene expression data from mouse embryonic GnRH neurons. This included an uncharacterized G-protein coupled receptor GPR83, which we demonstrate amplifies signaling of MC3R, a key sensor of nutritional status. Finally, we identified several genes, including ovary-expressed genes involved in DNA damage response that co-localize with signals associated with menopause timing, leading us to hypothesize that the ovarian reserve might signal centrally to trigger puberty. Collectively these findings extend our understanding of the biological complexity of puberty timing and highlight body size dependent and independent mechanisms that potentially link reproductive timing to later life disease.
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Affiliation(s)
- Katherine A Kentistou
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Lena R Kaisinger
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Stasa Stankovic
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, NO-0213, Oslo, Norway
| | - Edson M de Oliveira
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Andrea Messina
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Alexander S Busch
- Department of General Pediatrics, University of Münster, Münster, Germany
- Deptartment of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Hannes Helgason
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Federico Santon
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Konstantin M Petricek
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pharmacology, Berlin, Germany
| | - Yassine Zouaghi
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Isabel Huang-Doran
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Eirik Bratland
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, NO-5021, Bergen, Norway
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Eugene J Gardner
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Raina Jia
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Margie Riggan
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mojgan Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Nahid Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Jonath P Bradfield
- Quantinuum Research, Wayne, PA, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Diana L Cousminer
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Lude H Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Giorgia Girotto
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Chunyan He
- Department of Epidemiology and Biostatistics, Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
- Departments of Medical Oncology and Hematology, Sir Runrun Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Institute of Health Sciences, P.O.Box 5000, FI-90014 University of Oulu, Finland
- Biocenter Oulu, P.O.Box 5000, Aapistie 5A, FI-90014 University of Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, P.O.Box 20, FI-90220 Oulu, 90029 OYS, Finland
- Department of Children and Young People and Families, National Institute for Health and Welfare, Aapistie 1, Box 310, FI-90101 Oulu, Finland
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jian’an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Kathryn L Lunetta
- Boston University School of Public Health, Department of Biostatistics. Boston, Massachusetts 02118, USA
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
- NIHR Biomedical Research Centre at Guy’s and St. Thomas’ Foundation Trust, London, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Psychology, University of Queensland, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Christa Meisinger
- Epidemiology, Medical Faculty, University of Augsburg, University Hospital of Augsburg, Augsburg, Germany
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Teresa Nutile
- Institute of Genetics and Biophysics “A. Buzzati-Traverso”, CNR, Naples, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
| | - Ozren Polašek
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Eleonora Porcu
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy
- University of Sassari, Department of Biomedical Sciences, Sassari, Sassari 07100, Italy
| | - Susan M Ring
- MRC Integrative Epidemiology Unit at the University of Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, UK
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffele Hospital, Milano, Italy
| | - Albert V Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Toshiko Tanaka
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Carol A Wang
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales 2308, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
| | - Gonneke Willemsen
- Dept of Biological Psychology, Vrije Universiteit, Amsterdam; Amsterdam Public Health (APH) research institute, The Netherlands
| | - Marek Zygmunt
- Clinic of Gynaecology and Obstetrics, University Medicine Greifswald, Germany
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services Bethesda, MD, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital Toronto, Ontario, Canada
- Department of Molecular Genetics University of Toronto Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute University of California Irvine Irvine, CA, USA
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center Medical College of Wisconsin Milwaukee, WI, USA
| | - Catriona LK Barnes
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - Amy Berrington
- Division of Genetics and Epidemiology The Institute of Cancer Research, London, UK
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Federico Canzian
- Genomic Epidemiology Group German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH) University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology Mayo Clinic Rochester, MN, USA
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Laura Crisponi
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics Fox Chase Cancer Center Philadelphia, PA, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Miriam Dwek
- School of Life Sciences, University of Westminster, London, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Healthcare, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | | | - Liana Ferreli
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services Bethesda, MD, USA
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Pascal Guénel
- Team “Exposome and Heredity”, CESP, Gustave Roussy INSERM, University Paris-Saclay, UVSQ Villejuif, France
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roger J Hart
- Division of Obstetrics and Gynaecology, University of Western Australia, Western Australia, Australia
| | - Martha Hickey
- Department of Obstetrics and Gynaecology at the University of Melbourne and The Royal Women’s Hospital, Victoria, Australia
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne Melbourne, Victoria, Australia
| | - Jouke-Jan Hottenga
- Dept of Biological Psychology, Vrije Universiteit, Amsterdam; Amsterdam Public Health (APH) research institute, The Netherlands
| | - Frank B Hu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health School of Public Health, Boston, Massachusetts 02115, USA
| | - Hanna Hübner
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - David J Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - ABCTB Investigators
- Australian Breast Cancer Tissue Bank, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Helena Jernström
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine Stanford, CA, USA
- Department of Medicine, Division of Oncology Stanford Cancer Institute, Stanford University School of Medicine Stanford, CA, USA
| | - David Karasik
- Hebrew SeniorLife Institute for Aging Research, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Vessela N Kristensen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - James V Lacey
- Department of Computational and Quantitative Medicine, City of Hope Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope Duarte, CA, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Patrik KE Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dale R Nyholt
- School of Biomedical Sciences, Faculty of Health, Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Nadia Obi
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katie M O’Brien
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, NC, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics Memorial Sloan Kettering Cancer Center New York, NY, USA
- Clinical Genetics Service, Department of Medicine Memorial Sloan Kettering Cancer Center New York, NY, USA
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Rigshospitalet - University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of health and medical sciences, University of Copenhagen, Denmark
| | - Aarno Palotie
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Ole B Pedersen
- Department of Clinical Medicine, Faculty of health and medical sciences, University of Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology - IBE, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Giulia Pianigiani
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology “Georgi D. Efremov” MASA Skopje Republic of North Macedonia
| | - Anneli Pouta
- National Institute for Health and Welfare, Finland
| | - Alfred Pozarickij
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research Fondazione IRCCS, Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion, Faculty of Medicine, Haifa, Israel
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics “A. Buzzati-Traverso”, CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | | | - Dale P Sandler
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, NC, USA
| | - Sabine Schipf
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Kerrin Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Meir Stampfer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne Melbourne, Victoria, Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia Perth, Western Australia, Australia
| | - Rulla M Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Population Health Sciences Weill Cornell Medicine New York, NY, USA
| | - Lauren R Teras
- Department of Population Science American Cancer Society Atlanta, GA, USA
| | - Emmi Tikkanen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology Mayo Clinic Rochester, MN, USA
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Babette S Zemel
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center Vanderbilt University School of Medicine Nashville, TN, USA
| | - Ko W van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dorret I Boomsma
- Dept of Biological Psychology, Vrije Universiteit, Amsterdam; Amsterdam Public Health (APH) research institute, The Netherlands
- Amsterdam Reproduction & Development research institute, Amsterdam, The Netherlands
| | - Marina Ciullo
- Institute of Genetics and Biophysics “A. Buzzati-Traverso”, CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | | | - Francesco Cucca
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Sardinia 09042, Italy
- University of Sassari, Department of Biomedical Sciences, Sassari, Sassari 07100, Italy
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Struan FA Grant
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ivana Kolčić
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ellen A Nøhr
- Institute of Clinical Research, University of Southern Denmark, Department of Obstetrics & Gynecology, Odense University Hospital, Denmark
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Pennell
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales 2308, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
- Department of Maternity and Gynaecology, John Hunter Hospital, Newcastle, New South Wales 2305, Australia
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Antonietta Robino
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ulla Sovio
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Doris Stöckl
- Gesundheitsamt Fürstenfeldbruck, Regierung von Oberbayern, Fürstenfeldbruck, Germany
| | - Cathie Sudlow
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Medical Informatics, Usher Institute, University of Edinburgh
| | - Nic J Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, UK
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffele Hospital, Milano, Italy
| | - André Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Sheila Ulivi
- Institute for Maternal and Child Health – IRCCS ‘‘Burlo Garofolo”, Trieste, Italy
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | | | | | | | | | | | | | - Paul DP Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Pål Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020, Bergen, Norway
- Department of Pediatrics and Adolescents, Haukeland University Hospital, NO-5021, Bergen, Norway
| | | | - Joanne M Murabito
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA
- Boston University Chobanian & Avedisian School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA 02118, USA
| | - Anna Murray
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Despoina Manousaki
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Canada
| | - Anders Juul
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Nelly Pitteloud
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne 1005, Switzerland
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, NO-5021, Bergen, Norway
| | - Felix R Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - John RB Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Ken K Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
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12
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Solé-Navais P, Flatley C, Steinthorsdottir V, Vaudel M, Juodakis J, Chen J, Laisk T, LaBella AL, Westergaard D, Bacelis J, Brumpton B, Skotte L, Borges MC, Helgeland Ø, Mahajan A, Wielscher M, Lin F, Briggs C, Wang CA, Moen GH, Beaumont RN, Bradfield JP, Abraham A, Thorleifsson G, Gabrielsen ME, Ostrowski SR, Modzelewska D, Nohr EA, Hypponen E, Srivastava A, Talbot O, Allard C, Williams SM, Menon R, Shields BM, Sveinbjornsson G, Xu H, Melbye M, Lowe W, Bouchard L, Oken E, Pedersen OB, Gudbjartsson DF, Erikstrup C, Sørensen E, Lie RT, Teramo K, Hallman M, Juliusdottir T, Hakonarson H, Ullum H, Hattersley AT, Sletner L, Merialdi M, Rifas-Shiman SL, Steingrimsdottir T, Scholtens D, Power C, West J, Nyegaard M, Capra JA, Skogholt AH, Magnus P, Andreassen OA, Thorsteinsdottir U, Grant SFA, Qvigstad E, Pennell CE, Hivert MF, Hayes GM, Jarvelin MR, McCarthy MI, Lawlor DA, Nielsen HS, Mägi R, Rokas A, Hveem K, Stefansson K, Feenstra B, Njolstad P, Muglia LJ, Freathy RM, Johansson S, Zhang G, Jacobsson B. Genetic effects on the timing of parturition and links to fetal birth weight. Nat Genet 2023; 55:559-567. [PMID: 37012456 PMCID: PMC10101852 DOI: 10.1038/s41588-023-01343-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 02/22/2023] [Indexed: 04/05/2023]
Abstract
The timing of parturition is crucial for neonatal survival and infant health. Yet, its genetic basis remains largely unresolved. We present a maternal genome-wide meta-analysis of gestational duration (n = 195,555), identifying 22 associated loci (24 independent variants) and an enrichment in genes differentially expressed during labor. A meta-analysis of preterm delivery (18,797 cases, 260,246 controls) revealed six associated loci and large genetic similarities with gestational duration. Analysis of the parental transmitted and nontransmitted alleles (n = 136,833) shows that 15 of the gestational duration genetic variants act through the maternal genome, whereas 7 act both through the maternal and fetal genomes and 2 act only via the fetal genome. Finally, the maternal effects on gestational duration show signs of antagonistic pleiotropy with the fetal effects on birth weight: maternal alleles that increase gestational duration have negative fetal effects on birth weight. The present study provides insights into the genetic effects on the timing of parturition and the complex maternal-fetal relationship between gestational duration and birth weight.
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Affiliation(s)
- Pol Solé-Navais
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden.
| | - Christopher Flatley
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | | | - Marc Vaudel
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Julius Juodakis
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Jonas Bacelis
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Ben Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Maria C Borges
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Øyvind Helgeland
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Frederick Lin
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Catherine Briggs
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Carol A Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Gunn-Helen Moen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Australia
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | | | - Abin Abraham
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Dominika Modzelewska
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Ellen A Nohr
- Research Unit of Gynecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Elina Hypponen
- Australian Centre for Precision Health, Uni Clinical & Health Sciences, University of South Australia, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Amit Srivastava
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Center for the Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Octavious Talbot
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Catherine Allard
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CHUS), Sherbrooke, Québec, Canada
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ramkumar Menon
- Department of Obstetrics and Gynaecology, University of Texas Medical Branch, Galveston, TX, USA
| | - Beverley M Shields
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | | | - Huan Xu
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Center for the Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mads Melbye
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - William Lowe
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Ole B Pedersen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, University of Aarhus, Aarhus, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Rolv T Lie
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Kari Teramo
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
- University of Helsinki, Helsinki, Finland
| | - Mikko Hallman
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | | | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Line Sletner
- Department of Pediatric and Adolescents Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Mario Merialdi
- Maternal Newborn Health Innovations, PBC, Geneva, Switzerland
| | - Sheryl L Rifas-Shiman
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Thora Steingrimsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Obstetrics and Gynecology, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Denise Scholtens
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Christine Power
- Population, Policy, Practice. Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Jane West
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - John A Capra
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Statistics, University of California San Francisco, San Francisco, CA, USA
| | - Anne H Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ole A Andreassen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Struan F A Grant
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Divisions of Human Genetics and Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elisabeth Qvigstad
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Geoffrey M Hayes
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter of Oulu, University of Oulu, Linnanmaa, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Henriette S Nielsen
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals Rigshospitalet & Hvidovre Hospital, Hvidovre, Denmark
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Pål Njolstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Louis J Muglia
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Center for the Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Rachel M Freathy
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Stefan Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Center for the Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynaecology, Sahlgrenska Academy, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden.
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway.
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13
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Vašíček J, Skiadopoulou D, Kuznetsova KG, Wen B, Johansson S, Njølstad PR, Bruckner S, Käll L, Vaudel M. Finding haplotypic signatures in proteins. Gigascience 2022; 12:giad093. [PMID: 37919975 PMCID: PMC10622322 DOI: 10.1093/gigascience/giad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/24/2023] [Accepted: 10/08/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND The nonrandom distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different co-occurring sets of alleles can encode different amino acid sequences: protein haplotypes. These protein haplotypes are present in biological samples and detectable by mass spectrometry, but they are not accounted for in proteomic searches. Consequently, the impact of haplotypic variation on the results of proteomic searches and the discoverability of peptides specific to haplotypes remain unknown. FINDINGS Here, we study how common genetic haplotypes influence the proteomic search space and investigate the possibility to match peptides containing multiple amino acid substitutions to a publicly available data set of mass spectra. We found that for 12.42% of the discoverable amino acid substitutions encoded by common haplotypes, 2 or more substitutions may co-occur in the same peptide after tryptic digestion of the protein haplotypes. We identified 352 spectra that matched to such multivariant peptides, and out of the 4,582 amino acid substitutions identified, 6.37% were covered by multivariant peptides. However, the evaluation of the reliability of these matches remains challenging, suggesting that refined error rate estimation procedures are needed for such complex proteomic searches. CONCLUSIONS As these procedures become available and the ability to analyze protein haplotypes increases, we anticipate that proteomics will provide new information on the consequences of common variation, across tissues and time.
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Affiliation(s)
- Jakub Vašíček
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Dafni Skiadopoulou
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Ksenia G Kuznetsova
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Bo Wen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen 5021, Norway
| | - Stefan Bruckner
- Chair of Visual Analytics, Institute for Visual and Analytic Computing, University of Rostock, Rostock 18051, Germany
| | - Lukas Käll
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH–Royal Institute of Technology, Solna 17121, Sweden
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo 0473, Norway
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14
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Carrasco M, Wang C, Søviknes AM, Bjørlykke Y, Abadpour S, Paulo JA, Tjora E, Njølstad P, Ghabayen J, Nermoen I, Lyssenko V, Chera S, Ghila LM, Vaudel M, Scholz H, Ræder H. Spatial Environment Affects HNF4A Mutation-Specific Proteome Signatures and Cellular Morphology in hiPSC-Derived β-Like Cells. Diabetes 2022; 71:862-869. [PMID: 35043148 PMCID: PMC8965667 DOI: 10.2337/db20-1279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/03/2022] [Indexed: 11/13/2022]
Abstract
Studies of monogenic diabetes are particularly useful because we can gain insight into the molecular events of pancreatic β-cell failure. Maturity-onset diabetes of the young 1 (MODY1) is a form of monogenic diabetes caused by a mutation in the HNF4A gene. Human-induced pluripotent stem cells (hiPSCs) provide an excellent tool for disease modeling by subsequently directing differentiation toward desired pancreatic islet cells, but cellular phenotypes in terminally differentiated cells are notoriously difficult to detect. Re-creating a spatial (three-dimensional [3D]) environment may facilitate phenotype detection. We studied MODY1 by using hiPSC-derived pancreatic β-like patient and isogenic control cell lines in two different 3D contexts. Using size-adjusted cell aggregates and alginate capsules, we show that the 3D context is critical to facilitating the detection of mutation-specific phenotypes. In 3D cell aggregates, we identified irregular cell clusters and lower levels of structural proteins by proteome analysis, whereas in 3D alginate capsules, we identified altered levels of glycolytic proteins in the glucose sensing apparatus by proteome analysis. Our study provides novel knowledge on normal and abnormal function of HNF4A, paving the way for translational studies of new drug targets that can be used in precision diabetes medicine in MODY.
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Affiliation(s)
- Manuel Carrasco
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Center for Cancer Biomarkers, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Chencheng Wang
- Department of Transplant Medicine and Institute for Surgical Research, Oslo University Hospital, Oslo, Norway
- Hybrid Technology Hub–Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Anne M. Søviknes
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Yngvild Bjørlykke
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Shadab Abadpour
- Department of Transplant Medicine and Institute for Surgical Research, Oslo University Hospital, Oslo, Norway
- Hybrid Technology Hub–Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Erling Tjora
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Pål Njølstad
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Jonas Ghabayen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ingrid Nermoen
- Department of Endocrinology, Akershus University Hospital, Lorenskog, Norway
| | - Valeriya Lyssenko
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Simona Chera
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Luiza M. Ghila
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Hanne Scholz
- Department of Transplant Medicine and Institute for Surgical Research, Oslo University Hospital, Oslo, Norway
- Hybrid Technology Hub–Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Helge Ræder
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
- Corresponding author: Helge Ræder,
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15
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Helgeland Ø, Vaudel M, Sole-Navais P, Flatley C, Juodakis J, Bacelis J, Koløen IL, Knudsen GP, Johansson BB, Magnus P, Kjennerud TR, Juliusson PB, Stoltenberg C, Holmen OL, Andreassen OA, Jacobsson B, Njølstad PR, Johansson S. Characterization of the genetic architecture of infant and early childhood body mass index. Nat Metab 2022; 4:344-358. [PMID: 35315439 DOI: 10.1038/s42255-022-00549-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/09/2022] [Indexed: 02/08/2023]
Abstract
Early childhood obesity is a growing global concern; however, the role of common genetic variation on infant and child weight development is unclear. Here, we identify 46 loci associated with early childhood body mass index at specific ages, matching different child growth phases, and representing four major trajectory patterns. We perform genome-wide association studies across 12 time points from birth to 8 years in 28,681 children and their parents (27,088 mothers and 26,239 fathers) in the Norwegian Mother, Father and Child Cohort Study. Monogenic obesity genes are overrepresented near identified loci, and several complex association signals near LEPR, GLP1R, PCSK1 and KLF14 point towards a major influence for common variation affecting the leptin-melanocortin system in early life, providing a link to putative treatment strategies. We also demonstrate how different polygenic risk scores transition from birth to adult profiles through early child growth. In conclusion, our results offer a fine-grained characterization of a changing genetic landscape sustaining early childhood growth.
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Affiliation(s)
- Øyvind Helgeland
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marc Vaudel
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Pol Sole-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christopher Flatley
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Julius Juodakis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ingvild L Koløen
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | | | - Bente B Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ted Reichborn Kjennerud
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Petur B Juliusson
- Department of Health Registry Research and Development, National Institute of Public Health, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | | | - Oddgeir L Holmen
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bo Jacobsson
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Pål R Njølstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
| | - Stefan Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
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16
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Farag YM, Horro C, Vaudel M, Barsnes H. PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data. J Proteome Res 2021; 20:5419-5423. [PMID: 34709836 PMCID: PMC8650087 DOI: 10.1021/acs.jproteome.1c00678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mass spectrometry-based proteomics is a high-throughput technology generating ever-larger amounts of data per project. However, storing, processing, and interpreting these data can be a challenge. A key element in simplifying this process is the development of interactive frameworks focusing on visualization that can greatly simplify both the interpretation of data and the generation of new knowledge. Here we present PeptideShaker Online, a user-friendly web-based framework for the identification of mass spectrometry-based proteomics data, from raw file conversion to interactive visualization of the resulting data. Storage and processing of the data are performed via the versatile Galaxy platform (through SearchGUI, PeptideShaker, and moFF), while the interaction with the results happens via a locally installed web server, thus enabling researchers to process and interpret their own data without requiring advanced bioinformatics skills or direct access to compute-intensive infrastructures. The source code, additional documentation, and a fully functional demo is available at https://github.com/barsnes-group/peptide-shaker-online.
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Affiliation(s)
- Yehia Mokhtar Farag
- Proteomics Unit, Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.,Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
| | - Carlos Horro
- Proteomics Unit, Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.,Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Sciences, University of Bergen, 5020 Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.,Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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17
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Flatley C, Sole-Navais P, Vaudel M, Helgeland Ø, Modzelewska D, Johansson S, Jacobsson B, Njølstad P. Placental weight centiles adjusted for age, parity and fetal sex. Placenta 2021; 117:87-94. [PMID: 34773745 DOI: 10.1016/j.placenta.2021.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/29/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022]
Abstract
INTRODUCTION The weight of the placenta can be indicative of efficacy in nutrient and oxygen supply. Furthermore, it has been suggested that a measure of the placenta's ability to adequately supply nutrients to the fetus can be found in the relationship between birth weight and placental weight expressed as a ratio. Our aim was to develop age adjusted placenta weight and birth weight to placenta weight ratio reference curves that are stratified by maternal parity and fetal sex. METHODS We included singleton, non-anomalous births with a gestational age inclusive of 28 + 0 weeks to 42 + 6 weeks. Excluded were pregnancies of multiplicity, fetuses with congenital abnormalities, stillbirths and pregnancies that had placental complications (ie placenta previa or abruption). Generalised additive model for location, shape and scale (GAMLSS) was used to fit reference curves. RESULTS We stratified 97,882 pregnancies by maternal nulliparity status and fetal sex. Extensive assessment model goodness-of-fit showed appropriate modeling and accurate fit to the four parameters of distribution. Our results show accurate model fit of the reference curves to the data. We demonstrated that the influence that parity has on the placenta weight is far greater than that exerted by fetal sex, and that the difference is dependent on gestational age. DISCUSSION This is the largest presentation of age and parity adjusted placenta weight and feto-placental weight ratio reference ranges to date. The difference observed between nulliparous and multiparous pregnancies could be explained by biological memory and the remnants of maternal endo-myometrial vascularity after the first pregnancy.
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Affiliation(s)
- Christopher Flatley
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Pol Sole-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marc Vaudel
- Center of Diabetes Research, Department of Clinical Science, University of Bergen, Children and Youth Hospital, Bergen, Norway
| | - Øyvind Helgeland
- Center of Diabetes Research, Department of Clinical Science, University of Bergen, Children and Youth Hospital, Bergen, Norway; Division of Health Data and Digitalization, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Dominika Modzelewska
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Johansson
- Center of Diabetes Research, Department of Clinical Science, University of Bergen, Children and Youth Hospital, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Division of Health Data and Digitalization, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway; Region Västra Götaland, Sahlgrenska University Hospital, Department of Obstetrics and Gynecology, Gothenburg, Sweden
| | - Pål Njølstad
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway; Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen, Norway
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18
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Sole-Navais P, Bacelis J, Helgeland Ø, Modzelewska D, Vaudel M, Flatley C, Andreassen O, Njølstad PR, Muglia LJ, Johansson S, Zhang G, Jacobsson B. Autozygosity mapping and time-to-spontaneous delivery in Norwegian parent-offspring trios. Hum Mol Genet 2020; 29:3845-3858. [PMID: 33291140 PMCID: PMC7861013 DOI: 10.1093/hmg/ddaa255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 11/18/2022] Open
Abstract
Parental genetic relatedness may lead to adverse health and fitness outcomes in the offspring. However, the degree to which it affects human delivery timing is unknown. We use genotype data from ≃25 000 parent-offspring trios from the Norwegian Mother, Father and Child Cohort Study to optimize runs of homozygosity (ROH) calling by maximizing the correlation between parental genetic relatedness and offspring ROHs. We then estimate the effect of maternal, paternal and fetal autozygosity and that of autozygosity mapping (common segments and gene burden test) on the timing of spontaneous onset of delivery. The correlation between offspring ROH using a variety of parameters and parental genetic relatedness ranged between −0.2 and 0.6, revealing the importance of the minimum number of genetic variants included in an ROH and the use of genetic distance. The optimized compared to predefined parameters showed a ≃45% higher correlation between parental genetic relatedness and offspring ROH. We found no evidence of an effect of maternal, paternal nor fetal overall autozygosity on spontaneous delivery timing. Yet, through autozygosity mapping, we identified three maternal loci TBC1D1, SIGLECs and EDN1 gene regions reducing the median time-to-spontaneous onset of delivery by ≃2–5% (P-value < 2.3 × 10−6). We also found suggestive evidence of a fetal locus at 3q22.2, near the RYK gene region (P-value = 2.0 × 10−6). Autozygosity mapping may provide new insights on the genetic determinants of delivery timing beyond traditional genome-wide association studies, but particular and rigorous attention should be given to ROH calling parameter selection.
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Affiliation(s)
- Pol Sole-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg 41685, Sweden
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg 41685, Sweden
| | - Øyvind Helgeland
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Division of Health Data and Digitalization, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo 0213, Norway
| | - Dominika Modzelewska
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg 41685, Sweden
| | - Marc Vaudel
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen 5021, Norway
| | - Christopher Flatley
- Division of Health Data and Digitalization, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo 0213, Norway
| | - Ole Andreassen
- NORMENT, University of Oslo, Oslo 0450, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0450, Norway.,Department of Psychiatry, University of California San Diego, San Diego, CA 92093, USA
| | - Pål R Njølstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen 5021, Norway
| | - Louis J Muglia
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.,Division of Human Genetics, The Center for Prevention of Preterm Birth, Perinatal Institute, March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45267, USA
| | - Stefan Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Center for Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.,Division of Human Genetics, The Center for Prevention of Preterm Birth, Perinatal Institute, March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45267, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg 41685, Sweden.,Division of Health Data and Digitalization, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo 0213, Norway.,Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg 41685, Sweden
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19
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Gupta MK, Vethe H, Softic S, Rao TN, Wagh V, Shirakawa J, Barsnes H, Vaudel M, Takatani T, Kahraman S, Sakaguchi M, Martinez R, Hu J, Bjørlykke Y, Raeder H, Kulkarni RN. Leptin Receptor Signaling Regulates Protein Synthesis Pathways and Neuronal Differentiation in Pluripotent Stem Cells. Stem Cell Reports 2020; 15:1067-1079. [PMID: 33125875 PMCID: PMC7664055 DOI: 10.1016/j.stemcr.2020.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 01/05/2023] Open
Abstract
The role of leptin receptor (OB-R) signaling in linking pluripotency with growth and development and the consequences of dysfunctional leptin signaling on progression of metabolic disease is poorly understood. Using a global unbiased proteomics approach we report that embryonic fibroblasts (MEFs) carrying the db/db mutation exhibit metabolic abnormalities, while their reprogrammed induced pluripotent stem cells (iPSCs) show altered expression of proteins involved in embryonic development. An upregulation in expression of eukaryotic translation initiation factor 4e (Eif4e) and Stat3 binding to the Eif4e promoter was supported by enhanced protein synthesis in mutant iPSCs. Directed differentiation of db/db iPSCs toward the neuronal lineage showed defects. Gene editing to correct the point mutation in db/db iPSCs using CRISPR-Cas9, restored expression of neuronal markers and protein synthesis while reversing the metabolic defects. These data imply a direct role for OB-R in regulating metabolism in embryonic fibroblasts and key developmental pathways in iPSCs. Pluripotency markers are decreased in db/db iPSCs (lacking functional OB-R) Mouse db/db iPSCs exhibit higher protein synthesis mediated by the Stat3/Eif4e axis OB-R signaling regulates neuronal development markers—NOGGIN, NESTIN, GFAP CRISPR correction reverses defects in db/db iPSCs
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Affiliation(s)
- Manoj K Gupta
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Heidrun Vethe
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; KG Jebsen Center for Diabetes Research, Department of Clinical Medicine, University of Bergen, Bergen 5009, Norway
| | - Samir Softic
- Department of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA; Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Tata Nageswara Rao
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; University Clinic of Hematology, Department of Biomedical Research, Inselspital Bern and University of Bern, Bern, Switzerland
| | - Vilas Wagh
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jun Shirakawa
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Harald Barsnes
- KG Jebsen Center for Diabetes Research, Department of Clinical Medicine, University of Bergen, Bergen 5009, Norway; Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Medicine, University of Bergen, Bergen 5009, Norway; Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
| | - Tomozumi Takatani
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Sevim Kahraman
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Masaji Sakaguchi
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Rachael Martinez
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jiang Hu
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yngvild Bjørlykke
- KG Jebsen Center for Diabetes Research, Department of Clinical Medicine, University of Bergen, Bergen 5009, Norway; Department of Pediatrics, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Helge Raeder
- KG Jebsen Center for Diabetes Research, Department of Clinical Medicine, University of Bergen, Bergen 5009, Norway; Department of Pediatrics, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Rohit N Kulkarni
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02215, USA.
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20
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Abstract
![]()
Randomization
is used in experimental design to reduce the prevalence
of unanticipated confounders. Complete randomization can however create
imbalanced designs, for example, grouping all samples of the same
condition in the same batch. Block randomization is an approach that
can prevent severe imbalances in sample allocation with respect to
both known and unknown confounders. This feature provides the reader
with an introduction to blocking and randomization, and insights into
how to effectively organize samples during experimental design, with
special considerations with respect to proteomics.
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Affiliation(s)
- Bram Burger
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, 5007 Bergen, Norway.,Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5007 Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Sciences, University of Bergen, 5007 Bergen, Norway
| | - Harald Barsnes
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, 5007 Bergen, Norway.,Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5007 Bergen, Norway
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21
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Vogelezang S, Bradfield JP, Ahluwalia TS, Curtin JA, Lakka TA, Grarup N, Scholz M, van der Most PJ, Monnereau C, Stergiakouli E, Heiskala A, Horikoshi M, Fedko IO, Vilor-Tejedor N, Cousminer DL, Standl M, Wang CA, Viikari J, Geller F, Íñiguez C, Pitkänen N, Chesi A, Bacelis J, Yengo L, Torrent M, Ntalla I, Helgeland Ø, Selzam S, Vonk JM, Zafarmand MH, Heude B, Farooqi IS, Alyass A, Beaumont RN, Have CT, Rzehak P, Bilbao JR, Schnurr TM, Barroso I, Bønnelykke K, Beilin LJ, Carstensen L, Charles MA, Chawes B, Clément K, Closa-Monasterolo R, Custovic A, Eriksson JG, Escribano J, Groen-Blokhuis M, Grote V, Gruszfeld D, Hakonarson H, Hansen T, Hattersley AT, Hollensted M, Hottenga JJ, Hyppönen E, Johansson S, Joro R, Kähönen M, Karhunen V, Kiess W, Knight BA, Koletzko B, Kühnapfel A, Landgraf K, Langhendries JP, Lehtimäki T, Leinonen JT, Li A, Lindi V, Lowry E, Bustamante M, Medina-Gomez C, Melbye M, Michaelsen KF, Morgen CS, Mori TA, Nielsen TRH, Niinikoski H, Oldehinkel AJ, Pahkala K, Panoutsopoulou K, Pedersen O, Pennell CE, Power C, Reijneveld SA, Rivadeneira F, Simpson A, Sly PD, Stokholm J, Teo KK, Thiering E, Timpson NJ, Uitterlinden AG, van Beijsterveldt CEM, van Schaik BDC, Vaudel M, Verduci E, Vinding RK, Vogel M, Zeggini E, Sebert S, Lind MV, Brown CD, Santa-Marina L, Reischl E, Frithioff-Bøjsøe C, Meyre D, Wheeler E, Ong K, Nohr EA, Vrijkotte TGM, Koppelman GH, Plomin R, Njølstad PR, Dedoussis GD, Froguel P, Sørensen TIA, Jacobsson B, Freathy RM, Zemel BS, Raitakari O, Vrijheid M, Feenstra B, Lyytikäinen LP, Snieder H, Kirsten H, Holt PG, Heinrich J, Widén E, Sunyer J, Boomsma DI, Järvelin MR, Körner A, Davey Smith G, Holm JC, Atalay M, Murray C, Bisgaard H, McCarthy MI, Jaddoe VWV, Grant SFA, Felix JF. Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits. PLoS Genet 2020; 16:e1008718. [PMID: 33045005 PMCID: PMC7581004 DOI: 10.1371/journal.pgen.1008718] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/22/2020] [Accepted: 03/16/2020] [Indexed: 01/22/2023] Open
Abstract
The genetic background of childhood body mass index (BMI), and the extent to which the well-known associations of childhood BMI with adult diseases are explained by shared genetic factors, are largely unknown. We performed a genome-wide association study meta-analysis of BMI in 61,111 children aged between 2 and 10 years. Twenty-five independent loci reached genome-wide significance in the combined discovery and replication analyses. Two of these, located near NEDD4L and SLC45A3, have not previously been reported in relation to either childhood or adult BMI. Positive genetic correlations of childhood BMI with birth weight and adult BMI, waist-to-hip ratio, diastolic blood pressure and type 2 diabetes were detected (Rg ranging from 0.11 to 0.76, P-values <0.002). A negative genetic correlation of childhood BMI with age at menarche was observed. Our results suggest that the biological processes underlying childhood BMI largely, but not completely, overlap with those underlying adult BMI. The well-known observational associations of BMI in childhood with cardio-metabolic diseases in adulthood may reflect partial genetic overlap, but in light of previous evidence, it is also likely that they are explained through phenotypic continuity of BMI from childhood into adulthood.
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Affiliation(s)
- Suzanne Vogelezang
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jonathan P. Bradfield
- Quantinuum Research LLC, San Diego, California, United States of America
- Center for Applied Genomics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Tarunveer S. Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - John A. Curtin
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Timo A. Lakka
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Peter J. van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Claire Monnereau
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Evie Stergiakouli
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- School of Oral and Dental Sciences, University of Bristol, Bristol, United Kingdom
| | - Anni Heiskala
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Momoko Horikoshi
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Iryna O. Fedko
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Natalia Vilor-Tejedor
- ISGlobal, Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Diana L. Cousminer
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
| | - Carol A. Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, Australia
| | - Jorma Viikari
- Department of Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Carmen Íñiguez
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Statistics and Computational Research–Universitat de València, València, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Niina Pitkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Alessandra Chesi
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Obstetrics and Gynecology, Gothenburg Sweden
| | - Loic Yengo
- University Lille, Centre National de la Recherche Scientifique, Institut Pasteur de Lille, UMR 8199—European Genomic Institute for Diabetes, Lille, France
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Maties Torrent
- Area de Salut de Menorca ib-salut, Menorca, Spain
- Institut d'Investigacio Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Øyvind Helgeland
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Saskia Selzam
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Judith M. Vonk
- Department of Epidemiology, GRIAC (Groningen Research Institute for Asthma and COPD), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mohammed H. Zafarmand
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Obstetrics & Gynecology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Barbara Heude
- Université de Paris, CRESS, INSERM, INRA, Paris, France
| | - Ismaa Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Akram Alyass
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Robin N. Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
| | - Christian T. Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Rzehak
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Jose Ramon Bilbao
- University of the Basque Country (UPV/EHU), Leioa, Spain
- Biocrues-Bizkaia Health Research Institute, Barakaldo, Spain
- CIBER Diabetes y Enfermedades Metabólicas (CIBERDEM), Spain
| | - Theresia M. Schnurr
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Inês Barroso
- Wellcome Sanger Institute, Cambridge, United Kingdom
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Lawrence J. Beilin
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Lisbeth Carstensen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Karine Clément
- Nutrition and Obesities; systemic approaches research unit, Sorbonne University, INSERM, Pitie- Salpêtrière Hospital, Assistance Publique hôpital de Paris, Paris, France
| | - Ricardo Closa-Monasterolo
- Pediatrics, Nutrition and Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Johan G. Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics & Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Joaquin Escribano
- Pediatrics, Nutrition and Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Maria Groen-Blokhuis
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Dariusz Gruszfeld
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrew T. Hattersley
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
- NIHR Exeter Clinical Research Facility, College of Medicine and Health, University of Exeter, and Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Mette Hollensted
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Diabetes Academy, Odense, Denmark
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Elina Hyppönen
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, Australia
- Population, Policy and Practice, UCL Institute of Child Health, University College London, London, United Kingdom
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Stefan Johansson
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Raimo Joro
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, United Kingdom
| | - Wieland Kiess
- Center for Pediatric Research, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
| | - Bridget A. Knight
- NIHR Exeter Clinical Research Facility, College of Medicine and Health, University of Exeter, and Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Andreas Kühnapfel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Kathrin Landgraf
- Center for Pediatric Research, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jaakko T. Leinonen
- Institute For Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Aihuali Li
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Virpi Lindi
- University of Eastern Finland Library Kuopio, Kuopio, Finland
| | - Estelle Lowry
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu University Hospital, Oulu, Finland
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carolina Medina-Gomez
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Medicine, Stanford School of Medicine, Stanford, California, United States of America
| | - Kim F. Michaelsen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Camilla S. Morgen
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
- National Insitute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Trevor A. Mori
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Tenna R. H. Nielsen
- Department of Pediatrics, Hvidovre Hospital, Hvidovre, Denmark
- The Children’s Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
| | - Harri Niinikoski
- Department of Physiology, University of Turku, Turku, Finland
- Department of Pediatrics, University of Turku, Turku, Finland
| | - Albertine J. Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center, Groningen, the Netherlands
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Paavo Nurmi Centre, Sports and Exercise Medicine Unit, Department of Physical Activity and Health, University of Turku, Turku, Finland
| | - Kalliope Panoutsopoulou
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Craig E. Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, Australia
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sijmen A. Reijneveld
- Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Angela Simpson
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Peter D. Sly
- Child Health Research Centre, University of Queensland, Brisbane, Australia
- World Health Organization, WHO Collaborating Centre for Children’s Health and Environment, Brisbane, Queensland, Australia
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Kook K. Teo
- Department of Medicine, McMaster University, Hamilton, Canada; Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Elisabeth Thiering
- Institute of Epidemiology, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging NCHA), Leiden, the Netherlands
| | | | - Barbera D. C. van Schaik
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Elvira Verduci
- Department of Pediatrics, San Paolo Hospital, University of Milan, Milan, Italy
| | - Rebecca K. Vinding
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Mandy Vogel
- Center for Pediatric Research, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Eleftheria Zeggini
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu University Hospital, Oulu, Finland
- Section of Genomics of Common Disease, Department of Medicine, Imperial College London, London, United Kingdom
| | - Mads V. Lind
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Christopher D. Brown
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Loreto Santa-Marina
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiologia y Salud Publica-CIBERESP), Barcelona, Spain
- Biodonostia Health Research Institute, San Sebastian, Spain
- Subdirección Salud Pública de Gipuzkoa, San Sebastian, Spain
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen, Munich, Germany
| | - Christine Frithioff-Bøjsøe
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
- University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen N, Denmark
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Cambridge, United Kingdom
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Ken Ong
- Medical Research Council Epidemiology Unit & Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, England
| | - Ellen A. Nohr
- Research Unit for Gynaecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Tanja G. M. Vrijkotte
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gerard H. Koppelman
- University Medical Center Groningen, University of Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, the Netherlands
| | - Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Pål R. Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen, Norway
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - George D. Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Philippe Froguel
- University Lille, Centre National de la Recherche Scientifique, Institut Pasteur de Lille, UMR 8199—European Genomic Institute for Diabetes, Lille, France
- Section of Genomics of Common Disease, Department of Medicine, Imperial College London, London, United Kingdom
| | - Thorkild I. A. Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Obstetrics and Gynecology, Gothenburg Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Rachel M. Freathy
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Babette S. Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Patrick G. Holt
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Joachim Heinrich
- Institute of Epidemiology, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Inner City Clinic, University Hospital Munich, Ludwig-Maximilians-Universität of Munich, Munich, Germany
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Elisabeth Widén
- Institute For Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Jordi Sunyer
- ISGlobal, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health research institute and Amsterdam Reproduction & Development research Institute, Amsterdam, the Netherlands
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, United Kingdom
| | - Antje Körner
- Center for Pediatric Research, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Jens-Christian Holm
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
- University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen N, Denmark
| | - Mustafa Atalay
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
| | - Clare Murray
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Mark I. McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
- Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom
| | | | - Vincent W. V. Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Struan F. A. Grant
- Center for Applied Genomics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Janine F. Felix
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- * E-mail:
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22
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Verheggen K, Raeder H, Berven FS, Martens L, Barsnes H, Vaudel M. Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows. Mass Spectrom Rev 2020; 39:292-306. [PMID: 28902424 DOI: 10.1002/mas.21543] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines.
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Affiliation(s)
- Kenneth Verheggen
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Helge Raeder
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Harald Barsnes
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
- Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
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23
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Aasebø E, Berven FS, Bartaula-Brevik S, Stokowy T, Hovland R, Vaudel M, Døskeland SO, McCormack E, Batth TS, Olsen JV, Bruserud Ø, Selheim F, Hernandez-Valladares M. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12030709. [PMID: 32192169 PMCID: PMC7140113 DOI: 10.3390/cancers12030709] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematological cancer that mainly affects the elderly. Although complete remission (CR) is achieved for the majority of the patients after induction and consolidation therapies, nearly two-thirds relapse within a short interval. Understanding biological factors that determine relapse has become of major clinical interest in AML. We utilized liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify the protein changes and protein phosphorylation events associated with AML relapse in primary cells from 41 AML patients at time of diagnosis. Patients were defined as relapse-free if they had not relapsed within a five-year clinical follow-up after AML diagnosis. Relapse was associated with increased expression of RNA processing proteins and decreased expression of V-ATPase proteins. We also observed an increase in phosphorylation events catalyzed by cyclin-dependent kinases (CDKs) and casein kinase 2 (CSK2). The biological relevance of the proteome findings was supported by cell proliferation assays using inhibitors of V-ATPase (bafilomycin), CSK2 (CX-4945), CDK4/6 (abemaciclib) and CDK2/7/9 (SNS-032). While bafilomycin preferentially inhibited the cells from relapse patients, the kinase inhibitors were less efficient in these cells. This suggests that therapy against the upregulated kinases could also target the factors inducing their upregulation rather than their activity. This study, therefore, presents markers that could help predict AML relapse and direct therapeutic strategies.
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Affiliation(s)
- Elise Aasebø
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Sushma Bartaula-Brevik
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
| | - Randi Hovland
- Department for Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway;
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | | | - Emmet McCormack
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
| | - Tanveer S. Batth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; (T.S.B.); (J.V.O.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (E.A.); (S.B.-B.); (T.S.); (M.V.); (Ø.B.)
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5009 Bergen, Norway; (F.S.B.); (F.S.)
- Correspondence: ; Tel.: +47-5558-6368
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24
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Li K, Vaudel M, Zhang B, Ren Y, Wen B. PDV: an integrative proteomics data viewer. Bioinformatics 2020; 35:1249-1251. [PMID: 30169737 DOI: 10.1093/bioinformatics/bty770] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/20/2022] Open
Abstract
SUMMARY Data visualization plays critical roles in proteomics studies, ranging from quality control of MS/MS data to validation of peptide identification results. Herein, we present PDV, an integrative proteomics data viewer that can be used to visualize a wide range of proteomics data, including database search results, de novo sequencing results, proteogenomics files, MS/MS data in mzML/mzXML format and data from public proteomics repositories. PDV is a lightweight visualization tool that enables intuitive and fast exploration of diverse, large-scale proteomics datasets on standard desktop computers in both graphical user interface and command line modes. AVAILABILITY AND IMPLEMENTATION PDV software and the user manual are freely available at http://pdv.zhang-lab.org. The source code is available at https://github.com/wenbostar/PDV and is released under the GPL-3 license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kai Li
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Marc Vaudel
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yan Ren
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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25
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Loo LSW, Vethe H, Soetedjo AAP, Paulo JA, Jasmen J, Jackson N, Bjørlykke Y, Valdez IA, Vaudel M, Barsnes H, Gygi SP, Raeder H, Teo AKK, Kulkarni RN. Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors. Stem Cells 2020; 38:542-555. [PMID: 31828876 DOI: 10.1002/stem.3135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/15/2019] [Indexed: 12/25/2022]
Abstract
A comprehensive characterization of the molecular processes controlling cell fate decisions is essential to derive stable progenitors and terminally differentiated cells that are functional from human pluripotent stem cells (hPSCs). Here, we report the use of quantitative proteomics to describe early proteome adaptations during hPSC differentiation toward pancreatic progenitors. We report that the use of unbiased quantitative proteomics allows the simultaneous profiling of numerous proteins at multiple time points, and is a valuable tool to guide the discovery of signaling events and molecular signatures underlying cellular differentiation. We also monitored the activity level of pathways whose roles are pivotal in the early pancreas differentiation, including the Hippo signaling pathway. The quantitative proteomics data set provides insights into the dynamics of the global proteome during the transition of hPSCs from a pluripotent state toward pancreatic differentiation.
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Affiliation(s)
- Larry Sai Weng Loo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore.,School of Biological Sciences, Nanyang Technological University (NTU), Singapore
| | - Heidrun Vethe
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts.,KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Joanita Jasmen
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore
| | - Nicholas Jackson
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts
| | - Yngvild Bjørlykke
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ivan A Valdez
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Helge Raeder
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore.,School of Biological Sciences, Nanyang Technological University (NTU), Singapore.,Departments of Biochemistry and Medicine, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts
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26
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Bradfield JP, Vogelezang S, Felix JF, Chesi A, Helgeland Ø, Horikoshi M, Karhunen V, Lowry E, Cousminer DL, Ahluwalia TS, Thiering E, Boh ETH, Zafarmand MH, Vilor-Tejedor N, Wang CA, Joro R, Chen Z, Gauderman WJ, Pitkänen N, Parra EJ, Fernandez-Rhodes L, Alyass A, Monnereau C, Curtin JA, Have CT, McCormack SE, Hollensted M, Frithioff-Bøjsøe C, Valladares-Salgado A, Peralta-Romero J, Teo YY, Standl M, Leinonen JT, Holm JC, Peters T, Vioque J, Vrijheid M, Simpson A, Custovic A, Vaudel M, Canouil M, Lindi V, Atalay M, Kähönen M, Raitakari OT, van Schaik BDC, Berkowitz RI, Cole SA, Voruganti VS, Wang Y, Highland HM, Comuzzie AG, Butte NF, Justice AE, Gahagan S, Blanco E, Lehtimäki T, Lakka TA, Hebebrand J, Bonnefond A, Grarup N, Froguel P, Lyytikäinen LP, Cruz M, Kobes S, Hanson RL, Zemel BS, Hinney A, Teo KK, Meyre D, North KE, Gilliland FD, Bisgaard H, Bustamante M, Bonnelykke K, Pennell CE, Rivadeneira F, Uitterlinden AG, Baier LJ, Vrijkotte TGM, Heinrich J, Sørensen TIA, Saw SM, Pedersen O, Hansen T, Eriksson J, Widén E, McCarthy MI, Njølstad PR, Power C, Hyppönen E, Sebert S, Brown CD, Järvelin MR, Timpson NJ, Johansson S, Hakonarson H, Jaddoe VWV. A trans-ancestral meta-analysis of genome-wide association studies reveals loci associated with childhood obesity. Hum Mol Genet 2019; 28:3327-3338. [PMID: 31504550 PMCID: PMC6859434 DOI: 10.1093/hmg/ddz161] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/20/2019] [Accepted: 07/02/2019] [Indexed: 01/04/2023] Open
Abstract
Although hundreds of genome-wide association studies-implicated loci have been reported for adult obesity-related traits, less is known about the genetics specific for early-onset obesity and with only a few studies conducted in non-European populations to date. Searching for additional genetic variants associated with childhood obesity, we performed a trans-ancestral meta-analysis of 30 studies consisting of up to 13 005 cases (≥95th percentile of body mass index (BMI) achieved 2-18 years old) and 15 599 controls (consistently <50th percentile of BMI) of European, African, North/South American and East Asian ancestry. Suggestive loci were taken forward for replication in a sample of 1888 cases and 4689 controls from seven cohorts of European and North/South American ancestry. In addition to observing 18 previously implicated BMI or obesity loci, for both early and late onset, we uncovered one completely novel locus in this trans-ancestral analysis (nearest gene, METTL15). The variant was nominally associated with only the European subgroup analysis but had a consistent direction of effect in other ethnicities. We then utilized trans-ancestral Bayesian analysis to narrow down the location of the probable causal variant at each genome-wide significant signal. Of all the fine-mapped loci, we were able to narrow down the causative variant at four known loci to fewer than 10 single nucleotide polymorphisms (SNPs) (FAIM2, GNPDA2, MC4R and SEC16B loci). In conclusion, an ethnically diverse setting has enabled us to both identify an additional pediatric obesity locus and further fine-map existing loci.
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Affiliation(s)
- Jonathan P Bradfield
- Center for Applied Genomics, Children’s Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Quantinuum Research LLC, San Diego, CA, USA
| | - Suzanne Vogelezang
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alessandra Chesi
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Øyvind Helgeland
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Momoko Horikoshi
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Estelle Lowry
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, PO Box 8000, FI-90014 Oulun yliopisto, Finland
| | - Diana L Cousminer
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia
| | - Tarunveer S Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital 2820, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Thiering
- Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Epidemiology, Neuherberg, Germany
- Ludwig Maximilians University of Munich, Dr. von Hauner Children’s Hospital, Munich, Germany
| | - Eileen Tai-Hui Boh
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
| | - Mohammad H Zafarmand
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, The Netherlands
- Department of Clinical Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Natalia Vilor-Tejedor
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
| | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle
| | - Raimo Joro
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Finland
| | - Zhanghua Chen
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
| | - William J Gauderman
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
| | - Niina Pitkänen
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20521, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20014, Finland
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada
| | - Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, Pennsylvania State University
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Akram Alyass
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Claire Monnereau
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - John A Curtin
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust
| | - Christian T Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shana E McCormack
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mette Hollensted
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christine Frithioff-Bøjsøe
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
| | - Adan Valladares-Salgado
- Unidad de Investigacion Medica en Bioquımica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jesus Peralta-Romero
- Unidad de Investigacion Medica en Bioquımica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, 119077, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore
| | - Marie Standl
- Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Epidemiology, Neuherberg, Germany
| | - Jaakko T Leinonen
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland
| | - Jens-Christian Holm
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Triinu Peters
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Jesus Vioque
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
- University Miguel Hernandez, Alicante, Spain
- ISABIAL–FISABIO Foundation, Alicante, Spain
| | - Martine Vrijheid
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust
| | | | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Mickaël Canouil
- CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Virpi Lindi
- University of Eastern Finland Library, Kuopio, Finland
| | - Mustafa Atalay
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33521, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20521, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20014, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Finland
| | - Barbera D C van Schaik
- Department of Clinical Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Robert I Berkowitz
- Department of Child and Adolescent Psychiatry and Behavioral Sciences, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - V Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill
| | - Yujie Wang
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | | | | | - Nancy F Butte
- Department of Pediatrics, Baylor College of Medicine
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill
- Biomedical and Translational Informatics, Geisinger Health System
| | - Sheila Gahagan
- Center for Community Health, Department of Pediatrics, University of California at San Diego
| | - Estela Blanco
- Center for Community Health, Department of Pediatrics, University of California at San Diego
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Amélie Bonnefond
- CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, University of Lille, Lille, France
- Department of Medicine, Section of Genomics of Common Disease, Imperial College London, London, UK
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philippe Froguel
- CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, University of Lille, Lille, France
- Department of Medicine, Section of Genomics of Common Disease, Imperial College London, London, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere 33521, Finland
| | - Miguel Cruz
- Unidad de Investigacion Medica en Bioquımica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Sayuko Kobes
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes Digestive and Kidney Diseases, NIH, USA
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes Digestive and Kidney Diseases, NIH, USA
| | - Babette S Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Koon K Teo
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill
| | - Frank D Gilliland
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital 2820, University of Copenhagen, Copenhagen, Denmark
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
| | - Klaus Bonnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital 2820, University of Copenhagen, Copenhagen, Denmark
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle
| | - Fernando Rivadeneira
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Leslie J Baier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes Digestive and Kidney Diseases, NIH, USA
| | - Tanja G M Vrijkotte
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Joachim Heinrich
- Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Epidemiology, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig Maximilians University of Munich, University Hospital Munich, Munich, Germany
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Seang-Mei Saw
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Johan Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsink Finland
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU
| | - Pål R Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen, Norway
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Elina Hyppönen
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, PO Box 8000, FI-90014 Oulun yliopisto, Finland
- Biocenter Oulu, University of Oulu, Aapistie 5, 90220 Oulu, Finland
- Department for Genomics of Common Diseases, School of Medicine, Imperial College London, UK
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, W2 1PG, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, PO Box 8000, FI-90014 Oulun yliopisto, Finland
- Biocenter Oulu, University of Oulu, Aapistie 5, 90220 Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, OYS, Kajaanintie 50, 90220 Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, Middlesex UB8 3PH, UK
| | - Nicholas J Timpson
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Stefan Johansson
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Struan F A Grant for the Early Growth Genetics Consortium
- Center for Applied Genomics, Children’s Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Sánchez LFH, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M. PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping. Gigascience 2019; 8:giz088. [PMID: 31363752 PMCID: PMC6667378 DOI: 10.1093/gigascience/giz088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/03/2019] [Accepted: 06/30/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., gene sets) in pathway knowledge bases. However, the isoform and posttranslational modification states of proteins are lost when converting input and pathways into gene-centric lists. FINDINGS Based on the Reactome knowledge base, we built a network of protein-protein interactions accounting for the documented isoform and modification statuses of proteins. We then implemented a command line application called PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher) to query this network. PathwayMatcher supports multiple types of omics data as input and outputs the possibly affected biochemical reactions, subnetworks, and pathways. CONCLUSIONS PathwayMatcher enables refining the network representation of pathways by including proteoforms defined as protein isoforms with posttranslational modifications. The specificity of pathway analyses is hence adapted to different levels of granularity, and it becomes possible to distinguish interactions between different forms of the same protein.
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Affiliation(s)
- Luis Francisco Hernández Sánchez
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Children's Hospital, Haukeland University Hospital, 5021 Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, P.O Box 1400, 5021 Bergen, Norway
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Bram Burger
- Proteomics Unit, Department of Biomedicine, University of Bergen, Postbox 7804, 5020 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, P.O. Box 7803, 5020 Bergen, Norway
| | - Carlos Horro
- Proteomics Unit, Department of Biomedicine, University of Bergen, Postbox 7804, 5020 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, P.O. Box 7803, 5020 Bergen, Norway
| | - Antonio Fabregat
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Stefan Johansson
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Children's Hospital, Haukeland University Hospital, 5021 Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, P.O Box 1400, 5021 Bergen, Norway
| | - Pål Rasmus Njølstad
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Children's Hospital, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Postbox 7804, 5020 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, P.O. Box 7803, 5020 Bergen, Norway
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, No. 38, Life Science Park Road, Changping District, 102206 Beijing, China
| | - Marc Vaudel
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Children's Hospital, Haukeland University Hospital, 5021 Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, P.O Box 1400, 5021 Bergen, Norway
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28
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Grüning BA, Lampa S, Vaudel M, Blankenberg D. Software engineering for scientific big data analysis. Gigascience 2019; 8:giz054. [PMID: 31121028 PMCID: PMC6532757 DOI: 10.1093/gigascience/giz054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/20/2019] [Accepted: 04/18/2019] [Indexed: 11/14/2022] Open
Abstract
The increasing complexity of data and analysis methods has created an environment where scientists, who may not have formal training, are finding themselves playing the impromptu role of software engineer. While several resources are available for introducing scientists to the basics of programming, researchers have been left with little guidance on approaches needed to advance to the next level for the development of robust, large-scale data analysis tools that are amenable to integration into workflow management systems, tools, and frameworks. The integration into such workflow systems necessitates additional requirements on computational tools, such as adherence to standard conventions for robustness, data input, output, logging, and flow control. Here we provide a set of 10 guidelines to steer the creation of command-line computational tools that are usable, reliable, extensible, and in line with standards of modern coding practices.
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Affiliation(s)
- Björn A Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany
- Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstr. 49, D-79104 Freiburg, Germany
| | - Samuel Lampa
- Pharmaceutical Bioinformatics group, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Svante Arrhenius vag 16C, 106 91, Solna, Sweden
| | - Marc Vaudel
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Postboks 7804, 5020, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Postboks 7804, 5020, Bergen, Norway
| | - Daniel Blankenberg
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue / NE50, Cleveland, OH, USA
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Warrington NM, Beaumont RN, Horikoshi M, Day FR, Helgeland Ø, Laurin C, Bacelis J, Peng S, Hao K, Feenstra B, Wood AR, Mahajan A, Tyrrell J, Robertson NR, Rayner NW, Qiao Z, Moen GH, Vaudel M, Marsit CJ, Chen J, Nodzenski M, Schnurr TM, Zafarmand MH, Bradfield JP, Grarup N, Kooijman MN, Li-Gao R, Geller F, Ahluwalia TS, Paternoster L, Rueedi R, Huikari V, Hottenga JJ, Lyytikäinen LP, Cavadino A, Metrustry S, Cousminer DL, Wu Y, Thiering E, Wang CA, Have CT, Vilor-Tejedor N, Joshi PK, Painter JN, Ntalla I, Myhre R, Pitkänen N, van Leeuwen EM, Joro R, Lagou V, Richmond RC, Espinosa A, Barton SJ, Inskip HM, Holloway JW, Santa-Marina L, Estivill X, Ang W, Marsh JA, Reichetzeder C, Marullo L, Hocher B, Lunetta KL, Murabito JM, Relton CL, Kogevinas M, Chatzi L, Allard C, Bouchard L, Hivert MF, Zhang G, Muglia LJ, Heikkinen J, Morgen CS, van Kampen AHC, van Schaik BDC, Mentch FD, Langenberg C, Luan J, Scott RA, Zhao JH, Hemani G, Ring SM, Bennett AJ, Gaulton KJ, Fernandez-Tajes J, van Zuydam NR, Medina-Gomez C, de Haan HG, Rosendaal FR, Kutalik Z, Marques-Vidal P, Das S, Willemsen G, Mbarek H, Müller-Nurasyid M, Standl M, Appel EVR, Fonvig CE, Trier C, van Beijsterveldt CEM, Murcia M, Bustamante M, Bonas-Guarch S, Hougaard DM, Mercader JM, Linneberg A, Schraut KE, Lind PA, Medland SE, Shields BM, Knight BA, Chai JF, Panoutsopoulou K, Bartels M, Sánchez F, Stokholm J, Torrents D, Vinding RK, Willems SM, Atalay M, Chawes BL, Kovacs P, Prokopenko I, Tuke MA, Yaghootkar H, Ruth KS, Jones SE, Loh PR, Murray A, Weedon MN, Tönjes A, Stumvoll M, Michaelsen KF, Eloranta AM, Lakka TA, van Duijn CM, Kiess W, Körner A, Niinikoski H, Pahkala K, Raitakari OT, Jacobsson B, Zeggini E, Dedoussis GV, Teo YY, Saw SM, Montgomery GW, Campbell H, Wilson JF, Vrijkotte TGM, Vrijheid M, de Geus EJCN, Hayes MG, Kadarmideen HN, Holm JC, Beilin LJ, Pennell CE, Heinrich J, Adair LS, Borja JB, Mohlke KL, Eriksson JG, Widén EE, Hattersley AT, Spector TD, Kähönen M, Viikari JS, Lehtimäki T, Boomsma DI, Sebert S, Vollenweider P, Sørensen TIA, Bisgaard H, Bønnelykke K, Murray JC, Melbye M, Nohr EA, Mook-Kanamori DO, Rivadeneira F, Hofman A, Felix JF, Jaddoe VWV, Hansen T, Pisinger C, Vaag AA, Pedersen O, Uitterlinden AG, Järvelin MR, Power C, Hyppönen E, Scholtens DM, Lowe WL, Davey Smith G, Timpson NJ, Morris AP, Wareham NJ, Hakonarson H, Grant SFA, Frayling TM, Lawlor DA, Njølstad PR, Johansson S, Ong KK, McCarthy MI, Perry JRB, Evans DM, Freathy RM. Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors. Nat Genet 2019; 51:804-814. [PMID: 31043758 PMCID: PMC6522365 DOI: 10.1038/s41588-019-0403-1] [Citation(s) in RCA: 297] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
Abstract
Birth weight variation is influenced by fetal and maternal genetic and non-genetic factors, and has been reproducibly associated with future cardio-metabolic health outcomes. In expanded genome-wide association analyses of own birth weight (n = 321,223) and offspring birth weight (n = 230,069 mothers), we identified 190 independent association signals (129 of which are novel). We used structural equation modeling to decompose the contributions of direct fetal and indirect maternal genetic effects, then applied Mendelian randomization to illuminate causal pathways. For example, both indirect maternal and direct fetal genetic effects drive the observational relationship between lower birth weight and higher later blood pressure: maternal blood pressure-raising alleles reduce offspring birth weight, but only direct fetal effects of these alleles, once inherited, increase later offspring blood pressure. Using maternal birth weight-lowering genotypes to proxy for an adverse intrauterine environment provided no evidence that it causally raises offspring blood pressure, indicating that the inverse birth weight-blood pressure association is attributable to genetic effects, and not to intrauterine programming.
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Affiliation(s)
- Nicole M Warrington
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
| | - Momoko Horikoshi
- RIKEN Centre for Integrative Medical Sciences, Laboratory for Endocrinology, Metabolism and Kidney Diseases, Yokohama, Japan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Felix R Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Øyvind Helgeland
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Charles Laurin
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital Östra, Gothenburg, Sweden
| | - Shouneng Peng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
- European Centre for Environment and Human Health, University of Exeter, Truro, UK
| | - Neil R Robertson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - N William Rayner
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Zhen Qiao
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Gunn-Helen Moen
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Nodzenski
- Department of Preventive Medicine, Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Theresia M Schnurr
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mohammad H Zafarmand
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Jonathan P Bradfield
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Quantinuum Research, San Diego, CA, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marjolein N Kooijman
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark
| | - Tarunveer S Ahluwalia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ville Huikari
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alana Cavadino
- Section of Epidemiology and Biostatistics, School of Population Health, University of Auckland, Auckland, New Zealand
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sarah Metrustry
- Department of Twin Research, King's College London, St. Thomas' Hospital, London, UK
| | - Diana L Cousminer
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ying Wu
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Elisabeth Thiering
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Christian T Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Natalia Vilor-Tejedor
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelonabeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
| | - Peter K Joshi
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Jodie N Painter
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Queensland, Australia
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ronny Myhre
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Niina Pitkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Elisabeth M van Leeuwen
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Raimo Joro
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Vasiliki Lagou
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Neuroscience, Katholieke Universiteit Leuven, Leuven, Belgium
- VIB Center for Brain and Disease Research, Leuven, Belgium
| | - Rebecca C Richmond
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ana Espinosa
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
- Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Sheila J Barton
- Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Hazel M Inskip
- Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Loreto Santa-Marina
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
- Subdirección de Salud Pública y Adicciones de Gipuzkoa, San Sebastián, Spain
- Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
| | - Xavier Estivill
- Sidra Medicine Research Department, Sidra Medicine, Doha, Qatar
- Genomics Unit, Dexeus Woman's Health, Barcelona, Spain
| | - Wei Ang
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Western Australia, Australia
| | - Julie A Marsh
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Western Australia, Australia
| | | | - Letizia Marullo
- Department of Life Sciences and Biotechnology, Genetic Section, University of Ferrara, Ferrara, Italy
| | - Berthold Hocher
- Fifth Department of Medicine, University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Joanne M Murabito
- Framingham Heart Study, Framingham, MA, USA
- Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
- Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Catherine Allard
- Centre de recherche, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Luigi Bouchard
- Centre de recherche, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
- ECOGENE-21 and Lipid Clinic, Chicoutimi Hospital, Saguenay, Quebec, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA, USA
- Diabetes Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Universite de Sherbrooke, Sherbooke, Quebec, Canada
| | - Ge Zhang
- Human Genetics Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Louis J Muglia
- Human Genetics Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Jani Heikkinen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Camilla S Morgen
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Barbera D C van Schaik
- Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Susan M Ring
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Amanda J Bennett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Kyle J Gaulton
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Natalie R van Zuydam
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Carolina Medina-Gomez
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Hugoline G de Haan
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Pedro Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Shikta Das
- Medical Research Council Unit for Lifelong Health and Ageing at UCL, Institute of Cardiovascular Sciences, University College London, London, UK
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
| | - Hamdi Mbarek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
- Amsterdam Reproduction and Development, Amsterdam, the Netherlands
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany
- Division of Genetic Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Emil V R Appel
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cilius E Fonvig
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Children's Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - Caecilie Trier
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Children's Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
| | | | - Mario Murcia
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
- FISABIO-Universitat Jaume I-Universitat de València, Joint Research Unit of Epidemiology and Environmental Health, Valencia, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
| | - Sílvia Bonas-Guarch
- Joint BSC-CGR-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - David M Hougaard
- Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Josep M Mercader
- Joint BSC-CGR-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Allan Linneberg
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
| | - Katharina E Schraut
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Queensland, Australia
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Queensland, Australia
| | - Beverley M Shields
- NIHR Exeter Clinical Research Facility, University of Exeter College of Medicine and Health and Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Bridget A Knight
- NIHR Exeter Clinical Research Facility, University of Exeter College of Medicine and Health and Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
| | | | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
| | - Friman Sánchez
- Joint BSC-CGR-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
- Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - David Torrents
- Joint BSC-CGR-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Rebecca K Vinding
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sara M Willems
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Mustafa Atalay
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Bo L Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Peter Kovacs
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Inga Prokopenko
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Section of Genomics of Common Disease, Department of Medicine, Imperial College London, London, UK
| | - Marcus A Tuke
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
| | - Hanieh Yaghootkar
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
| | - Katherine S Ruth
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
| | - Samuel E Jones
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Anna Murray
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
| | - Anke Tönjes
- Medical Department, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Medical Department, University of Leipzig, Leipzig, Germany
| | - Kim F Michaelsen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Aino-Maija Eloranta
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Wieland Kiess
- Pediatric Research Center, Department of Women's andChild Health, University of Leipzig, Leipzig, Germany
| | - Antje Körner
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Pediatric Research Center, Department of Women's andChild Health, University of Leipzig, Leipzig, Germany
| | - Harri Niinikoski
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Department of Physiology, University of Turku, Turku, Finland
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Paavo Nurmi Centre, Sports and Exercise Medicine Unit, Department of Physical Activity and Health, University of Turku, Turku, Finland
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Bo Jacobsson
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital Östra, Gothenburg, Sweden
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Translational Genomics, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - George V Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Seang-Mei Saw
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Queensland, Australia
| | - Harry Campbell
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - James F Wilson
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tanja G M Vrijkotte
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
| | - Eco J C N de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
| | - M Geoffrey Hayes
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Haja N Kadarmideen
- Quantitative and Systems Genomics Group, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Jens-Christian Holm
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Children's Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
| | - Lawrence J Beilin
- School of Medicine, Royal Perth Hospital, University of Western Australia, Perth, Western Australia, Australia
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Joachim Heinrich
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational Social and Environmental Medicine, Inner City Clinic, University Hospital Munich, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Linda S Adair
- Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Judith B Borja
- USC-Office of Population Studies Foundation, University of San Carlos, Cebu City, Philippines
- Department of Nutrition and Dietetics, University of San Carlos, Cebu City, Philippines
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Johan G Eriksson
- National Institute for Health and Welfare, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Elisabeth E Widén
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
- NIHR Exeter Clinical Research Facility, University of Exeter College of Medicine and Health and Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Tim D Spector
- Department of Twin Research, King's College London, St. Thomas' Hospital, London, UK
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jorma S Viikari
- Division of Medicine, Turku University Hospital, Turku, Finland
- Department of Medicine, University of Turku, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
- Amsterdam Reproduction and Development, Amsterdam, the Netherlands
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Genomics of Complex Diseases, Imperial College London, London, UK
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Thorkild I A Sørensen
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark
- Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Fernando Rivadeneira
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charlotta Pisinger
- Research Center for Prevention and Health, Center for Sundhed, Rigshospitalet Glostrup, Copenhagen University, Glostrup, Denmark
| | - Allan A Vaag
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
- Cardiovascular, Renal and Metabolism, Translational Medicine Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - André G Uitterlinden
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Elina Hyppönen
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Denise M Scholtens
- Department of Preventive Medicine, Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - William L Lowe
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Nicholas J Timpson
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F A Grant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK
| | - Debbie A Lawlor
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Pål R Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Stefan Johansson
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ken K Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - David M Evans
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, UK.
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
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30
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Njølstad PR, Andreassen OA, Brunak S, Børglum AD, Dillner J, Esko T, Franks PW, Freimer N, Groop L, Heimer H, Hougaard DM, Hovig E, Hveem K, Jalanko A, Kaprio J, Knudsen GP, Melbye M, Metspalu A, Mortensen PB, Palmgren J, Palotie A, Reed W, Stefánsson H, Stitziel NO, Sullivan PF, Thorsteinsdóttir U, Vaudel M, Vuorio E, Werge T, Stoltenberg C, Stefánsson K. Roadmap for a precision-medicine initiative in the Nordic region. Nat Genet 2019; 51:924-930. [DOI: 10.1038/s41588-019-0391-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Zhang-James Y, Vaudel M, Mjaavatten O, Berven FS, Haavik J, Faraone SV. Effect of disease-associated SLC9A9 mutations on protein-protein interaction networks: implications for molecular mechanisms for ADHD and autism. ACTA ACUST UNITED AC 2019; 11:91-105. [PMID: 30927234 DOI: 10.1007/s12402-018-0281-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022]
Abstract
Na+/H+ Exchanger 9 (NHE9) is an endosomal membrane protein encoded by the Solute Carrier 9A, member 9 gene (SLC9A9). SLC9A9 has been implicated in attention deficit hyperactivity disorder (ADHD), autism spectrum disorders (ASDs), epilepsy, multiple sclerosis and cancers. To better understand the function of NHE9 and the effects of disease-associated variants on protein-protein interactions, we conducted a quantitative analysis of the NHE9 interactome using co-immunoprecipitation and isobaric labeling-based quantitative mass spectrometry. We identified 100 proteins that interact with NHE9. These proteins were enriched in known functional pathways for NHE9: the endocytosis, protein ubiquitination and phagosome pathways, as well as some novel pathways including oxidative stress, mitochondrial dysfunction, mTOR signaling, cell death and RNA processing pathways. An ADHD-associated mutation (A409P) significantly altered NHE9's interactions with a subset of proteins involved in caveolae-mediated endocytosis and MAP2K2-mediated downstream signaling. An ASD nonsense mutation in SLC9A9, R423X, produced no-detectable amount of NHE9, suggesting the overall loss of NHE9 functional networks. In addition, seven of the NHE9 interactors are products of known autism candidate genes (Simons Foundation Autism Research Initiative, SFARI Gene) and 90% of the NHE9 interactome overlap with SFARI protein interaction network PIN (p < 0.0001), supporting the role of NHE9 interactome in ASDs molecular mechanisms. Our results provide a detailed understanding of the functions of protein NHE9 and its disrupted interactions, possibly underlying ADHD and ASDs. Furthermore, our methodological framework proved useful for functional characterization of disease-associated genetic variants and suggestion of druggable targets.
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Affiliation(s)
- Yanli Zhang-James
- Departments of Psychiatry, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY, 13210, USA
| | - Marc Vaudel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Olav Mjaavatten
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway.,Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Stephen V Faraone
- Departments of Psychiatry, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY, 13210, USA. .,Neuroscience and Physiology, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY, 13210, USA.
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32
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Beaumont RN, Warrington NM, Cavadino A, Tyrrell J, Nodzenski M, Horikoshi M, Geller F, Myhre R, Richmond RC, Paternoster L, Bradfield JP, Kreiner-Møller E, Huikari V, Metrustry S, Lunetta KL, Painter JN, Hottenga JJ, Allard C, Barton SJ, Espinosa A, Marsh JA, Potter C, Zhang G, Ang W, Berry DJ, Bouchard L, Das S, Hakonarson H, Heikkinen J, Helgeland Ø, Hocher B, Hofman A, Inskip HM, Jones SE, Kogevinas M, Lind PA, Marullo L, Medland SE, Murray A, Murray JC, Njølstad PR, Nohr EA, Reichetzeder C, Ring SM, Ruth KS, Santa-Marina L, Scholtens DM, Sebert S, Sengpiel V, Tuke MA, Vaudel M, Weedon MN, Willemsen G, Wood AR, Yaghootkar H, Muglia LJ, Bartels M, Relton CL, Pennell CE, Chatzi L, Estivill X, Holloway JW, Boomsma DI, Montgomery GW, Murabito JM, Spector TD, Power C, Järvelin MR, Bisgaard H, Grant SFA, Sørensen TIA, Jaddoe VW, Jacobsson B, Melbye M, McCarthy MI, Hattersley AT, Hayes MG, Frayling TM, Hivert MF, Felix JF, Hyppönen E, Lowe WL, Evans DM, Lawlor DA, Feenstra B, Freathy RM. Genome-wide association study of offspring birth weight in 86 577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics. Hum Mol Genet 2019; 27:742-756. [PMID: 29309628 PMCID: PMC5886200 DOI: 10.1093/hmg/ddx429] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/15/2017] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies of birth weight have focused on fetal genetics, whereas relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated with birth weight that could highlight potentially relevant maternal determinants of fetal growth. We meta-analysed data on up to 8.7 million SNPs in up to 86 577 women of European descent from the Early Growth Genetics (EGG) Consortium and the UK Biobank. We used structural equation modelling (SEM) and analyses of mother–child pairs to quantify the separate maternal and fetal genetic effects. Maternal SNPs at 10 loci (MTNR1B, HMGA2, SH2B3, KCNAB1, L3MBTL3, GCK, EBF1, TCF7L2, ACTL9, CYP3A7) were associated with offspring birth weight at P < 5 × 10−8. In SEM analyses, at least 7 of the 10 associations were consistent with effects of the maternal genotype acting via the intrauterine environment, rather than via effects of shared alleles with the fetus. Variants, or correlated proxies, at many of the loci had been previously associated with adult traits, including fasting glucose (MTNR1B, GCK and TCF7L2) and sex hormone levels (CYP3A7), and one (EBF1) with gestational duration. The identified associations indicate that genetic effects on maternal glucose, cytochrome P450 activity and gestational duration, and potentially on maternal blood pressure and immune function, are relevant for fetal growth. Further characterization of these associations in mechanistic and causal analyses will enhance understanding of the potentially modifiable maternal determinants of fetal growth, with the goal of reducing the morbidity and mortality associated with low and high birth weights.
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Affiliation(s)
- Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Nicole M Warrington
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - Alana Cavadino
- Centre for Environmental and Preventive Medicine, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK.,European Centre for Environment and Human Health, University of Exeter, The Knowledge Spa, Truro TR1 3HD, UK
| | - Michael Nodzenski
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Momoko Horikoshi
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Ronny Myhre
- Division of Epidemiology, Department of Genes and Environment, Norwegian Institute of Public Health, Oslo, Norway
| | - Rebecca C Richmond
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Jonathan P Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eskil Kreiner-Møller
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark
| | - Ville Huikari
- Institute of Health Sciences, University of Oulu, Oulu, Finland
| | - Sarah Metrustry
- Department of Twin Research, King's College London, St. Thomas' Hospital, London, UK
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.,Framingham Heart Study, Framingham, MA, USA
| | - Jodie N Painter
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD 4029, Australia
| | - Jouke-Jan Hottenga
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands.,Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Sheila J Barton
- Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Ana Espinosa
- Pompeu Fabra University (UPF), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.,ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - Julie A Marsh
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Australia
| | - Catherine Potter
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Ge Zhang
- Human Genetics Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, OH, USA.,March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Wei Ang
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Australia
| | - Diane J Berry
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada.,ECOGENE-21 and Lipid Clinic, Chicoutimi Hospital, Saguenay, QC, Canada.,Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Shikta Das
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jani Heikkinen
- FIMM Institute for Molecular Medicine Finland, Helsinki University, Helsinki FI-00014, Finland
| | - Øyvind Helgeland
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Domain of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Berthold Hocher
- The First Affiliated Hospital of Jinan University, Guangzhou 510630, China.,Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Hazel M Inskip
- Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Samuel E Jones
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Manolis Kogevinas
- Pompeu Fabra University (UPF), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.,ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD 4029, Australia
| | - Letizia Marullo
- Genetic Section, Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD 4029, Australia
| | - Anna Murray
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Pål R Njølstad
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway.,Department of Pediatrics, Haukeland University Hospital, Bergen 5021, Norway
| | - Ellen A Nohr
- Research Unit of Obstetrics & Gynecology, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Christoph Reichetzeder
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany.,Center for Cardiovascular Research, Charité, Berlin, Germany
| | - Susan M Ring
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Katherine S Ruth
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Loreto Santa-Marina
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Subdirección de Salud Pública y Adicciones de Gipuzkoa, Donostia/San Sebastián, Spain.,Instituto de Investigación Sanitaria BIODONOSTIA, Donostia/San Sebastián, Spain
| | - Denise M Scholtens
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sylvain Sebert
- Institute of Health Sciences, University of Oulu, Oulu, Finland.,Department of Epidemiology and Biostatistics, School of Public Health, Medical Research Council-Health Protection Agency Centre for Environment and Health, Faculty of Medicine, Imperial College London, London, UK
| | - Verena Sengpiel
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, Sahgrenska University Hospital, Gothenburg, Sweden
| | - Marcus A Tuke
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Marc Vaudel
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Gonneke Willemsen
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands.,Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Hanieh Yaghootkar
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Louis J Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, OH, USA.,March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Meike Bartels
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands.,Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Craig E Pennell
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Australia
| | - Leda Chatzi
- Department of Social Medicine, University of Crete, Crete, Greece
| | - Xavier Estivill
- Pompeu Fabra University (UPF), Barcelona, Spain.,ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Dorret I Boomsma
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands.,Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD 4029, Australia
| | - Joanne M Murabito
- Framingham Heart Study, Framingham, MA, USA.,Section of General Internal Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Tim D Spector
- Department of Twin Research, King's College London, St. Thomas' Hospital, London, UK
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Marjo-Ritta Järvelin
- Institute of Health Sciences, University of Oulu, Oulu, Finland.,Department of Epidemiology and Biostatistics, School of Public Health, Medical Research Council-Health Protection Agency Centre for Environment and Health, Faculty of Medicine, Imperial College London, London, UK.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, FI-90220 Oulu, 90029 OYS, Finland.,Department of Children and Young People and Families, National Institute for Health and Welfare, FI-90101 Oulu, Finland
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark
| | - Struan F A Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thorkild I A Sørensen
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vincent W Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Bo Jacobsson
- Division of Epidemiology, Department of Genes and Environment, Norwegian Institute of Public Health, Oslo, Norway.,Department of Obstetrics and Gynecology, Sahlgrenska Academy, Sahgrenska University Hospital, Gothenburg, Sweden
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA, USA.,Diabetes Center, Massachussetts General Hospital, Boston, MA, USA.,Department of Medicine, Universite de Sherbrooke, QC, Canada
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Elina Hyppönen
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Centre for School of Population Health Research, School of Health Sciences, and Sansom Institute, University of South Australia, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, Australia
| | - William L Lowe
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David M Evans
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD, Australia.,Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Debbie A Lawlor
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK.,Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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33
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Burger B, Hernández Sánchez LF, Lereim RR, Barsnes H, Vaudel M. Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets. J Proteome Res 2018; 17:3801-3809. [PMID: 30251541 DOI: 10.1021/acs.jproteome.8b00464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Biochemical pathways are commonly used as a reference to conduct functional analysis on biomedical omics data sets, where experimental results are mapped to knowledgebases comprising known molecular interactions collected from the literature. Due to their central role, the content of the functional knowledgebases directly influences the outcome of pathway analyses. In this study, we investigate the structure of the current pathway knowledge, as exemplified by Reactome, discuss the consequences for biological interpretation, and outline possible improvements in the use of pathway knowledgebases. By providing a view of the underlying protein interaction network, we aim to help pathway analysis users manage their expectations and better identify possible artifacts in the results.
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Affiliation(s)
- Bram Burger
- Computational Biology Unit (CBU), Department of Informatics , University of Bergen , 5020 Bergen , Norway.,Proteomics Unit (PROBE), Department of Biomedicine , University of Bergen , 5020 Bergen , Norway
| | - Luis Francisco Hernández Sánchez
- KG Jebsen Center for Diabetes Research, Department of Clinical Science , University of Bergen , 5020 Bergen , Norway.,Center for Medical Genetics and Molecular Medicine , Haukeland University Hospital , 5020 Bergen , Norway
| | - Ragnhild Reehorst Lereim
- Computational Biology Unit (CBU), Department of Informatics , University of Bergen , 5020 Bergen , Norway.,Proteomics Unit (PROBE), Department of Biomedicine , University of Bergen , 5020 Bergen , Norway
| | - Harald Barsnes
- Computational Biology Unit (CBU), Department of Informatics , University of Bergen , 5020 Bergen , Norway.,Proteomics Unit (PROBE), Department of Biomedicine , University of Bergen , 5020 Bergen , Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science , University of Bergen , 5020 Bergen , Norway.,Center for Medical Genetics and Molecular Medicine , Haukeland University Hospital , 5020 Bergen , Norway
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34
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Muth T, Hartkopf F, Vaudel M, Renard BY. A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics. Proteomics 2018; 18:e1700150. [PMID: 29968278 DOI: 10.1002/pmic.201700150] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/23/2018] [Indexed: 01/15/2023]
Abstract
In shotgun proteomics, peptide and protein identification is most commonly conducted using database search engines, the method of choice when reference protein sequences are available. Despite its widespread use the database-driven approach is limited, mainly because of its static search space. In contrast, de novo sequencing derives peptide sequence information in an unbiased manner, using only the fragment ion information from the tandem mass spectra. In recent years, with the improvements in MS instrumentation, various new methods have been proposed for de novo sequencing. This review article provides an overview of existing de novo sequencing algorithms and software tools ranging from peptide sequencing to sequence-to-protein mapping. Various use cases are described for which de novo sequencing was successfully applied. Finally, limitations of current methods are highlighted and new directions are discussed for a wider acceptance of de novo sequencing in the community.
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Affiliation(s)
- Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Felix Hartkopf
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Marc Vaudel
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020, Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5020, Bergen, Norway
| | - Bernhard Y Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
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35
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Willems S, Bouyssié D, Deforce D, Dorfer V, Gorshkov V, Kopczynski D, Laukens K, Locard-Paulet M, Schwämmle V, Uszkoreit J, Valkenborg D, Vaudel M, Bittremieux W. Proceedings of the EuBIC developer's meeting 2018. J Proteomics 2018; 187:25-27. [PMID: 29864591 DOI: 10.1016/j.jprot.2018.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/27/2018] [Indexed: 11/18/2022]
Abstract
The inaugural European Bioinformatics Community (EuBIC) developer's meeting was held from January 9th to January 12th 2018 in Ghent, Belgium. While the meeting kicked off with an interactive keynote session featuring four internationally renowned experts in the field of computational proteomics, its primary focus were the hands-on hackathon sessions which featured six community-proposed projects revolving around three major topics: Here, we present an overview of the scientific program of the EuBIC developer's meeting and provide a starting point for follow-up on the covered projects.
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Affiliation(s)
- Sander Willems
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - David Bouyssié
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, UPS, Toulouse, France
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Viktoria Dorfer
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Dominik Kopczynski
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Marie Locard-Paulet
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, UPS, Toulouse, France
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Julian Uszkoreit
- Medizinisches Proteom-Center, Ruhr University Bochum, Bochum, Germany
| | - Dirk Valkenborg
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, Belgium; Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Wout Bittremieux
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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36
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Abstract
Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide sequences for later mapping to the originating proteins. We here present the latest developments in SearchGUI, a common open-source interface for the most frequently used freely available proteomics search and de novo engines that has evolved into a central component in numerous bioinformatics workflows.
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Affiliation(s)
| | - Marc Vaudel
- Center for Medical Genetics and Molecular Medicine , Haukeland University Hospital , 5021 Bergen , Norway
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37
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da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics 2018; 33:2580-2582. [PMID: 28379341 PMCID: PMC5870671 DOI: 10.1093/bioinformatics/btx192] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/29/2017] [Indexed: 12/16/2022] Open
Abstract
Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/.
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Affiliation(s)
| | - Björn A Grüning
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,Albert-Ludwigs-University, Department of Computer Science, Bioinformatics Group, Freiburg, Baden-Württemberg, 79110 Freiburg, Freiburg
| | - Saulo Alves Aflitos
- Wageningen Plant Research, Cluster Bioinformatics, Wageningen, 6700 AD, Gelderland, Netherlands
| | | | - Julian Uszkoreit
- Medizinisches Proteom-Center, Ruhr-University Bochum, Germany, 44801
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway.,(I) KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway, 5020; (II) Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway, 5020
| | - Pablo Moreno
- EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Laurent Gatto
- Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jonas Weber
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Mingze Bai
- EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Rafael C Jimenez
- EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Timo Sachsenberg
- Universität Tübingen, Wilhelm Schickard Institut für Informatik, Applied Bioinformatics Group,D-72076 Tübingen, Germany
| | - Julianus Pfeuffer
- Eberhard-Karls-Universität Tübingen, Department of Computer Science, Applied bioinformatics, 72076 Tübingen
| | - Roberto Vera Alvarez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Johannes Griss
- EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yasset Perez-Riverol
- EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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38
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Berland S, Toft-Bertelsen TL, Aukrust I, Byska J, Vaudel M, Bindoff LA, MacAulay N, Houge G. A de novo Ser111Thr variant in aquaporin-4 in a patient with intellectual disability, transient signs of brain ischemia, transient cardiac hypertrophy, and progressive gait disturbance. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002303. [PMID: 29437797 PMCID: PMC5793774 DOI: 10.1101/mcs.a002303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/06/2017] [Indexed: 11/25/2022] Open
Abstract
Aquaporin-4, encoded by AQP4, is the major water channel in the central nervous system and plays an important role in the brain's water balance, including edema formation and clearance. Using genomic copy-number analysis and trio-exome sequencing, we investigated a male patient with intellectual disability, hearing loss, and progressive gait dysfunction and found a de novo missense change Ser111Thr in AQP4 as the only suspicious finding. Perinatally, signs of brain ischemia were detected in relation to acute collapse 2 h after birth that resolved a few days later. At the age of 3 mo, cardiac hypertrophy was detected that persisted through childhood but was completely resolved by age 16. In theory, this neurodevelopmental disorder with transient cardiomyopathy could be caused by a disturbance of cellular water balance. Ser111 is an extremely conserved residue in the short cytoplasmic loop between AQP4 transmembrane helix 2 and 3, present across all AQP isoforms from plants to mammals, and it does not appear to be a phosphorylation site. We found that the Ser111Thr change does not affect water permeability or protein stability, suggesting another and possibly regulatory role. Although causality remains unproven, this case study draws attention to AQP4 as a candidate gene for a unique developmental disorder and to a specific serine as a residue of possibly great functional importance in many AQPs.
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Affiliation(s)
- Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen N-5021, Norway
| | | | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, Bergen N-5021, Norway
| | - Jan Byska
- Department of Informatics, University of Bergen, Bergen N-5020, Norway
| | - Marc Vaudel
- Department of Medical Genetics, Haukeland University Hospital, Bergen N-5021, Norway.,KG Jebsen Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen N-5020, Norway
| | - Laurence A Bindoff
- Department of Neurology, Haukeland University Hospital, Bergen N-5021, Norway.,Department of Clinical Medicine (K1), University of Bergen, Bergen N-5020, Norway
| | - Nanna MacAulay
- Department of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen N-5021, Norway
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39
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Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barsnes H, Vaudel M, Martens L, Grüning B, Cooke IR, Heydarian M, Reddy KL, Griffin TJ. An Accessible Proteogenomics Informatics Resource for Cancer Researchers. Cancer Res 2017; 77:e43-e46. [PMID: 29092937 DOI: 10.1158/0008-5472.can-17-0331] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/07/2017] [Accepted: 06/30/2017] [Indexed: 11/16/2022]
Abstract
Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry-based proteomics data to directly identify expressed, variant protein sequences that may have functional roles in cancer. This approach is computationally intensive, requiring integration of disparate software tools into sophisticated workflows, challenging its adoption by nonexpert, bench scientists. To address this need, we have developed an extensible, Galaxy-based resource aimed at providing more researchers access to, and training in, proteogenomic informatics. Our resource brings together software from several leading research groups to address two foundational aspects of proteogenomics: (i) generation of customized, annotated protein sequence databases from RNA-Seq data; and (ii) accurate matching of tandem mass spectrometry data to putative variants, followed by filtering to confirm their novelty. Directions for accessing software tools and workflows, along with instructional documentation, can be found at z.umn.edu/canresgithub. Cancer Res; 77(21); e43-46. ©2017 AACR.
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Affiliation(s)
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota.,Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, Minnesota
| | - Getiria Onsongo
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Candace R Guerrero
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Björn Grüning
- Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany.,Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
| | - Ira R Cooke
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Queensland, Australia
| | | | - Karen L Reddy
- Department of Biological Chemistry, Center for Epigenetics and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota.
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40
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Hernandez-Valladares M, Vaudel M, Selheim F, Berven F, Bruserud Ø. Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers. Expert Rev Proteomics 2017; 14:649-663. [DOI: 10.1080/14789450.2017.1352474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Frode Selheim
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Frode Berven
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Øystein Bruserud
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
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41
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Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR. The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. Mol Cell Proteomics 2017; 16:1275-1285. [PMID: 28515314 PMCID: PMC5500760 DOI: 10.1074/mcp.m117.068429] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/15/2017] [Indexed: 12/31/2022] Open
Abstract
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012-capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well-supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (1) scores associated with localization of modifications on peptides; (2) statistics performed at the level of peptides; (3) identification of cross-linked peptides; and (4) support for proteogenomics approaches. In addition, there is now improved support for the encoding of de novo sequencing of peptides, spectral library searches, and protein inference. As a key point, the underlying XML schema has only undergone very minor modifications to simplify as much as possible the transition from version 1.1 to version 1.2 for implementers, but there have been several notable updates to the format specification, implementation guidelines, controlled vocabularies and validation software. mzIdentML 1.2 can be described as backwards compatible, in that reading software designed for mzIdentML 1.1 should function in most cases without adaptation. We anticipate that these developments will provide a continued stable base for software teams working to implement the standard. All the related documentation is accessible at http://www.psidev.info/mzidentml.
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Affiliation(s)
- Juan Antonio Vizcaíno
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Gerhard Mayer
- §Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Simon Perkins
- ¶Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Harald Barsnes
- ‖Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
- **Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- ‡‡KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
| | - Marc Vaudel
- ‖Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
- ‡‡KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
- §§Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Yasset Perez-Riverol
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Tobias Ternent
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Julian Uszkoreit
- §Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Martin Eisenacher
- §Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Lutz Fischer
- ¶¶Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Juri Rappsilber
- ¶¶Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- ‖‖Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin, 13355 Berlin, Germany
| | - Eugen Netz
- Biomolecular Interactions group, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| | - Mathias Walzer
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Biomolecular Interactions group, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
- Dept. of Computer Science, University of Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Germany
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94143
| | - Fawaz Ghali
- ¶Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Salvador Martínez-Bartolomé
- Department of Chemical Physiology, The Scripps Research Institute, 10550, N. Torrey Pines Rd., La Jolla, California, 92037
| | | | - Andrew R Jones
- ¶Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK;
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42
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Kopczynski D, Barsnes H, Njølstad PR, Sickmann A, Vaudel M, Ahrends R. PeptideMapper: efficient and versatile amino acid sequence and tag mapping. Bioinformatics 2017; 33:2042-2044. [DOI: 10.1093/bioinformatics/btx122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/01/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Dominik Kopczynski
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V, Dortmund, Germany
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Pål R Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V, Dortmund, Germany
- College of Physical Sciences, University of Aberdeen, Old Aberdeen, UK
- Medizinische Fakultät, Ruhr-Universität Bochum, Bochum, Germany
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V, Dortmund, Germany
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43
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Opsahl JA, Vaudel M, Guldbrandsen A, Aasebø E, Van Pesch V, Franciotta D, Myhr KM, Barsnes H, Berle M, Torkildsen Ø, Kroksveen AC, Berven FS. Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis. Proteomics 2016; 16:1154-65. [PMID: 26841090 DOI: 10.1002/pmic.201500284] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 12/08/2015] [Accepted: 01/28/2016] [Indexed: 11/05/2022]
Abstract
The aims of the study were to: (i) identify differentially regulated proteins in cerebrospinal fluid (CSF) between multiple sclerosis (MS) patients and non-MS controls; (ii) examine the effect of matching the CSF samples on either total protein amount or volume, and compare four protein normalization strategies for CSF protein quantification. CSF from MS patients (n = 37) and controls (n = 64), consisting of other noninflammatory neurological diseases (n = 50) and non neurological spinal anesthetic subjects (n = 14), were analyzed using label-free proteomics, quantifying almost 800 proteins. In total, 122 proteins were significantly regulated (p < 0.05), where 77 proteins had p-value <0.01 or AUC value >0.75. Hierarchical clustering indicated that there were two main groups of MS patients, those with increased levels of inflammatory response proteins and decreased levels of proteins involved in neuronal tissue development (n = 30), and those with normal protein levels for both of these protein groups (n = 7). The main subgroup of controls clustering with the MS patients showing increased inflammation and decreased neuronal tissue development were patients suffering from chronic fatigue. Our data indicate that the preferable way to quantify proteins in CSF is to first match the samples on total protein amount and then normalize the data based on the median intensities, preferably from the CNS-enriched proteins.
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Affiliation(s)
- Jill A Opsahl
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Elise Aasebø
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Vincent Van Pesch
- Neurology Department, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Diego Franciotta
- Laboratory of Neuroimmunology, IRCCS, "C. Mondino" National Neurological Institute, Pavia, Italy
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Magnus Berle
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,Surgical Clinic, Haukeland University Hospital, Bergen, Norway
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.,The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Ann C Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
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44
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Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS. In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis. J Proteome Res 2016; 16:179-194. [PMID: 27728768 DOI: 10.1021/acs.jproteome.6b00659] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In the current study, we conducted a quantitative in-depth proteome and deglycoproteome analysis of cerebrospinal fluid (CSF) from relapsing-remitting multiple sclerosis (RRMS) and neurological controls using mass spectrometry and pathway analysis. More than 2000 proteins and 1700 deglycopeptides were quantified, with 484 proteins and 180 deglycopeptides significantly changed between pools of RRMS and pools of controls. Approximately 300 of the significantly changed proteins were assigned to various biological processes including inflammation, extracellular matrix organization, cell adhesion, immune response, and neuron development. Ninety-six significantly changed deglycopeptides mapped to proteins that were not found changed in the global protein study. In addition, four mapped to the proteins oligo-myelin glycoprotein and noelin, which were found oppositely changed in the global study. Both are ligands to the nogo receptor, and the glycosylation of these proteins appears to be affected by RRMS. Our study gives the most extensive overview of the RRMS affected processes observed from the CSF proteome to date, and the list of differential proteins will have great value for selection of biomarker candidates for further verification.
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Affiliation(s)
- Ann Cathrine Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Ragnhild Reehorst Lereim
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Kjell-Morten Myhr
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Øivind Torkildsen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
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45
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Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M. Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows. J Proteomics 2016; 145:214-225. [DOI: 10.1016/j.jprot.2016.03.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/23/2016] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
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46
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Abstract
Targeting subproteomes is a good strategy to decrease the complexity of a sample, for example in body fluid biomarker studies. Glycoproteins are proteins with carbohydrates of varying size and structure attached to the polypeptide chain, and it has been shown that glycosylation plays essential roles in several vital cellular processes, making glycosylation a particularly interesting field of study. Here, we describe a method for the enrichment of glycosylated peptides from trypsin digested proteins in human cerebrospinal fluid. We also describe how to perform the data analysis on the mass spectrometry data for such samples, focusing on site-specific identification of glycosylation sites, using user friendly open source software.
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Affiliation(s)
- Astrid Guldbrandsen
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Center for Diabetes Research, Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Ann Cathrine Kroksveen
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Marc Vaudel
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.
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47
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Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H. Exploring the potential of public proteomics data. Proteomics 2016; 16:214-25. [PMID: 26449181 PMCID: PMC4738454 DOI: 10.1002/pmic.201500295] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/25/2015] [Accepted: 09/28/2015] [Indexed: 12/22/2022]
Abstract
In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re-)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.
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Affiliation(s)
- Marc Vaudel
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Kenneth Verheggen
- Medical Biotechnology Center, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Attila Csordas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Helge Raeder
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, KG Jebsen Centre for Multiple Sclerosis Research, University of Bergen, Bergen, Norway
| | - Lennart Martens
- Medical Biotechnology Center, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
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48
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Lereim RR, Oveland E, Berven FS, Vaudel M, Barsnes H. Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results. Modern Proteomics – Sample Preparation, Analysis and Practical Applications 2016; 919:227-235. [DOI: 10.1007/978-3-319-41448-5_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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49
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Abstract
In quantitative proteomics, large lists of identified and quantified proteins are used to answer biological questions in a systemic approach. However, working with such extensive datasets can be challenging, especially when complex experimental designs are involved. Here, we demonstrate how to post-process large quantitative datasets, detect proteins of interest, and annotate the data with biological knowledge. The protocol presented can be achieved without advanced computational knowledge thanks to the user-friendly Perseus interface (available from the MaxQuant website, www.maxquant.org ). Various visualization techniques facilitating the interpretation of quantitative results in complex biological systems are also highlighted.
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Affiliation(s)
- Elise Aasebø
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Frode Selheim
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.
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50
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Vaudel M, Barsnes H, Ræder H, Berven FS. Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies. Advances in Experimental Medicine and Biology 2016; 926:65-75. [DOI: 10.1007/978-3-319-42316-6_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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