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Jurgens SJ, Wang X, Choi SH, Weng LC, Koyama S, Pirruccello JP, Nguyen T, Smadbeck P, Jang D, Chaffin M, Walsh R, Roselli C, Elliott AL, Wijdeveld LFJM, Biddinger KJ, Kany S, Rämö JT, Natarajan P, Aragam KG, Flannick J, Burtt NP, Bezzina CR, Lubitz SA, Lunetta KL, Ellinor PT. Rare coding variant analysis for human diseases across biobanks and ancestries. Nat Genet 2024; 56:1811-1820. [PMID: 39210047 DOI: 10.1038/s41588-024-01894-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 08/01/2024] [Indexed: 09/04/2024]
Abstract
Large-scale sequencing has enabled unparalleled opportunities to investigate the role of rare coding variation in human phenotypic variability. Here, we present a pan-ancestry analysis of sequencing data from three large biobanks, including the All of Us research program. Using mixed-effects models, we performed gene-based rare variant testing for 601 diseases across 748,879 individuals, including 155,236 with ancestry dissimilar to European. We identified 363 significant associations, which highlighted core genes for the human disease phenome and identified potential novel associations, including UBR3 for cardiometabolic disease and YLPM1 for psychiatric disease. Pan-ancestry burden testing represented an inclusive and useful approach for discovery in diverse datasets, although we also highlight the importance of ancestry-specific sensitivity analyses in this setting. Finally, we found that effect sizes for rare protein-disrupting variants were concordant between samples similar to European ancestry and other genetic ancestries (βDeming = 0.7-1.0). Our results have implications for multi-ancestry and cross-biobank approaches in sequencing association studies for human disease.
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Affiliation(s)
- Sean J Jurgens
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Wang
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Lu-Chen Weng
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Satoshi Koyama
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James P Pirruccello
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Cardiology, University of California, San Francisco, CA, USA
| | - Trang Nguyen
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Patrick Smadbeck
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Dongkeun Jang
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mark Chaffin
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Roddy Walsh
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Carolina Roselli
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amanda L Elliott
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry and Center for Genomic Medicine, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital,Harvard Medical School, Boston, MA, USA
- Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Leonoor F J M Wijdeveld
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Physiology, Amsterdam UMC location VU, Amsterdam, The Netherlands
| | - Kiran J Biddinger
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shinwan Kany
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cardiology, University Heart and Vascular Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Joel T Rämö
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Pradeep Natarajan
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Krishna G Aragam
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason Flannick
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Noël P Burtt
- Metabolism Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Connie R Bezzina
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Steven A Lubitz
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- NHLBI and Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA.
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2
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Cione E, Mahjoubin-Tehran M, Bacchetti T, Banach M, Ferretti G, Sahebkar A. Profiling of differentially expressed MicroRNAs in familial hypercholesterolemia via direct hybridization. Noncoding RNA Res 2024; 9:796-810. [PMID: 38590435 PMCID: PMC10999490 DOI: 10.1016/j.ncrna.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 04/10/2024] Open
Abstract
Background Individuals with homozygous familial hypercholesterolemia (HoFH) have a severe clinical problem in their first decade of life, which is not usually present in heterozygous FH (HeFH) individuals. For this latter group of patients, FH diagnosis is mostly severely delayed with a significant increase in the risk of angina, myocardial infarction, peripheral artery disease, stroke, and cardiovascular and all-cause mortality. Methods This study used various bioinformatics tools to analyze microarray data and identify critical miRNAs and their target genes associated with FH and its severity. Differentially expressed serum miRNAs from direct hybridization microarray data in three groups of subjects: healthy, HeFH, and HoFH. The differential expressed miRNAs were determined according to a log of fold-change (LFC) <-0.5 or >0.5 and of p < 0.05. Then, we assessed their target genes in silico. Gene ontology (GO) enrichment was applied by Cytoscape. The protein-protein interaction and co-expression network were analyzed by the STRING and GeneMANIA plugins of Cytoscape, respectively. Results We identified increased expression of circulating hsa-miR-604, hsa-miR-652-5p, and hsa-miR-4451 as well as reduced expression of hsa-miR-3140-3p, hsa-miR-550a-5p, and hsa-miR-363-3p in both group of FH vs. healthy subjects. Higher levels of hsa-miR-1183, hsa-miR-1185-1-3p, hsa-miR-122-5p, hsa-miR-19a-3p, hsa-miR-345-3p, and hsa-miR-34c-5p were detected in HeFH in respect to HoFH when compared to healthy subjects. Most upregulated miRNAs mainly affected gene related to cardiac myofibrillogenesis, cholesterol synthesis, RNA editing for apolipoprotein B, and associated with LDL-cholesterol levels. In contrast, down-regulated miRNAs mainly affected gene related to plasma biomarker for coronary artery disease, lipids metabolism, cell adhesion and migration, genetic predictors of type 2 diabetes and cholesterol metabolism. The essential genes were primarily enriched in GO regarding biological regulation, intracellular nucleic acid binding, and the KEGG pathway of TGF-β signaling. Conclusions The case-control nature of this study precluded the possibility of assessing the predictive role of the identified differentially expressed miRNAs for cardiovascular events. Therefore, the signature of miRNAs reflecting the pathogenesis of both HeFH and HoFH.
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Affiliation(s)
- Erika Cione
- Department of Pharmacy, Health, and Nutritional Sciences. Via Savinio, University of Calabria 87036 Rende (CS) Italy
| | - Maryam Mahjoubin-Tehran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tiziana Bacchetti
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy
| | - Maciej Banach
- Department of Preventive Cardiology and Lipidology, Medical University of Lodz (MUL) Lodz, Poland
- Cardiovascular Research Centre, University of Zielona Gora, Zielona Gora, Poland
- Ciccarone Center for the Prevention of Cardiovascular Disease, Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, 600 N. Wolfe St, Carnegie 591, Baltimore, MD 21287, USA
| | - Gianna Ferretti
- Department of Clinical Science and Odontostomatology, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy
- Center of Obesity, Marche Polytechnic University, 60131 Ancona, Italy
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Giontella A, Åkerlund M, Bronton K, Fava C, Lotta LA, Baras A, Overton JD, Jones M, Bergmann A, Kaufmann P, Ilina Y, Melander O. Deficiency of Peptidylglycine-alpha-amidating Monooxygenase, a Cause of Sarcopenic Diabetes Mellitus. J Clin Endocrinol Metab 2024:dgae510. [PMID: 39137152 DOI: 10.1210/clinem/dgae510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Indexed: 08/15/2024]
Abstract
CONTEXT Peptidylglycine-α-amidating monooxygenase (PAM) is a critical enzyme in the endocrine system responsible for activation, by amidation, of bioactive peptides. OBJECTIVE To define the clinical phenotype of carriers of genetic mutations associated with impaired PAM-amidating activity (PAM-AMA). DESIGN We used genetic and phenotypic data from cohort studies: the Malmö Diet and Cancer (MDC; 1991-1996; reexamination in 2002-2012), the Malmö Preventive Project (MPP; 2002-2006), and the UK Biobank (UKB; 2012). SETTING Exome-wide association analysis was used to identify loss-of-function (LoF) variants associated with reduced PAM-AMA and subsequently used for association with the outcomes. PATIENTS OR OTHER PARTICIPANTS This study included n∼4500 participants from a subcohort of the MDC (MDC-Cardiovascular cohort), n∼4500 from MPP, and n∼300,000 from UKB. MAIN OUTCOME MEASURES Endocrine-metabolic traits suggested by prior literature, muscle mass, muscle function, and sarcopenia. RESULTS Two LoF variants in the PAM gene, Ser539Trp (minor allele frequency: 0.7%) and Asp563Gly (5%), independently contributed to a decrease of 2.33 [95% confidence interval (CI): 2.52/2.15; P = 2.5E-140] and 0.98 (1.04/0.92; P = 1.12E-225) SD units of PAM-AMA, respectively. The cumulative effect of the LoF was associated with diabetes, reduced insulin secretion, and higher levels of GH and IGF-1. Moreover, carriers had reduced muscle mass and function, followed by a higher risk of sarcopenia. Indeed, the Ser539Trp mutation increased the risk of sarcopenia by 30% (odds ratio 1.31; 95% CI: 1.16/1.47; P = 9.8E-06), independently of age and diabetes. CONCLUSION PAM-AMA genetic deficiency results in a prediabetic sarcopenic phenotype. Early identification of PAM LoF carriers would allow targeted exercise interventions and calls for novel therapies that restore enzymatic activity.
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Affiliation(s)
- Alice Giontella
- Department of Clinical Sciences Malmö, Lund University, 205 02 Malmö, Sweden
- Department of Clinical Sciences Malmö, Lund University Diabetes Center, Lund University, 205 02 Malmö, Sweden
| | - Mikael Åkerlund
- Department of Clinical Sciences Malmö, Lund University, 205 02 Malmö, Sweden
- Department of Clinical Sciences Malmö, Lund University Diabetes Center, Lund University, 205 02 Malmö, Sweden
- Clinical Research Center, Skåne University Hospital, 205 02 Malmö, Sweden
| | - Kevin Bronton
- Department of Clinical Sciences Malmö, Lund University, 205 02 Malmö, Sweden
- Department of Emergency and Internal Medicine, Skåne University Hospital, 205 02 Malmö, Sweden
| | - Cristiano Fava
- Department of Clinical Sciences Malmö, Lund University, 205 02 Malmö, Sweden
- Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Luca A Lotta
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - John D Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Marcus Jones
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Yulia Ilina
- PAM Theragnostics GmbH, 16761 Hennigsdorf, Germany
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, 205 02 Malmö, Sweden
- Department of Clinical Sciences Malmö, Lund University Diabetes Center, Lund University, 205 02 Malmö, Sweden
- Clinical Research Center, Skåne University Hospital, 205 02 Malmö, Sweden
- Department of Emergency and Internal Medicine, Skåne University Hospital, 205 02 Malmö, Sweden
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4
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Curtis D. Assessment of ability of AlphaMissense to identify variants affecting susceptibility to common disease. Eur J Hum Genet 2024:10.1038/s41431-024-01675-y. [PMID: 39097650 DOI: 10.1038/s41431-024-01675-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 06/28/2024] [Accepted: 07/23/2024] [Indexed: 08/05/2024] Open
Abstract
An important issue in the analysis of rare variant association studies is the ability to annotate nonsynonymous variants in terms of their likely importance as affecting protein function. To address this, AlphaMissense was recently released and was shown to have good performance using benchmarks based on variants causing severe disease and on functional assays. Here, we assess the performance of AlphaMissense across 18 genes which had previously demonstrated association between rare coding variants and hyperlipidaemia, hypertension or type 2 diabetes. The strength of evidence in favour of association, expressed as the signed log p value (SLP), was compared between AlphaMissense and 43 other annotation methods. The results demonstrated marked variability between genes regarding the extent to which nonsynonymous variants contributed to evidence for association and also between the performance of different methods of annotating the nonsynonymous variants. Although AlphaMissense produced the highest SLP on average across genes, it produced the maximum SLP for only 4 genes. For some genes, other methods produced a considerably higher SLP and there were examples of genes where AlphaMissense produced no evidence for association while another method performed well. The marked inconsistency across genes means that it is difficult to decide on an optimal method of analysis of sequence data. The fact that different methods perform well for different genes suggests that if one wished to use sequence data for individual risk prediction then gene-specific annotation methods should be used.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, University College London, London, UK.
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5
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Wang G, Hua R, Chen X, He X, Dingming Y, Chen H, Zhang B, Dong Y, Liu M, Liu J, Liu T, Zhao J, Zhao YQ, Qiao L. MX1 and UBE2L6 are potential metaflammation gene targets in both diabetes and atherosclerosis. PeerJ 2024; 12:e16975. [PMID: 38406276 PMCID: PMC10893863 DOI: 10.7717/peerj.16975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/29/2024] [Indexed: 02/27/2024] Open
Abstract
Background The coexistence of diabetes mellitus (DM) and atherosclerosis (AS) is widespread, although the explicit metabolism and metabolism-associated molecular patterns (MAMPs) responsible for the correlation are still unclear. Methods Twenty-four genetically wild-type male Ba-Ma mini pigs were randomly divided into five groups distinguished by different combinations of 90 mg/kg streptozotocin (STZ) intravenous injection and high-cholesterol/lipid (HC) or high-lipid (HL) diet feeding for 9 months in total. Pigs in the STZ+HC and STZ+HL groups were injected with STZ first and then fed the HC or HL diet for 9 months. In contrast, pigs in the HC+STZ and HL+STZ groups were fed the HC or HL diet for 9 months and injected with STZ at 3 months. The controls were only fed a regular diet for 9 months. The blood glucose and abdominal aortic plaque observed through oil red O staining were used as evaluation indicators for successful modelling of DM and AS. A microarray gene expression analysis of all subjects was performed. Results Atherosclerotic lesions were observed only in the HC+STZ and STZ+HC groups. A total of 103 differentially expressed genes (DEGs) were identified as common between them. The most significantly enriched pathways of 103 common DEGs were influenza A, hepatitis C, and measles. The global and internal protein-protein interaction (PPI) networks of the 103 common DEGs consisted of 648 and 14 nodes, respectively. The top 10 hub proteins, namely, ISG15, IRG6, IRF7, IFIT3, MX1, UBE2L6, DDX58, IFIT2, USP18, and IFI44L, drive aspects of DM and AS. MX1 and UBE2L6 were the intersection of internal and global PPI networks. The expression of MX1 and UBE2L6 was 507.22 ± 342.56 and 96.99 ± 49.92 in the HC+STZ group, respectively, which was significantly higher than others and may be linked to the severity of hyperglycaemia-related atherosclerosis. Further PPI network analysis of calcium/micronutrients, including MX1 and UBE2L6, consisted of 58 and 18 nodes, respectively. The most significantly enriched KEGG pathways were glutathione metabolism, pyrimidine metabolism, purine metabolism, and metabolic pathways. Conclusions The global and internal PPI network of the 103 common DEGs consisted of 648 and 14 nodes, respectively. The intersection of the nodes of internal and global PPI networks was MX1 and UBE2L6, suggesting their key role in the comorbidity mechanism of DM and AS. This inference was partly verified by the overexpression of MX1 and UBE2L6 in the HC+STZ group but not others. Further calcium- and micronutrient-related enriched KEGG pathway analysis supported that MX1 and UBE2L6 may affect the inflammatory response through micronutrient metabolic pathways, conceptually named metaflammation. Collectively, MX1 and UBE2L6 may be potential common biomarkers for DM and AS that may reveal metaflammatory aspects of the pathological process, although proper validation is still needed to determine their contribution to the detailed mechanism.
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Affiliation(s)
- Guisheng Wang
- Department of Radiology, Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Rongrong Hua
- Department of Radiology, Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaoxia Chen
- Department of Radiology, Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xucheng He
- Department of Radiology, Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yao Dingming
- Department of Radiology, Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hua Chen
- Laboratory Animal Center, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Buhuan Zhang
- Department of Radiology, Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yuru Dong
- Department of Radiology, Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Muqing Liu
- Department of Radiology, Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jiaxiong Liu
- Department of Radiology, Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ting Liu
- Department of Radiology, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Jingwei Zhao
- Department of Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Qiong Zhao
- Laboratory Animal Center, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Li Qiao
- Department of International Business, Business College of Beijing Union University, Beijing, China
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Dallali H, Boukhalfa W, Kheriji N, Fassatoui M, Jmel H, Hechmi M, Gouiza I, Gharbi M, Kammoun W, Mrad M, Taoueb M, Krir A, Trabelsi H, Bahlous A, Jamoussi H, Messaoud O, Abid A, Kefi R. The first exome wide association study in Tunisia: identification of candidate loci and pathways with biological relevance for type 2 diabetes. Front Endocrinol (Lausanne) 2023; 14:1293124. [PMID: 38192426 PMCID: PMC10773763 DOI: 10.3389/fendo.2023.1293124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Introduction Type 2 diabetes (T2D) is a multifactorial disease involving genetic and environmental components. Several genome-wide association studies (GWAS) have been conducted to decipher potential genetic aberrations promoting the onset of this metabolic disorder. These GWAS have identified over 400 associated variants, mostly in the intronic or intergenic regions. Recently, a growing number of exome genotyping or exome sequencing experiments have identified coding variants associated with T2D. Such studies were mainly conducted in European populations, and the few candidate-gene replication studies in North African populations revealed inconsistent results. In the present study, we aimed to discover the coding genetic etiology of T2D in the Tunisian population. Methods We carried out a pilot Exome Wide Association Study (EWAS) on 50 Tunisian individuals. Single variant analysis was performed as implemented in PLINK on potentially deleterious coding variants. Subsequently, we applied gene-based and gene-set analyses using MAGMA software to identify genes and pathways associated with T2D. Potential signals were further replicated in an existing large in-silico dataset, involving up to 177116 European individuals. Results Our analysis revealed, for the first time, promising associations between T2D and variations in MYORG gene, implicated in the skeletal muscle fiber development. Gene-set analysis identified two candidate pathways having nominal associations with T2D in our study samples, namely the positive regulation of neuron apoptotic process and the regulation of mucus secretion. These two pathways are implicated in the neurogenerative alterations and in the inflammatory mechanisms of metabolic diseases. In addition, replication analysis revealed nominal associations of the regulation of beta-cell development and the regulation of peptidase activity pathways with T2D, both in the Tunisian subjects and in the European in-silico dataset. Conclusions The present study is the first EWAS to investigate the impact of single genetic variants and their aggregate effects on T2D risk in Africa. The promising disease markers, revealed by our pilot EWAS, will promote the understanding of the T2D pathophysiology in North Africa as well as the discovery of potential treatments.
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Affiliation(s)
- Hamza Dallali
- Genetic typing service, Institut Pasteur of Tunis, Tunis, Tunisia
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Wided Boukhalfa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Meriem Fassatoui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Haifa Jmel
- Genetic typing service, Institut Pasteur of Tunis, Tunis, Tunisia
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Ismail Gouiza
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- MitoLab Team, Unité MitoVasc, UMR CNRS 6015, INSERM U1083, SFR ICAT, University of Angers, Angers, France
| | - Mariem Gharbi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Wafa Kammoun
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Mehdi Mrad
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Marouen Taoueb
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Asma Krir
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Hajer Trabelsi
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Afef Bahlous
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Henda Jamoussi
- Research Unit on Obesity, Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Abdelmajid Abid
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Rym Kefi
- Genetic typing service, Institut Pasteur of Tunis, Tunis, Tunisia
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
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7
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Xue D, Narisu N, Taylor DL, Zhang M, Grenko C, Taylor HJ, Yan T, Tang X, Sinha N, Zhu J, Vandana JJ, Nok Chong AC, Lee A, Mansell EC, Swift AJ, Erdos MR, Zhong A, Bonnycastle LL, Zhou T, Chen S, Collins FS. Functional interrogation of twenty type 2 diabetes-associated genes using isogenic human embryonic stem cell-derived β-like cells. Cell Metab 2023; 35:1897-1914.e11. [PMID: 37858332 PMCID: PMC10841752 DOI: 10.1016/j.cmet.2023.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/26/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional roles of many loci remain unexplored. Here, we engineered isogenic knockout human embryonic stem cell lines for 20 genes associated with T2D risk. We examined the impacts of each knockout on β cell differentiation, functions, and survival. We generated gene expression and chromatin accessibility profiles on β cells derived from each knockout line. Analyses of T2D-association signals overlapping HNF4A-dependent ATAC peaks identified a likely causal variant at the FAIM2 T2D-association signal. Additionally, the integrative association analyses identified four genes (CP, RNASE1, PCSK1N, and GSTA2) associated with insulin production, and two genes (TAGLN3 and DHRS2) associated with β cell sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental line and identified a single likely functional variant at each of 23 T2D-association signals.
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Affiliation(s)
- Dongxiang Xue
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - D Leland Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meili Zhang
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Caleb Grenko
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry J Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN Cambridge, UK
| | - Tingfen Yan
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuming Tang
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Neelam Sinha
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiajun Zhu
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - J Jeya Vandana
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Angie Chi Nok Chong
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Angela Lee
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin C Mansell
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy J Swift
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael R Erdos
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron Zhong
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Lori L Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ting Zhou
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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8
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Nguyen NH, Sarangi S, McChesney EM, Sheng S, Durrant JD, Porter AW, Kleyman TR, Pitluk ZW, Brodsky JL. Genome mining yields putative disease-associated ROMK variants with distinct defects. PLoS Genet 2023; 19:e1011051. [PMID: 37956218 PMCID: PMC10695394 DOI: 10.1371/journal.pgen.1011051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/04/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023] Open
Abstract
Bartter syndrome is a group of rare genetic disorders that compromise kidney function by impairing electrolyte reabsorption. Left untreated, the resulting hyponatremia, hypokalemia, and dehydration can be fatal, and there is currently no cure. Bartter syndrome type II specifically arises from mutations in KCNJ1, which encodes the renal outer medullary potassium channel, ROMK. Over 40 Bartter syndrome-associated mutations in KCNJ1 have been identified, yet their molecular defects are mostly uncharacterized. Nevertheless, a subset of disease-linked mutations compromise ROMK folding in the endoplasmic reticulum (ER), which in turn results in premature degradation via the ER associated degradation (ERAD) pathway. To identify uncharacterized human variants that might similarly lead to premature degradation and thus disease, we mined three genomic databases. First, phenotypic data in the UK Biobank were analyzed using a recently developed computational platform to identify individuals carrying KCNJ1 variants with clinical features consistent with Bartter syndrome type II. In parallel, we examined genomic data in both the NIH TOPMed and ClinVar databases with the aid of Rhapsody, a verified computational algorithm that predicts mutation pathogenicity and disease severity. Subsequent phenotypic studies using a yeast screen to assess ROMK function-and analyses of ROMK biogenesis in yeast and human cells-identified four previously uncharacterized mutations. Among these, one mutation uncovered from the two parallel approaches (G228E) destabilized ROMK and targeted it for ERAD, resulting in reduced cell surface expression. Another mutation (T300R) was ERAD-resistant, but defects in channel activity were apparent based on two-electrode voltage clamp measurements in X. laevis oocytes. Together, our results outline a new computational and experimental pipeline that can be applied to identify disease-associated alleles linked to a range of other potassium channels, and further our understanding of the ROMK structure-function relationship that may aid future therapeutic strategies to advance precision medicine.
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Affiliation(s)
- Nga H. Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Srikant Sarangi
- Paradigm4, Inc., Waltham, Massachusetts, United States of America
| | - Erin M. McChesney
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Shaohu Sheng
- Renal-Electrolyte Division, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aidan W. Porter
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Thomas R. Kleyman
- Renal-Electrolyte Division, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Jeffrey L. Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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9
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Willems SM, Ng NHJ, Fernandez J, Fine RS, Wheeler E, Wessel J, Kitajima H, Marenne G, Sim X, Yaghootkar H, Wang S, Chen S, Chen Y, Chen YDI, Grarup N, Li-Gao R, Varga TV, Asimit JL, Feng S, Strawbridge RJ, Kleinbrink EL, Ahluwalia TS, An P, Appel EV, Arking DE, Auvinen J, Bielak LF, Bihlmeyer NA, Bork-Jensen J, Brody JA, Campbell A, Chu AY, Davies G, Demirkan A, Floyd JS, Giulianini F, Guo X, Gustafsson S, Jackson AU, Jakobsdottir J, Järvelin MR, Jensen RA, Kanoni S, Keinanen-Kiukaanniemi S, Li M, Lu Y, Luan J, Manning AK, Marten J, Meidtner K, Mook-Kanamori DO, Muka T, Pistis G, Prins B, Rice KM, Sanna S, Smith AV, Smith JA, Southam L, Stringham HM, Tragante V, van der Laan SW, Warren HR, Yao J, Yiorkas AM, Zhang W, Zhao W, Graff M, Highland HM, Justice AE, Marouli E, Medina-Gomez C, Afaq S, Alhejily WA, Amin N, Asselbergs FW, Bonnycastle LL, Bots ML, Brandslund I, Chen J, Danesh J, de Mutsert R, Dehghan A, Ebeling T, Elliott P, Farmaki AE, Faul JD, Franks PW, Franks S, Fritsche A, Gjesing AP, Goodarzi MO, Gudnason V, Hallmans G, Harris TB, Herzig KH, Hivert MF, Jørgensen T, Jørgensen ME, Jousilahti P, Kajantie E, Karaleftheri M, Kardia SLR, Kinnunen L, Koistinen HA, Komulainen P, Kovacs P, Kuusisto J, Laakso M, Lange LA, Launer LJ, Leong A, Lindström J, Manning Fox JE, Männistö S, Maruthur NM, Moilanen L, Mulas A, Nalls MA, Neville M, Pankow JS, Pattie A, Petersen ERB, Puolijoki H, Rasheed A, Redmond P, Renström F, Roden M, Saleheen D, Saltevo J, Savonen K, Sebert S, Skaaby T, Small KS, Stančáková A, Stokholm J, Strauch K, Tai ES, Taylor KD, Thuesen BH, Tönjes A, Tsafantakis E, Tuomi T, Tuomilehto J, Uusitupa M, Vääräsmäki M, Vaartjes I, Zoledziewska M, Abecasis G, Balkau B, Bisgaard H, Blakemore AI, Blüher M, Boeing H, Boerwinkle E, Bønnelykke K, Bottinger EP, Caulfield MJ, Chambers JC, Chasman DI, Cheng CY, Collins FS, Coresh J, Cucca F, de Borst GJ, Deary IJ, Dedoussis G, Deloukas P, den Ruijter HM, Dupuis J, Evans MK, Ferrannini E, Franco OH, Grallert H, Hansen T, Hattersley AT, Hayward C, Hirschhorn JN, Ikram A, Ingelsson E, Karpe F, Kaw KT, Kiess W, Kooner JS, Körner A, Lakka T, Langenberg C, Lind L, Lindgren CM, Linneberg A, Lipovich L, Liu CT, Liu J, Liu Y, Loos RJF, MacDonald PE, Mohlke KL, Morris AD, Munroe PB, Murray A, Padmanabhan S, Palmer CNA, Pasterkamp G, Pedersen O, Peyser PA, Polasek O, Porteous D, Province MA, Psaty BM, Rauramaa R, Ridker PM, Rolandsson O, Rorsman P, Rosendaal FR, Rudan I, Salomaa V, Schulze MB, Sladek R, Smith BH, Spector TD, Starr JM, Stumvoll M, van Duijn CM, Walker M, Wareham NJ, Weir DR, Wilson JG, Wong TY, Zeggini E, Zonderman AB, Rotter JI, Morris AP, Boehnke M, Florez JC, McCarthy MI, Meigs JB, Mahajan A, Scott RA, Gloyn AL, Barroso I. Large-scale exome array summary statistics resources for glycemic traits to aid effector gene prioritization. Wellcome Open Res 2023; 8:483. [PMID: 39280063 PMCID: PMC11399760 DOI: 10.12688/wellcomeopenres.18754.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 09/18/2024] Open
Abstract
Background Genome-wide association studies for glycemic traits have identified hundreds of loci associated with these biomarkers of glucose homeostasis. Despite this success, the challenge remains to link variant associations to genes, and underlying biological pathways. Methods To identify coding variant associations which may pinpoint effector genes at both novel and previously established genome-wide association loci, we performed meta-analyses of exome-array studies for four glycemic traits: glycated hemoglobin (HbA1c, up to 144,060 participants), fasting glucose (FG, up to 129,665 participants), fasting insulin (FI, up to 104,140) and 2hr glucose post-oral glucose challenge (2hGlu, up to 57,878). In addition, we performed network and pathway analyses. Results Single-variant and gene-based association analyses identified coding variant associations at more than 60 genes, which when combined with other datasets may be useful to nominate effector genes. Network and pathway analyses identified pathways related to insulin secretion, zinc transport and fatty acid metabolism. HbA1c associations were strongly enriched in pathways related to blood cell biology. Conclusions Our results provided novel glycemic trait associations and highlighted pathways implicated in glycemic regulation. Exome-array summary statistic results are being made available to the scientific community to enable further discoveries.
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Affiliation(s)
- Sara M Willems
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- General Medicine Center, Saarland University Faculty of Medicine, Homburg, 66421, Germany
| | - Natasha H J Ng
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, UK
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Juan Fernandez
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Rebecca S Fine
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Current address: Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, MA, 02210, USA
| | - Eleanor Wheeler
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jennifer Wessel
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Departments of Epidemiology & Medicine, Schools of Public Health & Medicine, Indiana University, Indianapolis, IN, 46202, USA
- Diabetes Translational Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- General Medicine Division, Massachusetts General Hospital, Boston, MA, USA
| | - Hidetoshi Kitajima
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Gaelle Marenne
- Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore, 117549, Singapore
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Shuai Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Sai Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yuning Chen
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Tibor V Varga
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, SE-205 02, Sweden
| | - Jennifer L Asimit
- Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Shuang Feng
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Rona J Strawbridge
- Mental Health and Wellbeing, School of Health and Wellbeing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8RZ, UK
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, 171 76, Sweden
| | - Erica L Kleinbrink
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201-1928, USA
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - Ping An
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, 63108, USA
| | - Emil V Appel
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juha Auvinen
- Center for Life Course Health Research, University of Oulu, Oulu, 90014, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nathan A Bihlmeyer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Audrey Y Chu
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
| | - James S Floyd
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, 75237, Sweden
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, 90014, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, W2 1PG, UK
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Richard A Jensen
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sirkka Keinanen-Kiukaanniemi
- Faculty of Medicine, Center for Life Course Health Research, University of Oulu, Oulu, Finland
- MRC and Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Man Li
- Division of Nephrology, Internal Medicine, School of Medicine, University of Utah, Salt Lake City, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, 10069, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Alisa K Manning
- Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Karina Meidtner
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, 14558, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, 85764, Germany
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Taulant Muka
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Giorgio Pistis
- Italian National Research Council, Institute of Genetics and Biomedic Research, Cittadella Universitaria, Monserrato, 09042, Italy
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bram Prins
- Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kenneth M Rice
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Serena Sanna
- Italian National Research Council, Institute of Genetics and Biomedic Research, Cittadella Universitaria, Monserrato, 09042, Italy
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, 9700 RB, The Netherlands
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Lorraine Southam
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Vinicius Tragante
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Helen R Warren
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Barts Cardiovascular Research Unit, Barts and The London School of Medicine & Dentistry, Queen Mary University, London, EC1M 6BQ, UK
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Andrianos M Yiorkas
- Section of Investigative Medicine, Department of Medicine, Imperial College London, London, W12 0NN, UK
- Department of Life Sciences, Brunel University London, London, UB8 3PH, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
- Human Genetics Center, The University of Texas School of Public Health; The University of Texas Graduate School of Biomedical Sciences at Houston;, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Eirini Marouli
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Carolina Medina-Gomez
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
| | - Saima Afaq
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Wesam A Alhejily
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Lori L Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Michiel L Bots
- Center for Circulatory Health, University Medical Center Utrecht, Utrecht, 3508GA, The Netherlands
| | - Ivan Brandslund
- Department of Clinical Biochemistry, Lillebaelt Hospital Vejle, Vejle, 7100, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, 5000, Denmark
| | - Ji Chen
- Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - John Danesh
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB18RN, UK
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, W2 1PG, UK
- UK Dementia Research Institute, Imperial College London, London, UK
| | | | - Paul Elliott
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, W2 1PG, UK
- Imperial College NIHR Biomedical Research Centre, London, UK
- Health Data Research UK, Imperial College London, London, UK
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, 17671, Greece
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Paul W Franks
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, SE-205 02, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Steve Franks
- Institute of Reproductive and Developmental Biology, Imperial College London, London, W12 0NN, UK
| | - Andreas Fritsche
- German Center for Diabetes Research (DZD), München-Neuherberg, 85764, Germany
- Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Medicine, Nephrology, and Clinical Chemistry, University Hospital of Tübingen, Tübingen, Germany
| | - Anette P Gjesing
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Göran Hallmans
- Department of Biobank Research, Umeå University, Umeå, SE-901 87, Sweden
| | | | - Karl-Heinz Herzig
- Institute of Biomedicine and Biocenter of Oulu, Faculty of Medicine, Medical Research Center Oulu and Oulu University Hospital, Oulu, Finland
- Department of Gastroenterology and Metabolism, Poznan University of Medical Sciences, Poznan, 60-572, Poland
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Torben Jørgensen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, 2000, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
- Faculty of Medicine, University of Aalborg, Aalborg, 9100, Denmark
| | - Marit E Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
- National Institute of Public Health, Southern Denmark University, Odense, 5000, Denmark
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Eero Kajantie
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, FI-00271, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Children's Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Leena Kinnunen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Heikki A Koistinen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, FI-00271, Finland
- University of Helsinki and Department of Medicine, Helsinki University Hospital, Helsinki, FI-00029, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U Helsinki, Helsinki, FI-00290, Finland
| | - Pirjo Komulainen
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, 70100, Finland
| | - Peter Kovacs
- Integrated Research and Treatment (IFB) Center Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Leslie A Lange
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Denver, Denver, CO, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Aaron Leong
- Division of General Internal Medicine, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jaana Lindström
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Jocelyn E Manning Fox
- Alberta Diabetes Institute IsletCore, University of Alberta, Edmonton, T6G 2E1, Canada
- Department of Pharmacology, University of Alberta, Edmonton, T6G 2E1, Canada
| | - Satu Männistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Nisa M Maruthur
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Medicine, Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
| | | | - Antonella Mulas
- Italian National Research Council, Institute of Genetics and Biomedic Research, Cittadella Universitaria, Monserrato, 09042, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, 07100, Italy
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, 20892, USA
- Data Tecnica International LLC, Glen Echo, MD, 20812, USA
| | - Matthew Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, UK
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Alison Pattie
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Eva R B Petersen
- Department of Clinical Biochemistry, Lillebaelt Hospital Vejle, Vejle, 7100, Denmark
| | - Hannu Puolijoki
- South Ostobothnia Central Hospital, Seinajoki, 60220, Finland
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Paul Redmond
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Frida Renström
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, SE-205 02, Sweden
- Department of Biobank Research, Umeå University, Umeå, SE-901 87, Sweden
| | - Michael Roden
- German Center for Diabetes Research (DZD), München-Neuherberg, 85764, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Institute for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Pakistan
- Department of Biostatistics and Epidemiology, University of Pennsylvania, 19104, USA
| | - Juha Saltevo
- Central Finland Central Hospital, Jyvaskyla, 40620, Finland
| | - Kai Savonen
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, 70100, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, 70029, Finland
| | - Sylvain Sebert
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Faculty of Medicine, Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Tea Skaaby
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, 2000, Denmark
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Alena Stančáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore, 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Betina H Thuesen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, 2000, Denmark
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, 04103, Germany
| | | | - Tiinamaija Tuomi
- Folkhälsan Research Centre, Helsinki, Finland
- Department of Endocrinology, Helsinki University Central Hospital, Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Jaakko Tuomilehto
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, FI-00271, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Saudi Diabetes Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Matti Uusitupa
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, 70210, Finland
| | - Marja Vääräsmäki
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Department of Welfare, Children, Adolescents and Families Unit, National Institute for Health and Welfare, Oulu, Finland
| | - Ilonca Vaartjes
- Center for Circulatory Health, University Medical Center Utrecht, Utrecht, 3508GA, The Netherlands
| | - Magdalena Zoledziewska
- Italian National Research Council, Institute of Genetics and Biomedic Research, Cittadella Universitaria, Monserrato, 09042, Italy
| | - Goncalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Beverley Balkau
- INSERM U1018, Centre de recherche en Épidémiologie et Santé des Populations (CESP), Villejuif, France
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra I Blakemore
- Section of Investigative Medicine, Department of Medicine, Imperial College London, London, W12 0NN, UK
- Department of Life Sciences, Brunel University London, London, UB8 3PH, UK
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, 04103, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG), Helmholtz Zentrum München, University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, 14558, Germany
| | - Eric Boerwinkle
- The Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas, 77030, USA
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, 10069, USA
| | - Mark J Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Barts Cardiovascular Research Unit, Barts and The London School of Medicine & Dentistry, Queen Mary University, London, EC1M 6BQ, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, W2 1PG, UK
- Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
- Harvard School of Medicine, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
| | - Francesco Cucca
- Italian National Research Council, Institute of Genetics and Biomedic Research, Cittadella Universitaria, Monserrato, 09042, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, 07100, Italy
| | - Gert J de Borst
- Department of Vascular Surgery, Division of Surgical Specialties, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, 17671, Greece
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hester M den Ruijter
- Experimental Cardiology Laboratory, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, 3584 CX, The Netherlands
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ele Ferrannini
- CNR Institute of Clinical Physiology, Department of Clinical & Experimental Medicine, University of Pisa, Pisa, Italy
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Harald Grallert
- German Center for Diabetes Research (DZD), München-Neuherberg, 85764, Germany
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Munich, Germany
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, 5000, Denmark
| | - Andrew T Hattersley
- University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Joel N Hirschhorn
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Departments of Pediatrics and Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, 94305, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, 94305, USA
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Kay-Tee Kaw
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Wieland Kiess
- Pediatric Research Center, Department of Women & Child Health, University of Leipzig, Leipzig, Germany
| | - Jaspal S Kooner
- Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
| | - Antje Körner
- Pediatric Research Center, Department of Women & Child Health, University of Leipzig, Leipzig, Germany
| | - Timo Lakka
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, 70100, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, 70029, Finland
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, 70211, Finland
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Lars Lind
- Department of Medical Sciences, Molecular Epidemiology; EpiHealth, Uppsala University, Uppsala, 75185, Sweden
| | - Cecilia M Lindgren
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX3 7BN, UK
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, 2000, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201-1928, USA
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jun Liu
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest University, Winston-Salem, NC, 27157, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, 10069, USA
- The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10069, USA
| | - Patrick E MacDonald
- Alberta Diabetes Institute IsletCore, University of Alberta, Edmonton, T6G 2E1, Canada
- Department of Pharmacology, University of Alberta, Edmonton, T6G 2E1, Canada
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Andrew D Morris
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Barts Cardiovascular Research Unit, Barts and The London School of Medicine & Dentistry, Queen Mary University, London, EC1M 6BQ, UK
| | - Alison Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Foresterhill Health Campus, Aberdeen, AB25 2ZD, UK
| | - Sandosh Padmanabhan
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD2 4BF, UK
| | - Gerard Pasterkamp
- Experimental Cardiology Laboratory, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, 3584 CX, The Netherlands
- Laboratory of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - David Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Michael A Province
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, 63108, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology, Health Systems and Population Health, University of Washington, Seattle, Seattle, WA, USA
| | - Rainer Rauramaa
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, 70100, Finland
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
- Harvard School of Medicine, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Olov Rolandsson
- Department of Public Health & Clinical Medicine, Section for Family Medicine, Umeå University, Umeå, SE-901 85, Sweden
| | - Patrik Rorsman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Igor Rudan
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, 14558, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, 85764, Germany
| | - Robert Sladek
- Department of Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, H3A 1B1, Canada
| | - Blair H Smith
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD2 4BF, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, 04103, Germany
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
| | - Mark Walker
- Institute of Cellular Medicine, The Medical School, Newcastle University, Newcastle, NE2 4HH, UK
| | - Nick J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich, Germany
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, OX3 7LE, UK
- Current address: Genentech, South San Francisco, CA, 94080, USA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Current address: Genentech, South San Francisco, CA, 94080, USA
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, OX3 7LE, UK
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - Inês Barroso
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter Medical School, Exeter, UK
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Vorstman JAS, Scherer SW. Contemplating syndromic autism. Genet Med 2023; 25:100919. [PMID: 37330697 DOI: 10.1016/j.gim.2023.100919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023] Open
Affiliation(s)
- Jacob A S Vorstman
- Department of Psychiatry, Hospital for Sick Children University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada.
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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11
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Zöller B, Manderstedt E, Lind‐Halldén C, Halldén C. Bioinformatic and rare-variant collapsing analyses for type 1 and type 2 diabetes in the UK Biobank reveal novel pleiotropic susceptibility loci. J Diabetes 2023; 15:799-802. [PMID: 37528512 PMCID: PMC10509505 DOI: 10.1111/1753-0407.13452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023] Open
Affiliation(s)
- Bengt Zöller
- Center for Primary Health Care Research, Department of Clinical SciencesLund University and Region SkåneMalmöSweden
| | - Eric Manderstedt
- Center for Primary Health Care Research, Department of Clinical SciencesLund University and Region SkåneMalmöSweden
| | - Christina Lind‐Halldén
- Department of Environmental Science and BioscienceKristianstad UniversityKristianstadSweden
| | - Christer Halldén
- Center for Primary Health Care Research, Department of Clinical SciencesLund University and Region SkåneMalmöSweden
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12
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DeForest N, Kavitha B, Hu S, Isaac R, Krohn L, Wang M, Du X, De Arruda Saldanha C, Gylys J, Merli E, Abagyan R, Najmi L, Mohan V, Flannick J, Peloso GM, Gordts PL, Heinz S, Deaton AM, Khera AV, Olefsky J, Radha V, Majithia AR. Human gain-of-function variants in HNF1A confer protection from diabetes but independently increase hepatic secretion of atherogenic lipoproteins. CELL GENOMICS 2023; 3:100339. [PMID: 37492105 PMCID: PMC10363808 DOI: 10.1016/j.xgen.2023.100339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/08/2023] [Accepted: 05/03/2023] [Indexed: 07/27/2023]
Abstract
Loss-of-function mutations in hepatocyte nuclear factor 1A (HNF1A) are known to cause rare forms of diabetes and alter hepatic physiology through unclear mechanisms. In the general population, 1:100 individuals carry a rare, protein-coding HNF1A variant, most of unknown functional consequence. To characterize the full allelic series, we performed deep mutational scanning of 11,970 protein-coding HNF1A variants in human hepatocytes and clinical correlation with 553,246 exome-sequenced individuals. Surprisingly, we found that ∼1:5 rare protein-coding HNF1A variants in the general population cause molecular gain of function (GOF), increasing the transcriptional activity of HNF1A by up to 50% and conferring protection from type 2 diabetes (odds ratio [OR] = 0.77, p = 0.007). Increased hepatic expression of HNF1A promoted a pro-atherogenic serum profile mediated in part by enhanced transcription of risk genes including ANGPTL3 and PCSK9. In summary, ∼1:300 individuals carry a GOF variant in HNF1A that protects carriers from diabetes but enhances hepatic secretion of atherogenic lipoproteins.
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Affiliation(s)
- Natalie DeForest
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Babu Kavitha
- Department of Molecular Genetics, Madras Diabetes Research Foundation, ICMR Centre for Advanced Research on Diabetes, Affiliated with University of Madras, Chennai, India
| | - Siqi Hu
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roi Isaac
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Minxian Wang
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaomi Du
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Camila De Arruda Saldanha
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jenny Gylys
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Edoardo Merli
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Laeya Najmi
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Viswanathan Mohan
- Department of Diabetology, Dr. Mohan’s Diabetes Specialties Centre (IDF Centre of Education) & Madras Diabetes Research Foundation (ICMR Centre for Advanced Research on Diabetes), Chennai, India
| | - Alnylam Human Genetics
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Genetics, Madras Diabetes Research Foundation, ICMR Centre for Advanced Research on Diabetes, Affiliated with University of Madras, Chennai, India
- Alnylam Pharmaceuticals, Cambridge, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Diabetology, Dr. Mohan’s Diabetes Specialties Centre (IDF Centre of Education) & Madras Diabetes Research Foundation (ICMR Centre for Advanced Research on Diabetes), Chennai, India
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - AMP-T2D Consortium
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Genetics, Madras Diabetes Research Foundation, ICMR Centre for Advanced Research on Diabetes, Affiliated with University of Madras, Chennai, India
- Alnylam Pharmaceuticals, Cambridge, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Diabetology, Dr. Mohan’s Diabetes Specialties Centre (IDF Centre of Education) & Madras Diabetes Research Foundation (ICMR Centre for Advanced Research on Diabetes), Chennai, India
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jason Flannick
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Philip L.S.M. Gordts
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
| | - Sven Heinz
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Amit V. Khera
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jerrold Olefsky
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Venkatesan Radha
- Department of Molecular Genetics, Madras Diabetes Research Foundation, ICMR Centre for Advanced Research on Diabetes, Affiliated with University of Madras, Chennai, India
| | - Amit R. Majithia
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
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13
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Chen CY, Tian R, Ge T, Lam M, Sanchez-Andrade G, Singh T, Urpa L, Liu JZ, Sanderson M, Rowley C, Ironfield H, Fang T, Daly M, Palotie A, Tsai EA, Huang H, Hurles ME, Gerety SS, Lencz T, Runz H. The impact of rare protein coding genetic variation on adult cognitive function. Nat Genet 2023:10.1038/s41588-023-01398-8. [PMID: 37231097 DOI: 10.1038/s41588-023-01398-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/13/2023] [Indexed: 05/27/2023]
Abstract
Compelling evidence suggests that human cognitive function is strongly influenced by genetics. Here, we conduct a large-scale exome study to examine whether rare protein-coding variants impact cognitive function in the adult population (n = 485,930). We identify eight genes (ADGRB2, KDM5B, GIGYF1, ANKRD12, SLC8A1, RC3H2, CACNA1A and BCAS3) that are associated with adult cognitive function through rare coding variants with large effects. Rare genetic architecture for cognitive function partially overlaps with that of neurodevelopmental disorders. In the case of KDM5B we show how the genetic dosage of one of these genes may determine the variability of cognitive, behavioral and molecular traits in mice and humans. We further provide evidence that rare and common variants overlap in association signals and contribute additively to cognitive function. Our study introduces the relevance of rare coding variants for cognitive function and unveils high-impact monogenic contributions to how cognitive function is distributed in the normal adult population.
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Affiliation(s)
- Chia-Yen Chen
- Research and Development, Biogen Inc, Cambridge, MA, USA.
| | - Ruoyu Tian
- Research and Development, Biogen Inc, Cambridge, MA, USA
- Dewpoint Therapeutics, Boston, MA, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Max Lam
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | | | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lea Urpa
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jimmy Z Liu
- Research and Development, Biogen Inc, Cambridge, MA, USA
- GlaxoSmithKline, Philadelphia, PA, USA
| | | | | | | | - Terry Fang
- Research and Development, Biogen Inc, Cambridge, MA, USA
| | - Mark Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ellen A Tsai
- Research and Development, Biogen Inc, Cambridge, MA, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | - Todd Lencz
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Heiko Runz
- Research and Development, Biogen Inc, Cambridge, MA, USA.
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14
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Xue D, Narisu N, Taylor DL, Zhang M, Grenko C, Taylor HJ, Yan T, Tang X, Sinha N, Zhu J, Vandana JJ, Chong ACN, Lee A, Mansell EC, Swift AJ, Erdos MR, Zhou T, Bonnycastle LL, Zhong A, Chen S, Collins FS. Functional interrogation of twenty type 2 diabetes-associated genes using isogenic hESC-derived β-like cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539774. [PMID: 37214922 PMCID: PMC10197532 DOI: 10.1101/2023.05.07.539774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional role of many loci has remained unexplored. In this study, we engineered isogenic knockout human embryonic stem cell (hESC) lines for 20 genes associated with T2D risk. We systematically examined β-cell differentiation, insulin production and secretion, and survival. We performed RNA-seq and ATAC-seq on hESC-β cells from each knockout line. Analyses of T2D GWAS signals overlapping with HNF4A-dependent ATAC peaks identified a specific SNP as a likely causal variant. In addition, we performed integrative association analyses and identified four genes ( CP, RNASE1, PCSK1N and GSTA2 ) associated with insulin production, and two genes ( TAGLN3 and DHRS2 ) associated with sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental hESC line, to identify a single likely functional variant at each of 23 T2D GWAS signals.
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15
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Nguyen NH, Sarangi S, McChesney EM, Sheng S, Porter AW, Kleyman TR, Pitluk ZW, Brodsky JL. Genome mining yields new disease-associated ROMK variants with distinct defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539609. [PMID: 37214976 PMCID: PMC10197530 DOI: 10.1101/2023.05.05.539609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bartter syndrome is a group of rare genetic disorders that compromise kidney function by impairing electrolyte reabsorption. Left untreated, the resulting hyponatremia, hypokalemia, and dehydration can be fatal. Although there is no cure for this disease, specific genes that lead to different Bartter syndrome subtypes have been identified. Bartter syndrome type II specifically arises from mutations in the KCNJ1 gene, which encodes the renal outer medullary potassium channel, ROMK. To date, over 40 Bartter syndrome-associated mutations in KCNJ1 have been identified. Yet, their molecular defects are mostly uncharacterized. Nevertheless, a subset of disease-linked mutations compromise ROMK folding in the endoplasmic reticulum (ER), which in turn results in premature degradation via the ER associated degradation (ERAD) pathway. To identify uncharacterized human variants that might similarly lead to premature degradation and thus disease, we mined three genomic databases. First, phenotypic data in the UK Biobank were analyzed using a recently developed computational platform to identify individuals carrying KCNJ1 variants with clinical features consistent with Bartter syndrome type II. In parallel, we examined ROMK genomic data in both the NIH TOPMed and ClinVar databases with the aid of a computational algorithm that predicts protein misfolding and disease severity. Subsequent phenotypic studies using a high throughput yeast screen to assess ROMK function-and analyses of ROMK biogenesis in yeast and human cells-identified four previously uncharacterized mutations. Among these, one mutation uncovered from the two parallel approaches (G228E) destabilized ROMK and targeted it for ERAD, resulting in reduced protein expression at the cell surface. Another ERAD-targeted ROMK mutant (L320P) was found in only one of the screens. In contrast, another mutation (T300R) was ERAD-resistant, but defects in ROMK activity were apparent after expression and two-electrode voltage clamp measurements in Xenopus oocytes. Together, our results outline a new computational and experimental pipeline that can be applied to identify disease-associated alleles linked to a range of other potassium channels, and further our understanding of the ROMK structure-function relationship that may aid future therapeutic strategies. Author Summary Bartter syndrome is a rare genetic disorder characterized by defective renal electrolyte handing, leading to debilitating symptoms and, in some patients, death in infancy. Currently, there is no cure for this disease. Bartter syndrome is divided into five types based on the causative gene. Bartter syndrome type II results from genetic variants in the gene encoding the ROMK protein, which is expressed in the kidney and assists in regulating sodium, potassium, and water homeostasis. Prior work established that some disease-associated ROMK mutants misfold and are destroyed soon after their synthesis in the endoplasmic reticulum (ER). Because a growing number of drugs have been identified that correct defective protein folding, we wished to identify an expanded cohort of similarly misshapen and unstable disease-associated ROMK variants. To this end, we developed a pipeline that employs computational analyses of human genome databases with genetic and biochemical assays. Next, we both confirmed the identity of known variants and uncovered previously uncharacterized ROMK variants associated with Bartter syndrome type II. Further analyses indicated that select mutants are targeted for ER-associated degradation, while another mutant compromises ROMK function. This work sets-the-stage for continued mining for ROMK loss of function alleles as well as other potassium channels, and positions select Bartter syndrome mutations for correction using emerging pharmaceuticals.
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16
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Bi W, Zhou W, Zhang P, Sun Y, Yue W, Lee S. Scalable mixed model methods for set-based association studies on large-scale categorical data analysis and its application to exome-sequencing data in UK Biobank. Am J Hum Genet 2023; 110:762-773. [PMID: 37019109 PMCID: PMC10183366 DOI: 10.1016/j.ajhg.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
The ongoing release of large-scale sequencing data in the UK Biobank allows for the identification of associations between rare variants and complex traits. SAIGE-GENE+ is a valid approach to conducting set-based association tests for quantitative and binary traits. However, for ordinal categorical phenotypes, applying SAIGE-GENE+ with treating the trait as quantitative or binarizing the trait can cause inflated type I error rates or power loss. In this study, we propose a scalable and accurate method for rare-variant association tests, POLMM-GENE, in which we used a proportional odds logistic mixed model to characterize ordinal categorical phenotypes while adjusting for sample relatedness. POLMM-GENE fully utilizes the categorical nature of phenotypes and thus can well control type I error rates while remaining powerful. In the analyses of UK Biobank 450k whole-exome-sequencing data for five ordinal categorical traits, POLMM-GENE identified 54 gene-phenotype associations.
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Affiliation(s)
- Wenjian Bi
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China; Center for Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China; Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China.
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Peipei Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, China
| | - Yaoyao Sun
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China; NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Weihua Yue
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China; NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China; Henan Key Lab of Biological Psychiatry, the Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China; Chinese Institute for Brain Research, Beijing, China
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, Korea.
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17
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Nag A, Dhindsa RS, Middleton L, Jiang X, Vitsios D, Wigmore E, Allman EL, Reznichenko A, Carss K, Smith KR, Wang Q, Challis B, Paul DS, Harper AR, Petrovski S. Effects of protein-coding variants on blood metabolite measurements and clinical biomarkers in the UK Biobank. Am J Hum Genet 2023; 110:487-498. [PMID: 36809768 PMCID: PMC10027475 DOI: 10.1016/j.ajhg.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Genome-wide association studies (GWASs) have established the contribution of common and low-frequency variants to metabolic blood measurements in the UK Biobank (UKB). To complement existing GWAS findings, we assessed the contribution of rare protein-coding variants in relation to 355 metabolic blood measurements-including 325 predominantly lipid-related nuclear magnetic resonance (NMR)-derived blood metabolite measurements (Nightingale Health Plc) and 30 clinical blood biomarkers-using 412,393 exome sequences from four genetically diverse ancestries in the UKB. Gene-level collapsing analyses were conducted to evaluate a diverse range of rare-variant architectures for the metabolic blood measurements. Altogether, we identified significant associations (p < 1 × 10-8) for 205 distinct genes that involved 1,968 significant relationships for the Nightingale blood metabolite measurements and 331 for the clinical blood biomarkers. These include associations for rare non-synonymous variants in PLIN1 and CREB3L3 with lipid metabolite measurements and SYT7 with creatinine, among others, which may not only provide insights into novel biology but also deepen our understanding of established disease mechanisms. Of the study-wide significant clinical biomarker associations, 40% were not previously detected on analyzing coding variants in a GWAS in the same cohort, reinforcing the importance of studying rare variation to fully understand the genetic architecture of metabolic blood measurements.
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Affiliation(s)
- Abhishek Nag
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ryan S Dhindsa
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Lawrence Middleton
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Xiao Jiang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dimitrios Vitsios
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Eleanor Wigmore
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Erik L Allman
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Anna Reznichenko
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Keren Carss
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Katherine R Smith
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Benjamin Challis
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Andrew R Harper
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Early Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia.
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18
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Gardner EJ, Kentistou KA, Stankovic S, Lockhart S, Wheeler E, Day FR, Kerrison ND, Wareham NJ, Langenberg C, O'Rahilly S, Ong KK, Perry JRB. Damaging missense variants in IGF1R implicate a role for IGF-1 resistance in the etiology of type 2 diabetes. CELL GENOMICS 2022; 2:None. [PMID: 36530175 PMCID: PMC9750938 DOI: 10.1016/j.xgen.2022.100208] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/12/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022]
Abstract
Type 2 diabetes (T2D) is a heritable metabolic disorder. While population studies have identified hundreds of common genetic variants associated with T2D, the role of rare (frequency < 0.1%) protein-coding variation is less clear. We performed exome sequence analysis in 418,436 (n = 32,374 T2D cases) individuals in the UK Biobank. We identified previously reported genes (GCK, GIGYF1, HNF1A) in addition to missense variants in ZEB2 (n = 31 carriers; odds ratio [OR] = 5.5 [95% confidence interval = 2.5-12.0]; p = 6.4 × 10-7), MLXIPL (n = 245; OR = 2.3 [1.6-3.2]; p = 3.2 × 10-7), and IGF1R (n = 394; OR = 2.4 [1.8-3.2]; p = 1.3 × 10-10). Carriers of damaging missense variants within IGF1R were also shorter (-2.2 cm [-1.8 to -2.7]; p = 1.2 × 10-19) and had higher circulating insulin-like growth factor-1 (IGF-1) protein levels (2.3 nmol/L [1.7-2.9]; p = 2.8 × 10-14), indicating relative IGF-1 resistance. A likely causal role of IGF-1 resistance was supported by Mendelian randomization analyses using common variants. These results increase understanding of the genetic architecture of T2D and highlight the growth hormone/IGF-1 axis as a potential therapeutic target.
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Affiliation(s)
- Eugene J Gardner
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Katherine A Kentistou
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Stasa Stankovic
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Samuel Lockhart
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Felix R Day
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Nicola D Kerrison
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.,Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stephen O'Rahilly
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.,NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Ken K Ong
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.,Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - John R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.,Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
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19
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Nag A, Dhindsa RS, Mitchell J, Vasavda C, Harper AR, Vitsios D, Ahnmark A, Bilican B, Madeyski-Bengtson K, Zarrouki B, Zoghbi AW, Wang Q, Smith KR, Alegre-Díaz J, Kuri-Morales P, Berumen J, Tapia-Conyer R, Emberson J, Torres JM, Collins R, Smith DM, Challis B, Paul DS, Bohlooly-Y M, Snowden M, Baker D, Fritsche-Danielson R, Pangalos MN, Petrovski S. Human genetics uncovers MAP3K15 as an obesity-independent therapeutic target for diabetes. SCIENCE ADVANCES 2022; 8:eadd5430. [PMID: 36383675 PMCID: PMC9668288 DOI: 10.1126/sciadv.add5430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/27/2022] [Indexed: 05/30/2023]
Abstract
We performed collapsing analyses on 454,796 UK Biobank (UKB) exomes to detect gene-level associations with diabetes. Recessive carriers of nonsynonymous variants in MAP3K15 were 30% less likely to develop diabetes (P = 5.7 × 10-10) and had lower glycosylated hemoglobin (β = -0.14 SD units, P = 1.1 × 10-24). These associations were independent of body mass index, suggesting protection against insulin resistance even in the setting of obesity. We replicated these findings in 96,811 Admixed Americans in the Mexico City Prospective Study (P < 0.05)Moreover, the protective effect of MAP3K15 variants was stronger in individuals who did not carry the Latino-enriched SLC16A11 risk haplotype (P = 6.0 × 10-4). Separately, we identified a Finnish-enriched MAP3K15 protein-truncating variant associated with decreased odds of both type 1 and type 2 diabetes (P < 0.05) in FinnGen. No adverse phenotypes were associated with protein-truncating MAP3K15 variants in the UKB, supporting this gene as a therapeutic target for diabetes.
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Affiliation(s)
- Abhishek Nag
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ryan S. Dhindsa
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Jonathan Mitchell
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Chirag Vasavda
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Andrew R. Harper
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dimitrios Vitsios
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Andrea Ahnmark
- Bioscience Metabolism, Early CVRM, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Bilada Bilican
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Katja Madeyski-Bengtson
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Bader Zarrouki
- Bioscience Metabolism, Early CVRM, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anthony W. Zoghbi
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Katherine R. Smith
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Jesus Alegre-Díaz
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Pablo Kuri-Morales
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Jaime Berumen
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Jonathan Emberson
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, England, UK
| | - Jason M. Torres
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, England, UK
| | - Rory Collins
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, England, UK
| | - David M. Smith
- Emerging Innovations, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Benjamin Challis
- Translational Science and Experimental Medicine, Early CVRM, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dirk S. Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Mohammad Bohlooly-Y
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mike Snowden
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - David Baker
- Bioscience Metabolism, Early CVRM, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
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20
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Karczewski KJ, Solomonson M, Chao KR, Goodrich JK, Tiao G, Lu W, Riley-Gillis BM, Tsai EA, Kim HI, Zheng X, Rahimov F, Esmaeeli S, Grundstad AJ, Reppell M, Waring J, Jacob H, Sexton D, Bronson PG, Chen X, Hu X, Goldstein JI, King D, Vittal C, Poterba T, Palmer DS, Churchhouse C, Howrigan DP, Zhou W, Watts NA, Nguyen K, Nguyen H, Mason C, Farnham C, Tolonen C, Gauthier LD, Gupta N, MacArthur DG, Rehm HL, Seed C, Philippakis AA, Daly MJ, Davis JW, Runz H, Miller MR, Neale BM. Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes. CELL GENOMICS 2022; 2:100168. [PMID: 36778668 PMCID: PMC9903662 DOI: 10.1016/j.xgen.2022.100168] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 07/16/2022] [Indexed: 01/20/2023]
Abstract
Genome-wide association studies have successfully discovered thousands of common variants associated with human diseases and traits, but the landscape of rare variations in human disease has not been explored at scale. Exome-sequencing studies of population biobanks provide an opportunity to systematically evaluate the impact of rare coding variations across a wide range of phenotypes to discover genes and allelic series relevant to human health and disease. Here, we present results from systematic association analyses of 4,529 phenotypes using single-variant and gene tests of 394,841 individuals in the UK Biobank with exome-sequence data. We find that the discovery of genetic associations is tightly linked to frequency and is correlated with metrics of deleteriousness and natural selection. We highlight biological findings elucidated by these data and release the dataset as a public resource alongside the Genebass browser for rapidly exploring rare-variant association results.
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Affiliation(s)
- Konrad J. Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia K. Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wenhan Lu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Hye In Kim
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xiuwen Zheng
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Fedik Rahimov
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Sahar Esmaeeli
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Mark Reppell
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Jeff Waring
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Howard Jacob
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | | | - Xing Chen
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xinli Hu
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Jacqueline I. Goldstein
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel King
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Vittal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Duncan S. Palmer
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claire Churchhouse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel P. Howrigan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas A. Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Huy Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cara Mason
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Farnham
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Charlotte Tolonen
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Laura D. Gauthier
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Namrata Gupta
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cotton Seed
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - J. Wade Davis
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Melissa R. Miller
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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21
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Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes. Nat Commun 2022; 13:5332. [PMID: 36088354 PMCID: PMC9464252 DOI: 10.1038/s41467-022-32864-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/22/2022] [Indexed: 12/05/2022] Open
Abstract
Here we present an exome-wide rare genetic variant association study for 30 blood biomarkers in 191,971 individuals in the UK Biobank. We compare gene-based association tests for separate functional variant categories to increase interpretability and identify 193 significant gene-biomarker associations. Genes associated with biomarkers were ~ 4.5-fold enriched for conferring Mendelian disorders. In addition to performing weighted gene-based variant collapsing tests, we design and apply variant-category-specific kernel-based tests that integrate quantitative functional variant effect predictions for missense variants, splicing and the binding of RNA-binding proteins. For these tests, we present a computationally efficient combination of the likelihood-ratio and score tests that found 36% more associations than the score test alone while also controlling the type-1 error. Kernel-based tests identified 13% more associations than their gene-based collapsing counterparts and had advantages in the presence of gain of function missense variants. We introduce local collapsing by amino acid position for missense variants and use it to interpret associations and identify potential novel gain of function variants in PIEZO1. Our results show the benefits of investigating different functional mechanisms when performing rare-variant association tests, and demonstrate pervasive rare-variant contribution to biomarker variability.
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22
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Deaton AM, Dubey A, Ward LD, Dornbos P, Flannick J, Yee E, Ticau S, Noetzli L, Parker MM, Hoffing RA, Willis C, Plekan ME, Holleman AM, Hinkle G, Fitzgerald K, Vaishnaw AK, Nioi P. Rare loss of function variants in the hepatokine gene INHBE protect from abdominal obesity. Nat Commun 2022; 13:4319. [PMID: 35896531 PMCID: PMC9329324 DOI: 10.1038/s41467-022-31757-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/01/2022] [Indexed: 02/07/2023] Open
Abstract
Identifying genetic variants associated with lower waist-to-hip ratio can reveal new therapeutic targets for abdominal obesity. We use exome sequences from 362,679 individuals to identify genes associated with waist-to-hip ratio adjusted for BMI (WHRadjBMI), a surrogate for abdominal fat that is causally linked to type 2 diabetes and coronary heart disease. Predicted loss of function (pLOF) variants in INHBE associate with lower WHRadjBMI and this association replicates in data from AMP-T2D-GENES. INHBE encodes a secreted protein, the hepatokine activin E. In vitro characterization of the most common INHBE pLOF variant in our study, indicates an in-frame deletion resulting in a 90% reduction in secreted protein levels. We detect associations with lower WHRadjBMI for variants in ACVR1C, encoding an activin receptor, further highlighting the involvement of activins in regulating fat distribution. These findings highlight activin E as a potential therapeutic target for abdominal obesity, a phenotype linked to cardiometabolic disease.
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Affiliation(s)
| | | | | | - Peter Dornbos
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jason Flannick
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Elaine Yee
- Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | - Paul Nioi
- Alnylam Pharmaceuticals, Cambridge, MA, USA
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23
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Middleton L, Harper AR, Nag A, Wang Q, Reznichenko A, Vitsios D, Petrovski S. Gene-SCOUT: identifying genes with similar continuous trait fingerprints from phenome-wide association analyses. Nucleic Acids Res 2022; 50:4289-4301. [PMID: 35474393 PMCID: PMC9071452 DOI: 10.1093/nar/gkac274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/31/2022] [Accepted: 04/09/2022] [Indexed: 12/24/2022] Open
Abstract
Large-scale phenome-wide association studies performed using densely-phenotyped cohorts such as the UK Biobank (UKB), reveal many statistically robust gene-phenotype relationships for both clinical and continuous traits. Here, we present Gene-SCOUT, a tool used to identify genes with similar continuous trait fingerprints to a gene of interest. A fingerprint reflects the continuous traits identified to be statistically associated with a gene of interest based on multiple underlying rare variant genetic architectures. Similarities between genes are evaluated by the cosine similarity measure, to capture concordant effect directionality, elucidating clusters of genes in a high dimensional space. The underlying gene-biomarker population-scale association statistics were obtained from a gene-level rare variant collapsing analysis performed on over 1500 continuous traits using 394 692 UKB participant exomes, with additional metabolomic trait associations provided through Nightingale Health's recent study of 121 394 of these participants. We demonstrate that gene similarity estimates from Gene-SCOUT provide stronger enrichments for clinical traits compared to existing methods. Furthermore, we provide a fully interactive web-resource (http://genescout.public.cgr.astrazeneca.com) to explore the pre-calculated exome-wide similarities. This resource enables a user to examine the biological relevance of the most similar genes for Gene Ontology (GO) enrichment and UKB clinical trait enrichment statistics, as well as a detailed breakdown of the traits underpinning a given fingerprint.
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Affiliation(s)
- Lawrence Middleton
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Andrew R Harper
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Abhishek Nag
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Anna Reznichenko
- Translational Science & Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Dimitrios Vitsios
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
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