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Hanssen F, Garcia MU, Folkersen L, Pedersen A, Lescai F, Jodoin S, Miller E, Seybold M, Wacker O, Smith N, Gabernet G, Nahnsen S. Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery. NAR Genom Bioinform 2024; 6:lqae031. [PMID: 38666213 PMCID: PMC11044436 DOI: 10.1093/nargab/lqae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2 emissions low. The code is available at https://nf-co.re/sarek.
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Affiliation(s)
- Friederike Hanssen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, 72076 Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
| | - Maxime U Garcia
- Seqera Labs, Carrer de Marià Aguilò, 28, Barcelona 08005, Spain
- Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Visionsgatan 4, Solna 17164, Sweden
- National Genomics Infrastructure, SciLifeLab, SciLifeLab, Tomtebodavägen 23, Solna 17165, Sweden
| | | | | | - Francesco Lescai
- Department of Biology and Biotechnology ”L. Spallanzani”, University of Pavia, via Ferrata, 9, Pavia, 27100 PV, Italy
| | - Susanne Jodoin
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Edmund Miller
- Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA
| | - Matthias Seybold
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Oskar Wacker
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Nicholas Smith
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, Garching, 85748 Bavaria, Germany
| | - Gisela Gabernet
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Pathology, Yale School of Medicine, 300 George, New Haven, CT 06510, USA
| | - Sven Nahnsen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, 72076 Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
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Santorsola M, Lescai F. The promise of explainable deep learning for omics data analysis: Adding new discovery tools to AI. N Biotechnol 2023; 77:1-11. [PMID: 37329982 DOI: 10.1016/j.nbt.2023.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/01/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Deep learning has already revolutionised the way a wide range of data is processed in many areas of daily life. The ability to learn abstractions and relationships from heterogeneous data has provided impressively accurate prediction and classification tools to handle increasingly big datasets. This has a significant impact on the growing wealth of omics datasets, with the unprecedented opportunity for a better understanding of the complexity of living organisms. While this revolution is transforming the way these data are analyzed, explainable deep learning is emerging as an additional tool with the potential to change the way biological data is interpreted. Explainability addresses critical issues such as transparency, so important when computational tools are introduced especially in clinical environments. Moreover, it empowers artificial intelligence with the capability to provide new insights into the input data, thus adding an element of discovery to these already powerful resources. In this review, we provide an overview of the transformative effects explainable deep learning is having on multiple sectors, ranging from genome engineering and genomics, from radiomics to drug design and clinical trials. We offer a perspective to life scientists, to better understand the potential of these tools, and a motivation to implement them in their research, by suggesting learning resources they can use to move their first steps in this field.
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Affiliation(s)
| | - Francesco Lescai
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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3
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Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian fusion and centromere repositioning contributed to the formation of satellite-free centromeres during the evolution of zebras. Mol Biol Evol 2022; 39:6650076. [PMID: 35881460 PMCID: PMC9356731 DOI: 10.1093/molbev/msac162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Centromeres are epigenetically specified by the histone H3 variant CENP-A and typically associated to highly repetitive satellite DNA. We previously discovered natural satellite-free neocentromeres in Equus caballus and E. asinus. Here, through ChIP-seq with an anti-CENP-A antibody, we found an extraordinarily high number of centromeres lacking satellite DNA in the zebras E. burchelli (15 of 22) and E. grevyi (13 of 23), demonstrating that the absence of satellite DNA at the majority of centromeres is compatible with genome stability and species survival and challenging the role of satellite DNA in centromere function. Nine satellite-free centromeres are shared between the two species in agreement with their recent separation. We assembled all centromeric regions and improved the reference genome of E. burchelli. Sequence analysis of the CENP-A binding domains revealed that they are LINE-1 and AT-rich with four of them showing DNA amplification. In the two zebras, satellite-free centromeres emerged from centromere repositioning or following Robertsonian fusion. In five chromosomes, the centromeric function arose near the fusion points, which are located within regions marked by traces of ancestral pericentromeric sequences. Therefore, besides centromere repositioning, Robertsonian fusions are an important source of satellite-free centromeres during evolution. Finally, in one case, a satellite-free centromere was seeded on an inversion breakpoint. At eleven chromosomes, whose primary constrictions seemed to be associated to satellite repeats by cytogenetic analysis, satellite-free neocentromeres were instead located near the ancestral inactivated satellite-based centromeres, therefore, the centromeric function has shifted away from a satellite repeat containing locus to a satellite-free new position.
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Affiliation(s)
- Eleonora Cappelletti
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesca M Piras
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Lorenzo Sola
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Marco Santagostino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Wasma A Abdelgadir
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Raimondi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesco Lescai
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Solomon G Nergadze
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
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4
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Singh T, Poterba T, Curtis D, Akil H, Al Eissa M, Barchas JD, Bass N, Bigdeli TB, Breen G, Bromet EJ, Buckley PF, Bunney WE, Bybjerg-Grauholm J, Byerley WF, Chapman SB, Chen WJ, Churchhouse C, Craddock N, Cusick CM, DeLisi L, Dodge S, Escamilla MA, Eskelinen S, Fanous AH, Faraone SV, Fiorentino A, Francioli L, Gabriel SB, Gage D, Gagliano Taliun SA, Ganna A, Genovese G, Glahn DC, Grove J, Hall MH, Hämäläinen E, Heyne HO, Holi M, Hougaard DM, Howrigan DP, Huang H, Hwu HG, Kahn RS, Kang HM, Karczewski KJ, Kirov G, Knowles JA, Lee FS, Lehrer DS, Lescai F, Malaspina D, Marder SR, McCarroll SA, McIntosh AM, Medeiros H, Milani L, Morley CP, Morris DW, Mortensen PB, Myers RM, Nordentoft M, O'Brien NL, Olivares AM, Ongur D, Ouwehand WH, Palmer DS, Paunio T, Quested D, Rapaport MH, Rees E, Rollins B, Satterstrom FK, Schatzberg A, Scolnick E, Scott LJ, Sharp SI, Sklar P, Smoller JW, Sobell JL, Solomonson M, Stahl EA, Stevens CR, Suvisaari J, Tiao G, Watson SJ, Watts NA, Blackwood DH, Børglum AD, Cohen BM, Corvin AP, Esko T, Freimer NB, Glatt SJ, Hultman CM, McQuillin A, Palotie A, Pato CN, Pato MT, Pulver AE, St Clair D, Tsuang MT, Vawter MP, Walters JT, Werge TM, Ophoff RA, Sullivan PF, Owen MJ, Boehnke M, O'Donovan MC, Neale BM, Daly MJ. Rare coding variants in ten genes confer substantial risk for schizophrenia. Nature 2022; 604:509-516. [PMID: 35396579 PMCID: PMC9805802 DOI: 10.1038/s41586-022-04556-w] [Citation(s) in RCA: 258] [Impact Index Per Article: 129.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 02/16/2022] [Indexed: 01/05/2023]
Abstract
Rare coding variation has historically provided the most direct connections between gene function and disease pathogenesis. By meta-analysing the whole exomes of 24,248 schizophrenia cases and 97,322 controls, we implicate ultra-rare coding variants (URVs) in 10 genes as conferring substantial risk for schizophrenia (odds ratios of 3-50, P < 2.14 × 10-6) and 32 genes at a false discovery rate of <5%. These genes have the greatest expression in central nervous system neurons and have diverse molecular functions that include the formation, structure and function of the synapse. The associations of the NMDA (N-methyl-D-aspartate) receptor subunit GRIN2A and AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptor subunit GRIA3 provide support for dysfunction of the glutamatergic system as a mechanistic hypothesis in the pathogenesis of schizophrenia. We observe an overlap of rare variant risk among schizophrenia, autism spectrum disorders1, epilepsy and severe neurodevelopmental disorders2, although different mutation types are implicated in some shared genes. Most genes described here, however, are not implicated in neurodevelopment. We demonstrate that genes prioritized from common variant analyses of schizophrenia are enriched in rare variant risk3, suggesting that common and rare genetic risk factors converge at least partially on the same underlying pathogenic biological processes. Even after excluding significantly associated genes, schizophrenia cases still carry a substantial excess of URVs, which indicates that more risk genes await discovery using this approach.
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Affiliation(s)
- Tarjinder Singh
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Timothy Poterba
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Curtis
- UCL Genetics Institute, University College London, London, UK
- Centre for Psychiatry, Queen Mary University London, London, UK
| | - Huda Akil
- Department of Psychiatry, Michigan Neuroscience Institute, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Mariam Al Eissa
- Division of Psychiatry, University College London, London, UK
| | | | - Nicholas Bass
- Division of Psychiatry, University College London, London, UK
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate College of Medicine, Brooklyn, NY, USA
| | - Gerome Breen
- Social Genetic and Developmental Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Evelyn J Bromet
- Department of Psychiatry and Behavioral Health, Health Sciences Center, Stony Brook University, Stony Brook, NY, USA
| | - Peter F Buckley
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - William E Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA
| | - Jonas Bybjerg-Grauholm
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - William F Byerley
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Sinéad B Chapman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wei J Chen
- College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Claire Churchhouse
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Caroline M Cusick
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lynn DeLisi
- Department of Psychiatry, Cambridge Health Alliance, Cambridge Hospital, Cambridge, MA, USA
| | - Sheila Dodge
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Saana Eskelinen
- University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Public Health Solutions, Mental Health Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Ayman H Fanous
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Stephen V Faraone
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | | | - Laurent Francioli
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Stacey B Gabriel
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Gage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sarah A Gagliano Taliun
- Faculté de Médecine, Université de Montréal, Montreal, Quebec, Canada
- Montréal Heart Institute, Montreal, Quebec, Canada
| | - Andrea Ganna
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Boston, MA, USA
| | - Jakob Grove
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Department of Biomedicine and Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Mei-Hua Hall
- McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Henrike O Heyne
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Matti Holi
- Department of Psychiatry, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - David M Hougaard
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Daniel P Howrigan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hai-Gwo Hwu
- Department of Psychiatry, National Taiwan University, Taipei, Taiwan
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- MIRECC, JP Peters VA Hospital, Bronx, NY, USA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - James A Knowles
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | | | - Douglas S Lehrer
- Department of Psychiatry, Wright State University, Dayton, OH, USA
| | - Francesco Lescai
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Dolores Malaspina
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen R Marder
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Helena Medeiros
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Lili Milani
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Christopher P Morley
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
- Department of Public Health and Preventive Medicine and Department of Family Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | | | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Merete Nordentoft
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Copenhagen Research Center for Mental Health, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niamh L O'Brien
- Division of Psychiatry, University College London, London, UK
| | - Ana Maria Olivares
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dost Ongur
- McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | | | - Duncan S Palmer
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tiina Paunio
- Department of Psychiatry, University of Helsinki, Helsinki, Finland
| | | | - Mark H Rapaport
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Brandi Rollins
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Alan Schatzberg
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Edward Scolnick
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Sally I Sharp
- Division of Psychiatry, University College London, London, UK
| | - Pamela Sklar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Janet L Sobell
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eli A Stahl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christine R Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Stanley J Watson
- Department of Psychiatry, Michigan Neuroscience Institute, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas A Watts
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Anders D Børglum
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Department of Biomedicine and Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Bruce M Cohen
- McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | | | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Nelson B Freimer
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stephen J Glatt
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | | | | | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Carlos N Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate College of Medicine, Brooklyn, NY, USA
| | - Michele T Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate College of Medicine, Brooklyn, NY, USA
| | - Ann E Pulver
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Ming T Tsuang
- Center for Behavioral Genomics, Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA
| | - James T Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Thomas M Werge
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, Erasmus Medical Center, Erasmus University, Rotterdam, the Netherlands
| | - Patrick F Sullivan
- Karolinska Institute, Solna, Sweden
- University of North Carolina, Chapel Hill, NC, USA
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
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5
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Dato S, Crocco P, Rambaldi Migliore N, Lescai F. Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging. Front Genet 2021; 12:689824. [PMID: 34178042 PMCID: PMC8225294 DOI: 10.3389/fgene.2021.689824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Aging is a complex phenotype influenced by a combination of genetic and environmental factors. Although many studies addressed its cellular and physiological age-related changes, the molecular causes of aging remain undetermined. Considering the biological complexity and heterogeneity of the aging process, it is now clear that full understanding of mechanisms underlying aging can only be achieved through the integration of different data types and sources, and with new computational methods capable to achieve such integration. Recent Advances In this review, we show that an omics vision of the age-dependent changes occurring as the individual ages can provide researchers with new opportunities to understand the mechanisms of aging. Combining results from single-cell analysis with systems biology tools would allow building interaction networks and investigate how these networks are perturbed during aging and disease. The development of high-throughput technologies such as next-generation sequencing, proteomics, metabolomics, able to investigate different biological markers and to monitor them simultaneously during the aging process with high accuracy and specificity, represents a unique opportunity offered to biogerontologists today. Critical Issues Although the capacity to produce big data drastically increased over the years, integration, interpretation and sharing of high-throughput data remain major challenges. In this paper we present a survey of the emerging omics approaches in aging research and provide a large collection of datasets and databases as a useful resource for the scientific community to identify causes of aging. We discuss their peculiarities, emphasizing the need for the development of methods focused on the integration of different data types. Future Directions We critically review the contribution of bioinformatics into the omics of aging research, and we propose a few recommendations to boost collaborations and produce new insights. We believe that significant advancements can be achieved by following major developments in bioinformatics, investing in diversity, data sharing and community-driven portable bioinformatics methods. We also argue in favor of more engagement and participation, and we highlight the benefits of new collaborations along these lines. This review aims at being a useful resource for many researchers in the field, and a call for new partnerships in aging research.
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Affiliation(s)
- Serena Dato
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | | | - Francesco Lescai
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
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6
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Satterstrom FK, Walters RK, Singh T, Wigdor EM, Lescai F, Demontis D, Kosmicki JA, Grove J, Stevens C, Bybjerg-Grauholm J, Bækvad-Hansen M, Palmer DS, Maller JB, Nordentoft M, Mors O, Robinson EB, Hougaard DM, Werge TM, Bo Mortensen P, Neale BM, Børglum AD, Daly MJ. Autism spectrum disorder and attention deficit hyperactivity disorder have a similar burden of rare protein-truncating variants. Nat Neurosci 2019; 22:1961-1965. [PMID: 31768057 PMCID: PMC6884695 DOI: 10.1038/s41593-019-0527-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
We analyze the exome sequences of approximately 8,000 children with autism spectrum disorder (ASD) and/or attention-deficit/hyperactivity disorder (ADHD) and 5,000 controls, and we find that ASD and ADHD have a similar burden of rare protein-truncating variants in evolutionarily constrained genes, both significantly higher than controls. This motivates a combined analysis across ASD and ADHD, which identifies microtubule-associated protein 1A (MAP1A) as a novel exome-wide significant gene conferring risk for childhood psychiatric disorders.
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Affiliation(s)
- F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Raymond K Walters
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emilie M Wigdor
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Francesco Lescai
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Jack A Kosmicki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Christine Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Duncan S Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Julian B Maller
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Mental Health Services in the Capital Region of Denmark, Mental Health Centre Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas M Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Benjamin M Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. .,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark. .,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.
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7
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Ganna A, Satterstrom FK, Zekavat SM, Das I, Kurki MI, Churchhouse C, Alfoldi J, Martin AR, Havulinna AS, Byrnes A, Thompson WK, Nielsen PR, Karczewski KJ, Saarentaus E, Rivas MA, Gupta N, Pietiläinen O, Emdin CA, Lescai F, Bybjerg-Grauholm J, Flannick J, Mercader JM, Udler M, Laakso M, Salomaa V, Hultman C, Ripatti S, Hämäläinen E, Moilanen JS, Körkkö J, Kuismin O, Nordentoft M, Hougaard DM, Mors O, Werge T, Mortensen PB, MacArthur D, Daly MJ, Sullivan PF, Locke AE, Palotie A, Børglum AD, Kathiresan S, Neale BM, Palotie A, Børglum AD, Kathiresan S, Neale BM. Quantifying the Impact of Rare and Ultra-rare Coding Variation across the Phenotypic Spectrum. Am J Hum Genet 2018; 102:1204-1211. [PMID: 29861106 DOI: 10.1016/j.ajhg.2018.05.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/02/2018] [Indexed: 10/14/2022] Open
Abstract
There is a limited understanding about the impact of rare protein-truncating variants across multiple phenotypes. We explore the impact of this class of variants on 13 quantitative traits and 10 diseases using whole-exome sequencing data from 100,296 individuals. Protein-truncating variants in genes intolerant to this class of mutations increased risk of autism, schizophrenia, bipolar disorder, intellectual disability, and ADHD. In individuals without these disorders, there was an association with shorter height, lower education, increased hospitalization, and reduced age at enrollment. Gene sets implicated from GWASs did not show a significant protein-truncating variants burden beyond what was captured by established Mendelian genes. In conclusion, we provide a thorough investigation of the impact of rare deleterious coding variants on complex traits, suggesting widespread pleiotropic risk.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aarno Palotie
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki 00290, Finland
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus 8210, Denmark; Department of Biomedicine - Human Genetics, Aarhus University, Aarhus 8210, Denmark
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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8
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Navarro AB, Lescai F. Editorial. N Biotechnol 2018; 40:185. [DOI: 10.1016/j.nbt.2017.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Løngren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Pontén T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sørensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Børglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature 2017; 548:87-91. [PMID: 28746312 DOI: 10.1038/nature23264] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 06/04/2017] [Indexed: 12/17/2022]
Abstract
Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.
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Affiliation(s)
- Lasse Maretty
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jacob Malte Jensen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jonas Andreas Sibbesen
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Siyang Liu
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.,BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Palle Villesen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Kirstine Belling
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Christian Theil Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jose M G Izarzugaza
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Marie Grosjean
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jakob Grove
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Thomas D Als
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Shujia Huang
- BGI-Shenzhen, Shenzhen 518083, China.,School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | | | - Ruiqi Xu
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Weijian Ye
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Junhua Rao
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jihua Sun
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Chen Ye
- BGI-Shenzhen, Shenzhen 518083, China
| | - Johan van Beusekom
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Thomas Espeseth
- Department of Psychology, University of Oslo, 0317 Oslo, Norway.,NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | - Esben Flindt
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rune M Friborg
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Anders E Halager
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Stephanie Le Hellard
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen 5021, Norway.,Dr E. Martens Research Group of Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen 5021, Norway
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Francesco Lescai
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Shengting Li
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Ole Lund
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Peter Løngren
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Maria Luisa Matey-Hernandez
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Ole Mors
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Christian N S Pedersen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Thomas Sicheritz-Pontén
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Patrick Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Ali Syed
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - David Westergaard
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Rachita Yadav
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Ning Li
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anders Krogh
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,BGI-Shenzhen, Shenzhen 518083, China
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark.,Department of Clinical Epidemiology, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, 2000 Frederiksberg, Denmark.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ramneek Gupta
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Simon Rasmussen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Søren Besenbacher
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Anders D Børglum
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Jun Wang
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Hans Eiberg
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Brunak
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mikkel Heide Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
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10
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Lescai F, Als TD, Li Q, Nyegaard M, Andorsdottir G, Biskopstø M, Hedemand A, Fiorentino A, O'Brien N, Jarram A, Liang J, Grove J, Pallesen J, Eickhardt E, Mattheisen M, Bolund L, Demontis D, Wang AG, McQuillin A, Mors O, Wang J, Børglum AD. Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder. Transl Psychiatry 2017; 7:e1034. [PMID: 28195573 PMCID: PMC5438033 DOI: 10.1038/tp.2017.3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 12/20/2022] Open
Abstract
Bipolar disorder affects about 1% of the world's population, and its estimated heritability is about 75%. Only few whole genome or whole-exome sequencing studies in bipolar disorder have been reported, and no rare coding variants have yet been robustly identified. The use of isolated populations might help finding variants with a recent origin, more likely to have drifted to higher frequency by chance. Following this approach, we investigated 28 bipolar cases and 214 controls from the Faroe Islands by whole exome sequencing, and the results were followed-up in a British sample of 2025 cases and 1358 controls. Seventeen variants in 16 genes in the single-variant analysis, and 3 genes in the gene-based statistics surpassed exome-wide significance in the discovery phase. The discovery findings were supported by enrichment analysis of common variants from genome-wide association studies (GWAS) data and interrogation of protein-protein interaction networks. The replication in the British sample confirmed the association with NOS1 (missense variant rs79487279) and NCL (gene-based test). A number of variants from the discovery set were not present in the replication sample, including a novel PITPNM2 missense variant, which is located in a highly significant schizophrenia GWAS locus. Likewise, PIK3C2A identified in the gene-based analysis is located in a combined bipolar and schizophrenia GWAS locus. Our results show support both for existing findings in the literature, as well as for new risk genes, and identify rare variants that might provide additional information on the underlying biology of bipolar disorder.
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Affiliation(s)
- F Lescai
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - T D Als
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Q Li
- BGI-Shenzhen, Shenzhen, China
| | - M Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - G Andorsdottir
- Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | - M Biskopstø
- Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | - A Hedemand
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - A Fiorentino
- Division of Psychiatry, University College London, London, UK
| | - N O'Brien
- Division of Psychiatry, University College London, London, UK
| | - A Jarram
- Division of Psychiatry, University College London, London, UK
| | - J Liang
- BGI-Shenzhen, Shenzhen, China
| | - J Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- BiRC—Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - J Pallesen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - E Eickhardt
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - M Mattheisen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - L Bolund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Aarhus University Hospital, Risskov, Aarhus, Denmark
| | - D Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - A G Wang
- Mental Health Centre Amager, Copenhagen, Denmark
| | | | - O Mors
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Aarhus University Hospital, Risskov, Aarhus, Denmark
| | - J Wang
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- BGI-Shenzhen, Shenzhen, China
| | - A D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH—The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ—Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
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11
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Gregersen NO, Lescai F, Liang J, Li Q, Als T, Buttenschøn HN, Hedemand A, Biskopstø M, Wang J, Wang AG, Børglum AD, Mors O, Demontis D. Whole-exome sequencing implicates DGKH as a risk gene for panic disorder in the Faroese population. Am J Med Genet B Neuropsychiatr Genet 2016; 171:1013-1022. [PMID: 27255576 DOI: 10.1002/ajmg.b.32464] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/20/2016] [Indexed: 12/12/2022]
Abstract
The demographic history of the isolated population of the Faroe Islands may have induced enrichment of variants rarely seen in outbred European populations, including enrichment of risk variants for panic disorder (PD). PD is a common mental disorder, characterized by recurring and unprovoked panic attacks, and genetic factors have been estimated to explain around 40% of the risk. In this study the potential enrichment of PD risk variants was explored based on whole-exome sequencing of 54 patients with PD and 211 control individuals from the Faroese population. No genome-wide significant associations were found, however several single variants and genes showed strong association with PD, where DGKH was found to be the strongest PD associated gene. Interestingly DGKH has previously demonstrated genome-wide significant association with bipolar disorder as well as evidence of association to other mental disorders. Additionally, we found an enrichment of PD risk variants in the Faroese population; variants with otherwise low frequency in more outbreed European populations. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Noomi O Gregersen
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Genetic Biobank of the Faroe Islands, Torshavn, Faroe Islands
| | - Francesco Lescai
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | | | | | - Thomas Als
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Henriette N Buttenschøn
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Anne Hedemand
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | | | - Jun Wang
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,BGI-Shenzhen, Shenzhen, China
| | - August G Wang
- Centre of Psychiatry Amager, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anders D Børglum
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Ditte Demontis
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
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12
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Demontis D, Lescai F, Børglum A, Glerup S, Østergaard SD, Mors O, Li Q, Liang J, Jiang H, Li Y, Wang J, Lesch KP, Reif A, Buitelaar JK, Franke B. Whole-Exome Sequencing Reveals Increased Burden of Rare Functional and Disruptive Variants in Candidate Risk Genes in Individuals With Persistent Attention-Deficit/Hyperactivity Disorder. J Am Acad Child Adolesc Psychiatry 2016; 55:521-3. [PMID: 27238071 DOI: 10.1016/j.jaac.2016.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/26/2016] [Accepted: 03/21/2016] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | | | | | - Ole Mors
- Aarhus University Hospital, Risskov, Denmark
| | | | | | | | | | | | | | | | - Jan K Buitelaar
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Barbara Franke
- Radboud University Medical Center, Nijmegen, The Netherlands
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13
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Poulsen JB, Lescai F, Grove J, Bækvad-Hansen M, Christiansen M, Hagen CM, Maller J, Stevens C, Li S, Li Q, Sun J, Wang J, Nordentoft M, Werge TM, Mortensen PB, Børglum AD, Daly M, Hougaard DM, Bybjerg-Grauholm J, Hollegaard MV. High-Quality Exome Sequencing of Whole-Genome Amplified Neonatal Dried Blood Spot DNA. PLoS One 2016; 11:e0153253. [PMID: 27089011 PMCID: PMC4835089 DOI: 10.1371/journal.pone.0153253] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/26/2016] [Indexed: 12/16/2022] Open
Abstract
Stored neonatal dried blood spot (DBS) samples from neonatal screening programmes are a valuable diagnostic and research resource. Combined with information from national health registries they can be used in population-based studies of genetic diseases. DNA extracted from neonatal DBSs can be amplified to obtain micrograms of an otherwise limited resource, referred to as whole-genome amplified DNA (wgaDNA). Here we investigate the robustness of exome sequencing of wgaDNA of neonatal DBS samples. We conducted three pilot studies of seven, eight and seven subjects, respectively. For each subject we analysed a neonatal DBS sample and corresponding adult whole-blood (WB) reference sample. Different DNA sample types were prepared for each of the subjects. Pilot 1: wgaDNA of 2x3.2mm neonatal DBSs (DBS_2x3.2) and raw DNA extract of the WB reference sample (WB_ref). Pilot 2: DBS_2x3.2, WB_ref and a WB_ref replica sharing DNA extract with the WB_ref sample. Pilot 3: DBS_2x3.2, WB_ref, wgaDNA of 2x1.6 mm neonatal DBSs and wgaDNA of the WB reference sample. Following sequencing and data analysis, we compared pairwise variant calls to obtain a measure of similarity—the concordance rate. Concordance rates were slightly lower when comparing DBS vs WB sample types than for any two WB sample types of the same subject before filtering of the variant calls. The overall concordance rates were dependent on the variant type, with SNPs performing best. Post-filtering, the comparisons of DBS vs WB and WB vs WB sample types yielded similar concordance rates, with values close to 100%. WgaDNA of neonatal DBS samples performs with great accuracy and efficiency in exome sequencing. The wgaDNA performed similarly to matched high-quality reference—whole-blood DNA—based on concordance rates calculated from variant calls. No differences were observed substituting 2x3.2 with 2x1.6 mm discs, allowing for additional reduction of sample material in future projects.
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Affiliation(s)
- Jesper Buchhave Poulsen
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Francesco Lescai
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Molecular Medicine, Statens Serum Institut, Copenhagen, Denmark
| | - Christian Munch Hagen
- Department for Congenital Disorders, Molecular Medicine, Statens Serum Institut, Copenhagen, Denmark
| | - Julian Maller
- Broad Institute, Stanley Center, Cambridge, Massachusetts, United States of America
| | - Christine Stevens
- Broad Institute, Stanley Center, Cambridge, Massachusetts, United States of America
| | - Shenting Li
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | | | | | - Jun Wang
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- BGI-Shenzhen, Shenzhen, China
| | - Merete Nordentoft
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- Mental Health Centre Copenhagen, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Mears Werge
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- Mental Health Centre Sct. Hans, Institute for Biological Psychiatry, Capital Region of Denmark, Roskilde, Denmark
| | - Preben Bo Mortensen
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-based Research, School of Business and Social Sciences, Aarhus University, Aarhus, Denmark
| | - Anders Dupont Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Mark Daly
- Broad Institute, Stanley Center, Cambridge, Massachusetts, United States of America
| | - David Michael Hougaard
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, The Danish Neonatal Screening Biobank, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
| | - Mads Vilhelm Hollegaard
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, The Danish Neonatal Screening Biobank, Statens Serum Institut, Copenhagen, Denmark
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14
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Rajkumar AP, Qvist P, Lazarus R, Lescai F, Ju J, Nyegaard M, Mors O, Børglum AD, Li Q, Christensen JH. Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq. BMC Genomics 2015; 16:548. [PMID: 26208977 PMCID: PMC4515013 DOI: 10.1186/s12864-015-1767-y] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 07/10/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Massively parallel cDNA sequencing (RNA-seq) experiments are gradually superseding microarrays in quantitative gene expression profiling. However, many biologists are uncertain about the choice of differentially expressed gene (DEG) analysis methods and the validity of cost-saving sample pooling strategies for their RNA-seq experiments. Hence, we performed experimental validation of DEGs identified by Cuffdiff2, edgeR, DESeq2 and Two-stage Poisson Model (TSPM) in a RNA-seq experiment involving mice amygdalae micro-punches, using high-throughput qPCR on independent biological replicate samples. Moreover, we sequenced RNA-pools and compared their results with sequencing corresponding individual RNA samples. RESULTS False-positivity rate of Cuffdiff2 and false-negativity rates of DESeq2 and TSPM were high. Among the four investigated DEG analysis methods, sensitivity and specificity of edgeR was relatively high. We documented the pooling bias and that the DEGs identified in pooled samples suffered low positive predictive values. CONCLUSIONS Our results highlighted the need for combined use of more sensitive DEG analysis methods and high-throughput validation of identified DEGs in future RNA-seq experiments. They indicated limited utility of sample pooling strategies for RNA-seq in similar setups and supported increasing the number of biological replicate samples.
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Affiliation(s)
- Anto P Rajkumar
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- Mental Health of Older Adults and Dementia Clinical Academic Group, South London and Maudsley NHS foundation trust, London, UK.
- Wolfson Centre for Age Related Diseases, Institute of Psychiatry, Psychology, & Neuroscience, King's College, London, UK.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
| | - Per Qvist
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
| | - Ross Lazarus
- Computational Biology, Baker IDI heart and diabetes institute, Victoria, 8008, Australia.
| | - Francesco Lescai
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
| | - Jia Ju
- Beijing Genomics Institute, Shenzhen, 518083, China.
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
| | - Ole Mors
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
- Research Department P, Aarhus University Hospital, Risskov, Denmark.
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
- Research Department P, Aarhus University Hospital, Risskov, Denmark.
- Translational Neuropsychiatry Unit, Aarhus University, Aarhus, 8240, Denmark.
| | - Qibin Li
- Beijing Genomics Institute, Shenzhen, 518083, China.
| | - Jane H Christensen
- Department of Biomedicine, Aarhus University, 6, Bartholins Allé, Aarhus C, Aarhus, 8000, Denmark.
- The Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, 8000, Denmark.
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, 8000, Denmark.
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15
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Le Quesne Stabej P, Williams HJ, James C, Tekman M, Stanescu HC, Kleta R, Ocaka L, Lescai F, Storr HL, Bitner-Glindzicz M, Bacchelli C, Conway GS. STAG3 truncating variant as the cause of primary ovarian insufficiency. Eur J Hum Genet 2015; 24:135-8. [PMID: 26059840 PMCID: PMC4795223 DOI: 10.1038/ejhg.2015.107] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/09/2015] [Accepted: 04/03/2015] [Indexed: 12/30/2022] Open
Abstract
Primary ovarian insufficiency (POI) is a distressing cause of infertility in young women. POI is heterogeneous with only a few causative genes having been discovered so far. Our objective was to determine the genetic cause of POI in a consanguineous Lebanese family with two affected sisters presenting with primary amenorrhoea and an absence of any pubertal development. Multipoint parametric linkage analysis was performed. Whole-exome sequencing was done on the proband. Linkage analysis identified a locus on chromosome 7 where exome sequencing successfully identified a homozygous two base pair duplication (c.1947_48dupCT), leading to a truncated protein p.(Y650Sfs*22) in the STAG3 gene, confirming it as the cause of POI in this family. Exome sequencing combined with linkage analyses offers a powerful tool to efficiently find novel genetic causes of rare, heterogeneous disorders, even in small single families. This is only the second report of a STAG3 variant; the first STAG3 variant was recently described in a phenotypically similar family with extreme POI. Identification of an additional family highlights the importance of STAG3 in POI pathogenesis and suggests it should be evaluated in families affected with POI.
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Affiliation(s)
| | - Hywel J Williams
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Chela James
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | | | | | - Robert Kleta
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK.,Division of Medicine, UCL, London, UK
| | - Louise Ocaka
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Francesco Lescai
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Helen L Storr
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Chiara Bacchelli
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Gerard S Conway
- Reproductive Medicine Unit, Institute for Women's Health, University College London Hospitals, London, UK
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16
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Williams HJ, Hurst JR, Ocaka L, James C, Pao C, Chanudet E, Lescai F, Stanescu HC, Kleta R, Rosser E, Bacchelli C, Beales P. The use of whole-exome sequencing to disentangle complex phenotypes. Eur J Hum Genet 2015; 24:298-301. [PMID: 26059842 PMCID: PMC4717198 DOI: 10.1038/ejhg.2015.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 03/11/2015] [Accepted: 04/24/2015] [Indexed: 12/30/2022] Open
Abstract
The success of whole-exome sequencing to identify mutations causing single-gene disorders has been well documented. In contrast whole-exome sequencing has so far had limited success in the identification of variants causing more complex phenotypes that seem unlikely to be due to the disruption of a single gene. We describe a family where two male offspring of healthy first cousin parents present a complex phenotype consisting of peripheral neuropathy and bronchiectasis that has not been described previously in the literature. Due to the fact that both children had the same problems in the context of parental consanguinity we hypothesised illness resulted from either X-linked or autosomal recessive inheritance. Through the use of whole-exome sequencing we were able to simplify this complex phenotype and identified a causative mutation (p.R1070*) in the gene periaxin (PRX), a gene previously shown to cause peripheral neuropathy (Dejerine-Sottas syndrome) when this mutation is present. For the bronchiectasis phenotype we were unable to identify a causal single mutation or compound heterozygote, reflecting the heterogeneous nature of this phenotype. In conclusion, in this study we show that whole-exome sequencing has the power to disentangle complex phenotypes through the identification of causative genetic mutations for distinct clinical disorders that were previously masked.
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Affiliation(s)
- Hywel J Williams
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - John R Hurst
- UCL Respiratory Medicine, UCL Medical School, London, UK
| | - Louise Ocaka
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - Chela James
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - Caroline Pao
- Paediatric Respiratory Medicine, Royal London Hospital, Whitechapel, London, UK
| | - Estelle Chanudet
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - Francesco Lescai
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | | | - Robert Kleta
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK.,UCL Respiratory Medicine, UCL Medical School, London, UK
| | | | - Elisabeth Rosser
- Department of Clinical Genetics, Great Ormond St Hospital, London, UK
| | - Chiara Bacchelli
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - Philip Beales
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
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17
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Besenbacher S, Liu S, Izarzugaza JMG, Grove J, Belling K, Bork-Jensen J, Huang S, Als TD, Li S, Yadav R, Rubio-García A, Lescai F, Demontis D, Rao J, Ye W, Mailund T, Friborg RM, Pedersen CNS, Xu R, Sun J, Liu H, Wang O, Cheng X, Flores D, Rydza E, Rapacki K, Damm Sørensen J, Chmura P, Westergaard D, Dworzynski P, Sørensen TIA, Lund O, Hansen T, Xu X, Li N, Bolund L, Pedersen O, Eiberg H, Krogh A, Børglum AD, Brunak S, Kristiansen K, Schierup MH, Wang J, Gupta R, Villesen P, Rasmussen S. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nat Commun 2015; 6:5969. [PMID: 25597990 PMCID: PMC4309431 DOI: 10.1038/ncomms6969] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/25/2014] [Indexed: 02/06/2023] Open
Abstract
Building a population-specific catalogue of single nucleotide variants (SNVs), indels and structural variants (SVs) with frequencies, termed a national pan-genome, is critical for further advancing clinical and public health genetics in large cohorts. Here we report a Danish pan-genome obtained from sequencing 10 trios to high depth (50 × ). We report 536k novel SNVs and 283k novel short indels from mapping approaches and develop a population-wide de novo assembly approach to identify 132k novel indels larger than 10 nucleotides with low false discovery rates. We identify a higher proportion of indels and SVs than previous efforts showing the merits of high coverage and de novo assembly approaches. In addition, we use trio information to identify de novo mutations and use a probabilistic method to provide direct estimates of 1.27e−8 and 1.5e−9 per nucleotide per generation for SNVs and indels, respectively. The generation of a national pan-genome, a population-specific catalogue of genetic variation, may advance the impact of clinical genetics studies. Here the Besenbacher et al. carry out deep sequencing and de novo assembly of 10 parent–child trios to generate a Danish pan-genome that provides insight into structural variation, de novo mutation rates and variant calling.
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Affiliation(s)
- Søren Besenbacher
- Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus, Denmark
| | - Siyang Liu
- 1] BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark [2] Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - José M G Izarzugaza
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Jakob Grove
- 1] Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus, Denmark [2] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark [3] The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark [4] Department of Biomedicine, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Kirstine Belling
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Jette Bork-Jensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1-3, DK-2100 Copenhagen, Denmark
| | - Shujia Huang
- 1] BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark [2] School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | - Thomas D Als
- 1] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark [2] The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark [3] Department of Biomedicine, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Shengting Li
- 1] BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark [2] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark [3] The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark [4] Department of Biomedicine, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Rachita Yadav
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Arcadio Rubio-García
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Francesco Lescai
- 1] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark [2] The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark [3] Department of Biomedicine, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Ditte Demontis
- 1] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark [2] The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark [3] Department of Biomedicine, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Junhua Rao
- BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark
| | - Weijian Ye
- BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark
| | - Thomas Mailund
- 1] Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus, Denmark [2] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Rune M Friborg
- 1] Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus, Denmark [2] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Christian N S Pedersen
- Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus, Denmark
| | - Ruiqi Xu
- BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark
| | - Jihua Sun
- BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark
| | - Hao Liu
- BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark
| | - Ou Wang
- BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark
| | - Xiaofang Cheng
- BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark
| | - David Flores
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Emil Rydza
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Kristoffer Rapacki
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - John Damm Sørensen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Piotr Chmura
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - David Westergaard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Piotr Dworzynski
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Thorkild I A Sørensen
- 1] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1-3, DK-2100 Copenhagen, Denmark [2] Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, The Capital Region, Nordre Fasanvej 57, Hovedvejen 5, DK2000 Copenhagen, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Torben Hansen
- 1] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1-3, DK-2100 Copenhagen, Denmark [2] Faculty of Health Sciences, University of Southern Denmark, DK-5000 Odense, Denmark
| | - Xun Xu
- BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark
| | - Ning Li
- BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark
| | - Lars Bolund
- 1] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark [2] Department of Biomedicine, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1-3, DK-2100 Copenhagen, Denmark
| | - Hans Eiberg
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Anders Krogh
- 1] Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark [2] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
| | - Anders D Børglum
- 1] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark [2] The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark [3] Department of Biomedicine, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Karsten Kristiansen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Mikkel H Schierup
- 1] Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus, Denmark [2] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Jun Wang
- 1] BGI Europe, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark [2] Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark [3] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Ramneek Gupta
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
| | - Palle Villesen
- 1] Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus, Denmark [2] Centre for Integrative Sequencing, iSEQ, Aarhus University, Bartholins Allé 6, building 1242, DK-8000 Aarhus, Denmark
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, DK-2800 Kgs Lyngby, Denmark
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18
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Waters AM, Asfahani R, Carroll P, Bicknell L, Lescai F, Bright A, Chanudet E, Brooks A, Christou-Savina S, Osman G, Walsh P, Bacchelli C, Chapgier A, Vernay B, Bader DM, Deshpande C, O' Sullivan M, Ocaka L, Stanescu H, Stewart HS, Hildebrandt F, Otto E, Johnson CA, Szymanska K, Katsanis N, Davis E, Kleta R, Hubank M, Doxsey S, Jackson A, Stupka E, Winey M, Beales PL. The kinetochore protein, CENPF, is mutated in human ciliopathy and microcephaly phenotypes. J Med Genet 2015; 52:147-56. [PMID: 25564561 PMCID: PMC4345935 DOI: 10.1136/jmedgenet-2014-102691] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background Mutations in microtubule-regulating genes are associated with disorders of neuronal migration and microcephaly. Regulation of centriole length has been shown to underlie the pathogenesis of certain ciliopathy phenotypes. Using a next-generation sequencing approach, we identified mutations in a novel centriolar disease gene in a kindred with an embryonic lethal ciliopathy phenotype and in a patient with primary microcephaly. Methods and results Whole exome sequencing data from a non-consanguineous Caucasian kindred exhibiting mid-gestation lethality and ciliopathic malformations revealed two novel non-synonymous variants in CENPF, a microtubule-regulating gene. All four affected fetuses showed segregation for two mutated alleles [IVS5-2A>C, predicted to abolish the consensus splice-acceptor site from exon 6; c.1744G>T, p.E582X]. In a second unrelated patient exhibiting microcephaly, we identified two CENPF mutations [c.1744G>T, p.E582X; c.8692 C>T, p.R2898X] by whole exome sequencing. We found that CENP-F colocalised with Ninein at the subdistal appendages of the mother centriole in mouse inner medullary collecting duct cells. Intraflagellar transport protein-88 (IFT-88) colocalised with CENP-F along the ciliary axonemes of renal epithelial cells in age-matched control human fetuses but did not in truncated cilia of mutant CENPF kidneys. Pairwise co-immunoprecipitation assays of mitotic and serum-starved HEKT293 cells confirmed that IFT88 precipitates with endogenous CENP-F. Conclusions Our data identify CENPF as a new centriolar disease gene implicated in severe human ciliopathy and microcephaly related phenotypes. CENP-F has a novel putative function in ciliogenesis and cortical neurogenesis.
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Affiliation(s)
- Aoife M Waters
- Institute of Child Health, University College London, London, UK Department of Nephrology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Rowan Asfahani
- Institute of Child Health, University College London, London, UK
| | - Paula Carroll
- Institute of Genetics & Molecular Medicine, Edinburgh, UK
| | | | - Francesco Lescai
- Institute of Child Health, University College London, London, UK
| | | | - Estelle Chanudet
- Institute of Child Health, University College London, London, UK
| | - Anthony Brooks
- Institute of Child Health, University College London, London, UK
| | | | - Guled Osman
- Institute of Child Health, University College London, London, UK
| | - Patrick Walsh
- Institute of Child Health, University College London, London, UK
| | - Chiara Bacchelli
- Institute of Child Health, University College London, London, UK
| | - Ariane Chapgier
- Institute of Child Health, University College London, London, UK
| | - Bertrand Vernay
- Institute of Child Health, University College London, London, UK
| | - David M Bader
- Department of Cell and Developmental Biology, Vanderbilt University, USA
| | - Charu Deshpande
- Department of Clinical Genetics, Evelina Children's Hospital, London, UK
| | - Mary O' Sullivan
- Institute of Child Health, University College London, London, UK
| | - Louise Ocaka
- Institute of Child Health, University College London, London, UK
| | - Horia Stanescu
- Centre for Nephrology, Royal Free Hospital, University College London, London, UK
| | - Helen S Stewart
- Department of Clinical Genetics, Oxford Radcliffe Hospitals NHS Trust, Churchill Hospital, Oxford, UK
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, USA
| | - Edgar Otto
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Colin A Johnson
- Department of Pediatrics, Leeds Institute of Biomedical and Clinical Sciences, Leeds, UK
| | - Katarzyna Szymanska
- Department of Pediatrics, Leeds Institute of Biomedical and Clinical Sciences, Leeds, UK
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Department of Cell Biology, Duke University Medical Center
| | - Erica Davis
- Center for Human Disease Modeling, Department of Cell Biology, Duke University Medical Center
| | - Robert Kleta
- Centre for Nephrology, Royal Free Hospital, University College London, London, UK
| | - Mike Hubank
- Institute of Child Health, University College London, London, UK
| | | | - Andrew Jackson
- Institute of Genetics & Molecular Medicine, Edinburgh, UK MRC Human Genetics, University of Edinburgh, Edinburgh, UK
| | - Elia Stupka
- Institute of Child Health, University College London, London, UK
| | - Mark Winey
- Molecular, Ceullular, and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Philip L Beales
- Institute of Child Health, University College London, London, UK
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19
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Thomas AC, Williams H, Setó-Salvia N, Bacchelli C, Jenkins D, O'Sullivan M, Mengrelis K, Ishida M, Ocaka L, Chanudet E, James C, Lescai F, Anderson G, Morrogh D, Ryten M, Duncan AJ, Pai YJ, Saraiva JM, Ramos F, Farren B, Saunders D, Vernay B, Gissen P, Straatmaan-Iwanowska A, Baas F, Wood NW, Hersheson J, Houlden H, Hurst J, Scott R, Bitner-Glindzicz M, Moore GE, Sousa SB, Stanier P. Mutations in SNX14 cause a distinctive autosomal-recessive cerebellar ataxia and intellectual disability syndrome. Am J Hum Genet 2014; 95:611-21. [PMID: 25439728 DOI: 10.1016/j.ajhg.2014.10.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/13/2014] [Indexed: 12/30/2022] Open
Abstract
Intellectual disability and cerebellar atrophy occur together in a large number of genetic conditions and are frequently associated with microcephaly and/or epilepsy. Here we report the identification of causal mutations in Sorting Nexin 14 (SNX14) found in seven affected individuals from three unrelated consanguineous families who presented with recessively inherited moderate-severe intellectual disability, cerebellar ataxia, early-onset cerebellar atrophy, sensorineural hearing loss, and the distinctive association of progressively coarsening facial features, relative macrocephaly, and the absence of seizures. We used homozygosity mapping and whole-exome sequencing to identify a homozygous nonsense mutation and an in-frame multiexon deletion in two families. A homozygous splice site mutation was identified by Sanger sequencing of SNX14 in a third family, selected purely by phenotypic similarity. This discovery confirms that these characteristic features represent a distinct and recognizable syndrome. SNX14 encodes a cellular protein containing Phox (PX) and regulator of G protein signaling (RGS) domains. Weighted gene coexpression network analysis predicts that SNX14 is highly coexpressed with genes involved in cellular protein metabolism and vesicle-mediated transport. All three mutations either directly affected the PX domain or diminished SNX14 levels, implicating a loss of normal cellular function. This manifested as increased cytoplasmic vacuolation as observed in cultured fibroblasts. Our findings indicate an essential role for SNX14 in neural development and function, particularly in development and maturation of the cerebellum.
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Affiliation(s)
- Anna C Thomas
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Hywel Williams
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Núria Setó-Salvia
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Chiara Bacchelli
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Dagan Jenkins
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Mary O'Sullivan
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | | | - Miho Ishida
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Louise Ocaka
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Estelle Chanudet
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Chela James
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Francesco Lescai
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Glenn Anderson
- Histopathology Department, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Deborah Morrogh
- NE Thames Regional Genetics Laboratory Service, London WC1N 3BH, UK
| | - Mina Ryten
- UCL Institute of Neurology, London WC1N 3BG, UK; Department of Clinical Genetics, Guy's Hospital, London SE1 9RT, UK
| | - Andrew J Duncan
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Yun Jin Pai
- Developmental Biology and Cancer, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Jorge M Saraiva
- Serviço de Genética Médica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, 3000-602 Coimbra, Portugal
| | - Fabiana Ramos
- Serviço de Genética Médica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Bernadette Farren
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Dawn Saunders
- Radiology, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Bertrand Vernay
- Developmental Biology and Cancer, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Paul Gissen
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | | | - Frank Baas
- Department of Genome Analysis, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, the Netherlands
| | | | | | | | - Jane Hurst
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Richard Scott
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Maria Bitner-Glindzicz
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Gudrun E Moore
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Sérgio B Sousa
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Serviço de Genética Médica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal.
| | - Philip Stanier
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK.
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20
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Kelberman D, Islam L, Lakowski J, Bacchelli C, Chanudet E, Lescai F, Patel A, Stupka E, Buck A, Wolf S, Beales PL, Jacques TS, Bitner-Glindzicz M, Liasis A, Lehmann OJ, Kohlhase J, Nischal KK, Sowden JC. Mutation of SALL2 causes recessive ocular coloboma in humans and mice. Hum Mol Genet 2014; 23:2511-26. [PMID: 24412933 PMCID: PMC3990155 DOI: 10.1093/hmg/ddt643] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ocular coloboma is a congenital defect resulting from failure of normal closure of the optic fissure during embryonic eye development. This birth defect causes childhood blindness worldwide, yet the genetic etiology is poorly understood. Here, we identified a novel homozygous mutation in the SALL2 gene in members of a consanguineous family affected with non-syndromic ocular coloboma variably affecting the iris and retina. This mutation, c.85G>T, introduces a premature termination codon (p.Glu29*) predicted to truncate the SALL2 protein so that it lacks three clusters of zinc-finger motifs that are essential for DNA-binding activity. This discovery identifies SALL2 as the third member of the Drosophila homeotic Spalt-like family of developmental transcription factor genes implicated in human disease. SALL2 is expressed in the developing human retina at the time of, and subsequent to, optic fissure closure. Analysis of Sall2-deficient mouse embryos revealed delayed apposition of the optic fissure margins and the persistence of an anterior retinal coloboma phenotype after birth. Sall2-deficient embryos displayed correct posterior closure toward the optic nerve head, and upon contact of the fissure margins, dissolution of the basal lamina occurred and PAX2, known to be critical for this process, was expressed normally. Anterior closure was disrupted with the fissure margins failing to meet, or in some cases misaligning leading to a retinal lesion. These observations demonstrate, for the first time, a role for SALL2 in eye morphogenesis and that loss of function of the gene causes ocular coloboma in humans and mice.
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21
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Lescai F, Marasco E, Bacchelli C, Stanier P, Mantovani V, Beales P. Identification and validation of loss of function variants in clinical contexts. Mol Genet Genomic Med 2013; 2:58-63. [PMID: 24498629 PMCID: PMC3907911 DOI: 10.1002/mgg3.42] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/05/2013] [Indexed: 12/20/2022] Open
Abstract
The choice of an appropriate variant calling pipeline for exome sequencing data is becoming increasingly more important in translational medicine projects and clinical contexts. Within GOSgene, which facilitates genetic analysis as part of a joint effort of the University College London and the Great Ormond Street Hospital, we aimed to optimize a variant calling pipeline suitable for our clinical context. We implemented the GATK/Queue framework and evaluated the performance of its two callers: the classical UnifiedGenotyper and the new variant discovery tool HaplotypeCaller. We performed an experimental validation of the loss-of-function (LoF) variants called by the two methods using Sequenom technology. UnifiedGenotyper showed a total validation rate of 97.6% for LoF single-nucleotide polymorphisms (SNPs) and 92.0% for insertions or deletions (INDELs), whereas HaplotypeCaller was 91.7% for SNPs and 55.9% for INDELs. We confirm that GATK/Queue is a reliable pipeline in translational medicine and clinical context. We conclude that in our working environment, UnifiedGenotyper is the caller of choice, being an accurate method, with a high validation rate of error-prone calls like LoF variants. We finally highlight the importance of experimental validation, especially for INDELs, as part of a standard pipeline in clinical environments.
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Affiliation(s)
- Francesco Lescai
- University College London, Institute of Child Health, GOSgene team London, U.K ; Department of Biomedicine, Human Genetics, Aarhus University Aarhus, Denmark
| | - Elena Marasco
- CRBA Centro Ricerca Biomedica Applicata, Azienda Ospedaliero-Universitaria Policlinico S. Orsola - Malpighi Bologna, Italy
| | - Chiara Bacchelli
- University College London, Institute of Child Health, GOSgene team London, U.K
| | - Philip Stanier
- University College London, Institute of Child Health, GOSgene team London, U.K
| | - Vilma Mantovani
- Department of Biomedicine, Human Genetics, Aarhus University Aarhus, Denmark
| | - Philip Beales
- University College London, Institute of Child Health, GOSgene team London, U.K
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22
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Webb EA, AlMutair A, Kelberman D, Bacchelli C, Chanudet E, Lescai F, Andoniadou CL, Banyan A, Alsawaid A, Alrifai MT, Alahmesh MA, Balwi M, Mousavy-Gharavy SN, Lukovic B, Burke D, McCabe MJ, Kasia T, Kleta R, Stupka E, Beales PL, Thompson DA, Chong WK, Alkuraya FS, Martinez-Barbera JP, Sowden JC, Dattani MT. ARNT2 mutation causes hypopituitarism, post-natal microcephaly, visual and renal anomalies. ACTA ACUST UNITED AC 2013; 136:3096-105. [PMID: 24022475 DOI: 10.1093/brain/awt218] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We describe a previously unreported syndrome characterized by secondary (post-natal) microcephaly with fronto-temporal lobe hypoplasia, multiple pituitary hormone deficiency, seizures, severe visual impairment and abnormalities of the kidneys and urinary tract in a highly consanguineous family with six affected children. Homozygosity mapping and exome sequencing revealed a novel homozygous frameshift mutation in the basic helix-loop-helix transcription factor gene ARNT2 (c.1373_1374dupTC) in affected individuals. This mutation results in absence of detectable levels of ARNT2 transcript and protein from patient fibroblasts compared with controls, consistent with nonsense-mediated decay of the mutant transcript and loss of ARNT2 function. We also show expression of ARNT2 within the central nervous system, including the hypothalamus, as well as the renal tract during human embryonic development. The progressive neurological abnormalities, congenital hypopituitarism and post-retinal visual pathway dysfunction in affected individuals demonstrates for the first time the essential role of ARNT2 in the development of the hypothalamo-pituitary axis, post-natal brain growth, and visual and renal function in humans.
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Affiliation(s)
- Emma A Webb
- 1 Developmental Endocrinology Research Group, UCL Institute of Child Health and Department of Endocrinology, Great Ormond Street Hospital for Children, London, WC1N 1EH, UK
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23
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Lescai F, Bonfiglio S, Bacchelli C, Chanudet E, Waters A, Sisodiya SM, Kasperavičiūtė D, Williams J, Harold D, Hardy J, Kleta R, Cirak S, Williams R, Achermann JC, Anderson J, Kelsell D, Vulliamy T, Houlden H, Wood N, Sheerin U, Tonini GP, Mackay D, Hussain K, Sowden J, Kinsler V, Osinska J, Brooks T, Hubank M, Beales P, Stupka E. Characterisation and validation of insertions and deletions in 173 patient exomes. PLoS One 2012; 7:e51292. [PMID: 23251486 PMCID: PMC3522676 DOI: 10.1371/journal.pone.0051292] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/01/2012] [Indexed: 01/01/2023] Open
Abstract
Recent advances in genomics technologies have spurred unprecedented efforts in genome and exome re-sequencing aiming to unravel the genetic component of rare and complex disorders. While in rare disorders this allowed the identification of novel causal genes, the missing heritability paradox in complex diseases remains so far elusive. Despite rapid advances of next-generation sequencing, both the technology and the analysis of the data it produces are in its infancy. At present there is abundant knowledge pertaining to the role of rare single nucleotide variants (SNVs) in rare disorders and of common SNVs in common disorders. Although the 1,000 genome project has clearly highlighted the prevalence of rare variants and more complex variants (e.g. insertions, deletions), their role in disease is as yet far from elucidated.We set out to analyse the properties of sequence variants identified in a comprehensive collection of exome re-sequencing studies performed on samples from patients affected by a broad range of complex and rare diseases (N = 173). Given the known potential for Loss of Function (LoF) variants to be false positive, we performed an extensive validation of the common, rare and private LoF variants identified, which indicated that most of the private and rare variants identified were indeed true, while common novel variants had a significantly higher false positive rate. Our results indicated a strong enrichment of very low-frequency insertion/deletion variants, so far under-investigated, which might be difficult to capture with low coverage and imputation approaches and for which most of study designs would be under-powered. These insertions and deletions might play a significant role in disease genetics, contributing specifically to the underlining rare and private variation predicted to be discovered through next generation sequencing.
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Affiliation(s)
- Francesco Lescai
- UCL Genomics, University College London, London, United Kingdom
- Division of Research Strategy, University College London, London, United Kingdom
- GOSgene, UCL Institute of Child Health, University College London, London, United Kingdom
| | - Silvia Bonfiglio
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Bacchelli
- GOSgene, UCL Institute of Child Health, University College London, London, United Kingdom
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Estelle Chanudet
- GOSgene, UCL Institute of Child Health, University College London, London, United Kingdom
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Aoife Waters
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Sanjay M. Sisodiya
- UCL Institute of Neurology, University College London, London, United Kingdom
| | | | - Julie Williams
- Department of Psychological Medicine, Cardiff University, Cardiff, United Kingdom
| | - Denise Harold
- Department of Psychological Medicine, Cardiff University, Cardiff, United Kingdom
| | - John Hardy
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Robert Kleta
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Sebahattin Cirak
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Richard Williams
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - John C. Achermann
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - John Anderson
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - David Kelsell
- Blizard Institute of Cell and Molecular Science, Barts and The London, London, United Kingdom
| | - Tom Vulliamy
- Blizard Institute of Cell and Molecular Science, Barts and The London, London, United Kingdom
| | - Henry Houlden
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Nicholas Wood
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Una Sheerin
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Gian Paolo Tonini
- Translational Oncopathology, National Cancer Research Institute (IST), Genova, Italy
| | - Donna Mackay
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Khalid Hussain
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Jane Sowden
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Veronica Kinsler
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Justyna Osinska
- UCL Genomics, University College London, London, United Kingdom
| | - Tony Brooks
- UCL Genomics, University College London, London, United Kingdom
| | - Mike Hubank
- UCL Genomics, University College London, London, United Kingdom
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Philip Beales
- GOSgene, UCL Institute of Child Health, University College London, London, United Kingdom
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Elia Stupka
- UCL Genomics, University College London, London, United Kingdom
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
- Cancer Institute, University College London, London, United Kingdom
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24
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Ellinghaus E, Stanulla M, Richter G, Ellinghaus D, te Kronnie G, Cario G, Cazzaniga G, Horstmann M, Panzer Grümayer R, Cavé H, Trka J, Cinek O, Teigler-Schlegel A, ElSharawy A, Häsler R, Nebel A, Meissner B, Bartram T, Lescai F, Franceschi C, Giordan M, Nürnberg P, Heinzow B, Zimmermann M, Schreiber S, Schrappe M, Franke A. Identification of germline susceptibility loci in ETV6-RUNX1-rearranged childhood acute lymphoblastic leukemia. Leukemia 2012; 26:902-9. [PMID: 22076464 PMCID: PMC3356560 DOI: 10.1038/leu.2011.302] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 09/03/2011] [Accepted: 09/21/2011] [Indexed: 02/08/2023]
Abstract
Acute lymphoblastic leukemia (ALL) is a malignant disease of the white blood cells. The etiology of ALL is believed to be multifactorial and likely to involve an interplay of environmental and genetic variables. We performed a genome-wide association study of 355 750 single-nucleotide polymorphisms (SNPs) in 474 controls and 419 childhood ALL cases characterized by a t(12;21)(p13;q22) - the most common chromosomal translocation observed in childhood ALL - which leads to an ETV6-RUNX1 gene fusion. The eight most strongly associated SNPs were followed-up in 951 ETV6-RUNX1-positive cases and 3061 controls from Germany/Austria and Italy, respectively. We identified a novel, genome-wide significant risk locus at 3q28 (TP63, rs17505102, P(CMH)=8.94 × 10(-9), OR=0.65). The separate analysis of the combined German/Austrian sample only, revealed additional genome-wide significant associations at 11q11 (OR8U8, rs1945213, P=9.14 × 10(-11), OR=0.69) and 8p21.3 (near INTS10, rs920590, P=6.12 × 10(-9), OR=1.36). These associations and another association at 11p11.2 (PTPRJ, rs3942852, P=4.95 × 10(-7), OR=0.72) remained significant in the German/Austrian replication panel after correction for multiple testing. Our findings demonstrate that germline genetic variation can specifically contribute to the risk of ETV6-RUNX1-positive childhood ALL. The identification of TP63 and PTPRJ as susceptibility genes emphasize the role of the TP53 gene family and the importance of proteins regulating cellular processes in connection with tumorigenesis.
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Affiliation(s)
- E Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - M Stanulla
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany, on behalf of the German Berlin-Frankfurt-Münster Study Group for Treatment of Childhood Acute Lymphoblastic Leukemia
| | - G Richter
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - D Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - G te Kronnie
- Department of Pediatrics, Laboratory of Pediatric Hematology/Oncology, University of Padua, Padua, Italy
| | - G Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany, on behalf of the German Berlin-Frankfurt-Münster Study Group for Treatment of Childhood Acute Lymphoblastic Leukemia
| | - G Cazzaniga
- M. Tettamanti Research Center, Children's Hospital, University of Milan-Bicocca, Monza, Italy
| | - M Horstmann
- Clinic of Pediatric Hematology and Oncology, University Medical Center, and Research Center Children's Cancer Center, Hamburg, Germany
| | - R Panzer Grümayer
- St Anna Children's Hospital and Children's Cancer Research Institute, Vienna, Austria
| | - H Cavé
- Department of Genetics, Hôpital Robert Debré, Paris, France
| | - J Trka
- Department of Pediatric Hematology/Oncology, Second Faculty of Medicine, Charles University Prague, Prague, Czech Republic
| | - O Cinek
- Department of Pediatrics, Second Faculty of Medicine, Charles University Prague, Prague, Czech Republic
| | - A Teigler-Schlegel
- Oncogenetic Laboratory, Department of Pediatric Hematology and Oncology, Justus-Liebig-University, Giessen, Germany
| | - A ElSharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - R Häsler
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - A Nebel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - B Meissner
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany, on behalf of the German Berlin-Frankfurt-Münster Study Group for Treatment of Childhood Acute Lymphoblastic Leukemia
| | - T Bartram
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany, on behalf of the German Berlin-Frankfurt-Münster Study Group for Treatment of Childhood Acute Lymphoblastic Leukemia
| | - F Lescai
- Division of Research Strategy, University College London, London, UK
| | - C Franceschi
- Department of Experimental Pathology, University of Bologna, Bologna, Italy
| | - M Giordan
- Department of Pediatrics, Laboratory of Pediatric Hematology/Oncology, University of Padua, Padua, Italy
| | - P Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - B Heinzow
- State Social Services Agency Schleswig-Holstein, Kiel, Germany
- University of Notre Dame, Sydney Medical School, Sydney, Australia
| | - M Zimmermann
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - S Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
- Department of General Internal Medicine, University Hospital Schleswig-Holstein, Christian-Albrechts-University Kiel, Kiel, Germany
- Popgen Biobank, University Hospital Schleswig-Holstein, Christian-Albrechts-University Kiel, Kiel, Germany
| | - M Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany, on behalf of the German Berlin-Frankfurt-Münster Study Group for Treatment of Childhood Acute Lymphoblastic Leukemia
| | - A Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
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25
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Lescai F, Chiamenti AM, Codemo A, Pirazzini C, D'Agostino G, Ruaro C, Ghidoni R, Benussi L, Galimberti D, Esposito F, Marchegiani F, Cardelli M, Olivieri F, Nacmias B, Sorbi S, Tagliavini F, Albani D, Martinelli Boneschi F, Binetti G, Santoro A, Forloni G, Scarpini E, Crepaldi G, Gabelli C, Franceschi C. An APOE haplotype associated with decreased ε4 expression increases the risk of late onset Alzheimer's disease. J Alzheimers Dis 2011; 24:235-45. [PMID: 21263195 DOI: 10.3233/jad-2011-101764] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This paper addresses a tenet of the literature on APOE, i.e., the relationship between the effects of the ε4, one of the established genetic risk factor for Alzheimer's disease (AD), and its expression levels as determined by APOE promoter polymorphisms. Five polymorphisms (-491 rs449647, -427 rs769446, -219 rs405509, and ε rs429358-rs7412) were studied in 1308 AD patients and 1082 control individuals from the Central-Northern Italy. Major findings of the present study are the following: 1) the variants -219T and ε4 increase the risk for late onset AD (LOAD) when they are both present in cis on the same chromosome (in phase); 2) the correlation between the haplotype (-219T/ε4) and AD risk persists when the data are stratified by age; 3) this haplotype likely anticipates the age of onset of the disease. These data, while confirming the association between -219T and AD, highlight the importance of the phase of the alleles for the observed effects on AD risk, suggesting that this information has to be taken into account when assessing the AD genetic risk. Moreover, the data help to clarify the apparent discrepancy that emerges from the genetic analysis where an SNP characterizing the haplotype responsible for an increased risk for LOAD is coherently associated with a reduced expression of ApoE levels. Our data are compatible with the hypothesis of a complex role of ApoE in the AD pathogenesis, with positive and negative effects occurring concomitantly according to its expression levels and its protein-protein interactions largely unclarified.
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Affiliation(s)
- Francesco Lescai
- Division of Research Strategy and UCL Cancer Institute, University College London, London, UK.
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26
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Taccioli C, Tegnér J, Maselli V, Gomez-Cabrero D, Altobelli G, Emmett W, Lescai F, Gustincich S, Stupka E. ParkDB: a Parkinson's disease gene expression database. Database (Oxford) 2011; 2011:bar007. [PMID: 21593080 PMCID: PMC3098727 DOI: 10.1093/database/bar007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Parkinson’s disease (PD) is a common, adult-onset, neuro-degenerative disorder characterized by the degeneration of cardinal motor signs mainly due to the loss of dopaminergic neurons in the substantia nigra. To date, researchers still have limited understanding of the key molecular events that provoke neurodegeneration in this disease. Here, we present ParkDB, the first queryable database dedicated to gene expression in PD. ParkDB contains a complete set of re-analyzed, curated and annotated microarray datasets. This resource enables scientists to identify and compare expression signatures involved in PD and dopaminergic neuron differentiation under different biological conditions and across species. Database URL:http://www2.cancer.ucl.ac.uk/Parkinson_Db2/
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Affiliation(s)
- Cristian Taccioli
- UCL, Department of Cancer Biology, University College London, Gower Street, London, UK
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27
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Lescai F, Pirazzini C, D'Agostino G, Santoro A, Ghidoni R, Benussi L, Galimberti D, Federica E, Marchegiani F, Cardelli M, Olivieri F, Nacmias B, Sorbi S, Bagnoli S, Tagliavini F, Albani D, Martinelli Boneschi F, Binetti G, Forloni G, Quadri P, Scarpini E, Franceschi C. Failure to replicate an association of rs5984894 SNP in the PCDH11X gene in a collection of 1,222 Alzheimer's disease affected patients. J Alzheimers Dis 2010; 21:385-8. [PMID: 20555150 DOI: 10.3233/jad-2010-091516] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A recent genome-wide study on late-onset Alzheimer's disease identified a SNP (rs5984894) on Xq21.3 in the PCDH11X gene strongly associated with LOAD individuals of European descent from the United States. We genotyped the same polymorphism in 1222 cases and 938 controls from central-northern Italy and could not confirm the association on the Italian population: multivariate logistic regression adjusted for gender and APOE epsilon4 allele resulted in a global p value of 0.56.
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Affiliation(s)
- Francesco Lescai
- Division of Research Strategy, University College London, London, UK.
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28
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Cevenini E, Bellavista E, Tieri P, Castellani G, Lescai F, Francesconi M, Mishto M, Santoro A, Valensin S, Salvioli S, Capri M, Zaikin A, Monti D, de Magalhães JP, Franceschi C. Systems biology and longevity: an emerging approach to identify innovative anti-aging targets and strategies. Curr Pharm Des 2010; 16:802-13. [PMID: 20388091 DOI: 10.2174/138161210790883660] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 10/16/2009] [Indexed: 11/22/2022]
Abstract
Human aging and longevity are complex and multi-factorial traits that result from a combination of environmental, genetic, epigenetic and stochastic factors, each contributing to the overall phenotype. The multi-factorial process of aging acts at different levels of complexity, from molecule to cell, from organ to organ systems and finally to organism, giving rise to the dynamic "aging mosaic". At present, an increasing amount of experimental data on genetics, genomics, proteomics and other -omics are available thanks to new high-throughput technologies but a comprehensive model for the study of human aging and longevity is still lacking. Systems biology represents a strategy to integrate and quantify the existing knowledge from different sources into predictive models, to be later tested and then implemented with new experimental data for validation and refinement in a recursive process. The ultimate goal is to compact the new acquired knowledge into a single picture, ideally able to characterize the phenotype at systemic/organism level. In this review we will briefly discuss the aging phenotype in a systems biology perspective, showing four specific examples at different levels of complexity, from a systemic process (inflammation) to a cascade-process pathways (coagulation) and from cellular organelle (proteasome) to single gene-network (PON-1), which could also represent targets for anti-aging strategies.
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Affiliation(s)
- E Cevenini
- CIG - Interdepartmental Centre L Galvani, University of Bologna, Bologna, Italy
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29
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Abstract
A consistent debate is ongoing on genome-wide association studies (GWAs). A key point is the capability to identify low-penetrance variations across the human genome. Among the phenomena reducing the power of these analyses, phenocopy level (PE) hampers very seriously the investigation of complex diseases, as well known in neurological disorders, cancer, and likely of primary importance in human ageing. PE seems to be the norm, rather than the exception, especially when considering the role of epigenetics and environmental factors towards phenotype. Despite some attempts, no recognized solution has been proposed, particularly to estimate the effects of phenocopies on the study planning or its analysis design. We present a simulation, where we attempt to define more precisely how phenocopy impacts on different analytical methods under different scenarios. With our approach the critical role of phenocopy emerges, and the more the PE level increases the more the initial difficulty in detecting gene-gene interactions is amplified. In particular, our results show that strong main effects are not hampered by the presence of an increasing amount of phenocopy in the study sample, despite progressively reducing the significance of the association, if the study is sufficiently powered. On the opposite, when purely epistatic effects are simulated, the capability of identifying the association depends on several parameters, such as the strength of the interaction between the polymorphic variants, the penetrance of the polymorphism and the alleles (minor or major) which produce the combined effect and their frequency in the population. We conclude that the neglect of the possible presence of phenocopies in complex traits heavily affects the analysis of their genetic data.
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Affiliation(s)
- Francesco Lescai
- Division of Research Strategy, University College London, London, United Kingdom.
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30
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Lescai F, Pourçain CS. Supporting careers of young researchers in the biosciences. N Biotechnol 2010. [DOI: 10.1016/j.nbt.2010.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Kaiser P, Danilowicz E, Vallés MF, Keller D, Lescai F. Youth careers in life sciences in Europe. N Biotechnol 2010. [DOI: 10.1016/j.nbt.2010.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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Lescai F, Marchegiani F, Franceschi C. PON1 is a longevity gene: results of a meta-analysis. Ageing Res Rev 2009; 8:277-84. [PMID: 19376276 DOI: 10.1016/j.arr.2009.04.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 04/06/2009] [Accepted: 04/07/2009] [Indexed: 11/17/2022]
Abstract
Paraoxonase 1 (PON1) is one of the most studied genes regarding cardiovascular risk, oxidative stress and inflammation. Several lines of evidence suggests that PON1 promotes an atheroprotective effect. Patients carrying PON1 codon 192 QQ genotype display a higher risk of cardiovascular events, the major cause of mortality in the elderly: it can be predicted that gene variants increasing the risk of mortality will be under-represented in long-living individuals. We first reported that PON1 R allele (R+) carriers are significantly more represented in Italian centenarians; subsequently this topic has been addressed by many other groups, and here we report a meta-analysis on 11 studies in different populations selected by a review of the literature available in PubMed and testing the effect of the Q192R polymorphism on human ageing. QUORUM guidelines for meta-analysis have been followed, and a total number of 5962 subjects have been included: 2795 young controls (<65 years of age) and 3167 old subjects (>65 years of age). The Mantel-Haenszel weighting for pooling in presence of a fixed effects model has been applied. The meta-analysis of R carriers showed a significant result with an overall OR of 1.16 (1.04-1.30, 95% CI, p=0.006). The meta-analysis of QR genotype also showed a significant result, with an overall OR of 1.14 (1.02-1.27, 95% CI, p=0.016). The results show that PON1 gene variants at codon 192 impact on the probability of attaining longevity, and that subjects carrying RR and QR genotypes (R+ carriers) are favoured in reaching extreme ages. These results likely represent the counterpart of the effects observed on cardiovascular diseases (CVD), as centenarians and nonagenarians escaped or delayed the onset of the major age-related diseases, including CVD.
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Affiliation(s)
- Francesco Lescai
- CIG-Centre L. Galvani for Biophysics, Bioinformatics and Biocomplexity, Alma Mater Studiorum Università di Bologna, Bologna, Italy.
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33
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Lescai F, Franceschi C. The impact of phenocopy on the genetic analysis of complex traits. N Biotechnol 2009. [DOI: 10.1016/j.nbt.2009.06.836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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34
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Lescai F, Blanché H, Nebel A, Beekman M, Sahbatou M, Flachsbart F, Slagboom E, Schreiber S, Sorbi S, Passarino G, Franceschi C. Human longevity and 11p15.5: a study in 1321 centenarians. Eur J Hum Genet 2009; 17:1515-9. [PMID: 19367319 DOI: 10.1038/ejhg.2009.54] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The 11p15.5 chromosomal region (2.8 Mb) is of particular interest as it encloses five genes (HRAS1, SIRT3, TH, INS and IGF2), the variability of which was found to be associated with life extension by association studies. Mostly important, the above genes are homologous of genes that modulate lifespan in model organisms. We scanned the area in four European sample groups for a total of 1321 centenarians and 1140 younger subjects, who shared with centenarians ethnicity and geographical origin, with a set of 239 SNPs. No significant results (P<0.05) have been found on the earlier associated loci (ie, TH, IGF2, INS and HRAS1), and this study could not confirm the earlier findings on each of those genes. A meta-analysis was carried out on the SIRT3 SNP data; a total number of 2461 samples were included, but no positive association was found except for one SNP having a significant effect (rs939915). The same meta-analysis approach has been applied to the other 229 markers, and six SNPs have been found significant for the frequent genotype (rs4073591, DEAF1-rs4073590, KRTAP5-6-rs11040489, rs4930001, TSPAN32-rs800140 and rs16928120). This experience, although unable to confirm the earlier findings of the literature, highlights all the common difficulties of such studies in human longevity. Despite the rather negative findings presented here, the results derived from unprecedented studies involving such a large number of centenarians should be disseminated, thus contributing to set up adequate strategies to disentangle complex and likely heterogeneous phenotypes.
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Affiliation(s)
- Francesco Lescai
- Centro Interdipartimentale 'L.Galvani' per Studi Integrati di Bioinformatica, Biofisica e Biocomplessità - Alma Mater Studiorum Università di Bologna, Italy.
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Lescai F. Marie Curie fellowships unraveled. N Biotechnol 2009; 25:186-7. [DOI: 10.1016/j.nbt.2008.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 12/25/2008] [Indexed: 11/28/2022]
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Abstract
BACKGROUND The aging phenotype in humans is very heterogeneous and can be described as a complex mosaic resulting from the interaction of a variety of environmental, stochastic and genetic-epigenetic variables. Therefore, each old person must be considered as a singleton, and consequently the definition of 'aging phenotype' is very difficult. OBJECTIVE We discuss the phenotype of centenarians, the best example of successful aging, as well as other models exploited to study human aging and longevity, such as families enriched in long-living subjects, twins and cohorts of unrelated subjects. METHODS A critical review of literature available until March 2008. CONCLUSIONS No single model can be considered the gold standard for the study of aging and longevity, instead the combination of results obtained from different models must be considered in order to better understand these complex phenomena. We propose that a systems biology concept such as that of 'bow-tie' architecture, useful for managing information flow, could help in this demanding task.
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Affiliation(s)
- E Cevenini
- University of Bologna, Department of Experimental Pathology, Via S. Giacomo 12, 40126 Bologna, Italy
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Lescai F. Helping young independent scientists: the EMBO Young Investigator Programme Interview with Gerlind Wallon, Deputy Executive Director, EMBO Young Investigator Programme. N Biotechnol 2008; 25:120-1. [PMID: 18723133 DOI: 10.1016/j.nbt.2008.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 08/08/2008] [Indexed: 11/17/2022]
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Di Bona D, Plaia A, Vasto S, Cavallone L, Lescai F, Franceschi C, Licastro F, Colonna-Romano G, Lio D, Candore G, Caruso C. Association between the interleukin-1beta polymorphisms and Alzheimer's disease: a systematic review and meta-analysis. ACTA ACUST UNITED AC 2008; 59:155-63. [PMID: 18675847 DOI: 10.1016/j.brainresrev.2008.07.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/04/2008] [Accepted: 07/08/2008] [Indexed: 11/26/2022]
Abstract
The pro-inflammatory cytokine interleukin(IL)-1beta is a main component in inflammatory pathways and is overexpressed in the brain of Alzheimer's disease (AD) patients. Several studies report associations between IL-1beta polymorphisms and AD, but findings from different studies are controversial. Our aim was to verify the correlation between the single nucleotide polymorphisms (SNPs) of the IL-1beta, at sites -511 and +3953, and AD by meta-analysis. Computerized bibliographic searches of PUBMED and AlzGene database (http://www.alzgene.org) were supplemented with manual searches of reference lists. There is evidence for association between IL-1beta +3953 SNP and AD, with an OR=1.60 (95% C.I.: 1.16-2.22; Z=2.83 p=0.005) for TT genotype. No significant difference in genotype distribution of the IL-1beta -511 SNP in AD was obtained, but high between-study heterogeneity was found. To reduce heterogeneity, subgroup analyses were performed using, as stratifying variables, characteristics of the population under study (age, gender, type of AD diagnosis, Mini Mental State Examination of the controls) and characteristics related to the study design (statistical power of individual studies). The frequency of the IL-1beta -511 TT genotype resulted significantly higher than other genotypes only when the Caucasian studies with the highest statistical power were included in the subgroup analysis (OR=1.32; 95% C.I.: 1.03-1.69; p=0.03), with no evidence of between-study heterogeneity. Our data support an association between the TT genotype of IL-1beta +3953 SNP and AD, and suggest a possible association of the -511 TT genotype. Unreplicability of the results seems to be due mainly to the lack of statistical power of the individual studies.
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Affiliation(s)
- Danilo Di Bona
- Istituto di Biomedicina ed Immunologia Molecolare (IBIM), CNR, Palermo Università di Palermo, Italy
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Cardelli M, Cavallone L, Marchegiani F, Oliveri F, Dato S, Montesanto A, Lescai F, Lisa R, De Benedictis G, Franceschi C. A genetic-demographic approach reveals male-specific association between survival and tumor necrosis factor (A/G)-308 polymorphism. J Gerontol A Biol Sci Med Sci 2008; 63:454-60. [PMID: 18511747 DOI: 10.1093/gerona/63.5.454] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The (A/G)-308 polymorphism of the tumor necrosis factor alpha gene (TNF) is associated with age-related diseases, but its influence on longevity is controversial. We genotyped for this polymorphism 747 Italian volunteers (401 women and 346 men, age 19-110 years). By applying a genetic-demographic (GD) approach we found that, in men, the survival function of allele A carriers is lower than that of noncarriers at all the ages (p =.044). After defining (by exploiting again demographic information) three age classes, we found that the frequency of men carrying the A allele decreases with age (p =.019), thus confirming the GD analysis results. The same analyses gave negative results in women. Therefore, allele A has a detrimental effect on life expectancy, and this effect is specific to men. A haplotype analysis carried out in men by screening the TNFa, TNFc, and TNFe microsatellite polymorphisms (spanning about 20 kb) confirmed the association of the TNF region with life expectancy.
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Affiliation(s)
- Maurizio Cardelli
- Department of Gerontological Research, Italian National Research Center on Aging, Ancona, Italy.
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Lescai F. The Young European Biotech Network (YEBN). N Biotechnol 2008; 25:34. [PMID: 18504012 DOI: 10.1016/j.nbt.2008.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Francesco Lescai
- The Babraham Institute, Babraham, Cambridge CB2 4AT, United Kingdom.
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Sevini F, Santoro A, Raule N, Lescai F, Franceschi C. Role of mitochondrial DNA in longevity, aging and age-related diseases in humans: a reappraisal. Ital J Biochem 2007; 56:243-253. [PMID: 19192621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The genetic variability of H. sapiens mitochondrial DNA (mtDNA) can be either germ-line inherited or somatically acquired, and its effect on aging and longevity as well as on the pathogenesis of complex age-related diseases is a hot topic. Here we illustrate the complexity of such studies, related to the large genetic variability of mtDNA in different populations and the fact that the rate of the aging process is different in different cells, tissues and organs. As far as concern Alzheimer's disease, the accumulation of somatic mutations in several tissues have been investigated, as well as the inherited mtDNA variability. However, the issue is still controversial and further studies are needed to clarify the role of mtDNA variants in Alzheimer's disease. This review is aimed to summarize the most recent advances in this field. By high throughput mtDNA sequencing and the study of large cohorts of ethnically homogeneous subjects/patients, it is now possible to perform high dimensionality studies in order to clarify the genetic associations among several inherited mtDNA variants and longevity or age-associated diseases in humans.
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Affiliation(s)
- Federica Sevini
- Interdepartmental Center for Studies on Biophysics, Bioinformatics and Biocomplexity L. Galvani (CIG), Bologna, Italy.
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Salvioli S, Olivieri F, Marchegiani F, Cardelli M, Santoro A, Bellavista E, Mishto M, Invidia L, Capri M, Valensin S, Sevini F, Cevenini E, Celani L, Lescai F, Gonos E, Caruso C, Paolisso G, De Benedictis G, Monti D, Franceschi C. Genes, ageing and longevity in humans: problems, advantages and perspectives. Free Radic Res 2007; 40:1303-23. [PMID: 17090420 DOI: 10.1080/10715760600917136] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many epidemiological data indicate the presence of a strong familial component of longevity that is largely determined by genetics, and a number of possible associations between longevity and allelic variants of genes have been described. A breakthrough strategy to get insight into the genetics of longevity is the study of centenarians, the best example of successful ageing. We review the main results regarding nuclear genes as well as the mitochondrial genome, focusing on the investigations performed on Italian centenarians, compared to those from other countries. These studies produced interesting results on many putative "longevity genes". Nevertheless, many discrepancies are reported, likely due to the population-specific interactions between gene pools and environment. New approaches, including large-scale studies using high-throughput techniques, are urgently needed to overcome the limits of traditional association studies performed on a limited number of polymorphisms in order to make substantial progress to disentangle the genetics of a trait as complex as human longevity.
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Affiliation(s)
- S Salvioli
- Department of Experimental Pathology, University of Bologna, Bologna, Italy
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Capri M, Monti D, Salvioli S, Lescai F, Pierini M, Altilia S, Sevini F, Valensin S, Ostan R, Bucci L, Franceschi C. Complexity of Anti-immunosenescence Strategies in Humans. Artif Organs 2006; 30:730-42. [PMID: 17026572 DOI: 10.1111/j.1525-1594.2006.00295.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Immunosenescence is characterized by three main aspects: (i) the shrinkage of the T cell repertoire and the accumulation of oligoclonal expansions (megaclones) of memory/effector cells directed toward ubiquitary infectious agents; (ii) the involution of the thymus and the exhaustion of naïve T cells; and (iii) a chronic inflammatory status called inflamm-aging. We present here possible strategies to counteract these main aspects of immunosenescence in humans with particular attention to the reduction of antigenic load by pathogens, such as CMV, and the normalization of intestinal microflora, the possible utilization of IL-7 to reverse thymic involution, the purging of megaclones, the forced expression of CD28 on T lymphocytes, the reduction of inflamm-aging and the administration of nutrients such as vitamin D. Possible drawbacks of all these strategies are discussed. Finally, the complexity of a rejuvenation approach is stressed, with particular attention to the inhibitory role played by the "old microenvironment" on the performance of progenitor cells, the best candidate to counteract the decline in regenerative potential characteristic of organs and tissues from old organisms.
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Affiliation(s)
- Miriam Capri
- Department of Experimental Pathology, University of Bologna, Bologna, Italy
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Lescai F, Conti L, Bartolozzi M, Ramazzotti G, Mazzi M, Sarnicola V, Franceschi C. Genotype of inflammatory cytokines in limbal stem cell graft in Italian patients. Biochem Biophys Res Commun 2005; 332:95-100. [PMID: 15896304 DOI: 10.1016/j.bbrc.2005.04.106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Accepted: 04/20/2005] [Indexed: 11/29/2022]
Abstract
We tested the hypothesis that the genetic capability to mount an inflammatory response might contribute to the inter-individual variability of limbal stem cell graft (LSCG) outcome. Two functional polymorphisms in the IL-6 and TNF-alpha promoter regions were genotyped in 35 patients. A new score system (clinical assessment score, CAS) was set up in order to classify patients' clinical profile, and the main parameters relevant for LSCG as well as for the follow-up of the patients. Patients carrying at both loci a genotype associated with a lower production of both cytokines were classified as "low producers" (LP), while all the others were classified as "intermediate or high producers" (HP). LP patients did not show any difference in CAS before and after transplantation while a significant difference was present in HP patients. A similar trend was evident in the 35 months of follow-up. Polymorphisms of IL-6 and TNF-alpha can be used to identify subgroups of patients with higher risk of unsuccessful outcome.
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Affiliation(s)
- Francesco Lescai
- Department of Experimental Pathology, University of Bologna, Bologna, Italy.
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Lescai F, Quarta M. Italian biotechnologists organize. Nature 2003; 425:644. [PMID: 14534594 DOI: 10.1038/nj6958-644a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Franceschi C, Valensin S, Lescai F, Olivieri F, Licastro F, Grimaldi LM, Monti D, De Benedictis G, Bonafè M. Neuroinflammation and the genetics of Alzheimer's disease: the search for a pro-inflammatory phenotype. Aging (Milano) 2001; 13:163-70. [PMID: 11442299 DOI: 10.1007/bf03351475] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of interleukin 1 (IL-1) and interleukin 6 (IL-6) in the pathogenesis of Alzheimer's disease (AD) is reviewed within the framework of "inflamm-aging", i.e., the characteristic chronic pro-inflammatory status which develops in old age, and neuroinflammation, i.e., the peculiar inflammatory process which is present in the brain of AD patients. In particular, the data suggesting that several IL-1 and IL-6 gene polymorphisms can contribute to the risk of developing AD are reviewed. The possibility as well as the difficulty in identifying a pro-inflammatory phenotype, and its importance for the prevention, diagnosis and therapy of AD and other age-related pathologies are discussed.
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Affiliation(s)
- C Franceschi
- Department of Experimental Pathology, University of Bologna, Italy.
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Franceschi C, Motta L, Valensin S, Rapisarda R, Franzone A, Berardelli M, Motta M, Monti D, Bonafè M, Ferrucci L, Deiana L, Pes GM, Carru C, Desole MS, Barbi C, Sartoni G, Gemelli C, Lescai F, Olivieri F, Marchegiani F, Cardelli M, Cavallone L, Gueresi P, Cossarizza A, Troiano L, Pini G, Sansoni P, Passeri G, Lisa R, Spazzafumo L, Amadio L, Giunta S, Stecconi R, Morresi R, Viticchi C, Mattace R, De Benedictis G, Baggio G. Do men and women follow different trajectories to reach extreme longevity? Italian Multicenter Study on Centenarians (IMUSCE). Aging (Milano) 2000; 12:77-84. [PMID: 10902049 DOI: 10.1007/bf03339894] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gender accounts for important differences in the incidence and prevalence of a variety of age-related diseases. Considering people of far advanced age, demographic data document a clear-cut prevalence of females compared to males, suggesting that sex-specific mortality rates follow different trajectories during aging. In the present investigation, we report data from a nationwide study on Italian centenarians (a total of 1162 subjects), and from two studies on centenarians living in two distinct zones of Italy, i.e., the island of Sardinia (a total of 222 subjects) and the Mantova province (Northern Italy) (a total of 43 subjects). The female/male ratio was about 2:1 in Sardinia, 4:1 in the whole of Italy, and about 7:1 in the Mantova province. Thus, a complex interaction of environmental, historical and genetic factors, differently characterizing the various parts of Italy, likely plays an important role in determining the gender-specific probability of achieving longevity. Gender differences in the health status of centenarians are also reported, and an innovative score method to classify long-lived people in different health categories, according to clinical and functional parameters, is proposed. Our data indicate that not only is this selected group of people, as a whole, highly heterogeneous, but also that a marked gender difference exists, since male centenarians are less heterogeneous and more healthy than female centenarians. Immunological factors regarding the age-related increase in pro-inflammatory status, and the frequency of HLA ancestral haplotypes also show gender differences that likely contribute to the different strategies that men and women seem to follow to achieve longevity. Concerning the different impact of genetic factors on the probability of reaching the extreme limits of the human life-span, emerging evidence (regarding mtDNA haplogroups, Thyrosine Hydroxilase, and IL-6 genes) suggests that female longevity is less dependent on genetics than male longevity, and that female centenarians likely exploited a healthier life-style and more favorable environmental conditions, owing to gender-specific cultural and anthropological characteristics of the Italian society in the last 100 years.
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Affiliation(s)
- C Franceschi
- Department of Experimental Pathology, University of Bologna.
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