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Koenig Z, Yohannes MT, Nkambule LL, Zhao X, Goodrich JK, Kim HA, Wilson MW, Tiao G, Hao SP, Sahakian N, Chao KR, Walker MA, Lyu Y, Rehm HL, Neale BM, Talkowski ME, Daly MJ, Brand H, Karczewski KJ, Atkinson EG, Martin AR. A harmonized public resource of deeply sequenced diverse human genomes. bioRxiv 2024:2023.01.23.525248. [PMID: 36747613 PMCID: PMC9900804 DOI: 10.1101/2023.01.23.525248] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Underrepresented populations are often excluded from genomic studies due in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequenced to high coverage, are valuable genomic resources because of the global diversity they capture and their open data sharing policies. Here, we harmonized a high quality set of 4,094 whole genomes from HGDP and 1kGP with data from the Genome Aggregation Database (gnomAD) and identified over 153 million high-quality SNVs, indels, and SVs. We performed a detailed ancestry analysis of this cohort, characterizing population structure and patterns of admixture across populations, analyzing site frequency spectra, and measuring variant counts at global and subcontinental levels. We also demonstrate substantial added value from this dataset compared to the prior versions of the component resources, typically combined via liftover and variant intersection; for example, we catalog millions of new genetic variants, mostly rare, compared to previous releases. In addition to unrestricted individual-level public release, we provide detailed tutorials for conducting many of the most common quality control steps and analyses with these data in a scalable cloud-computing environment and publicly release this new phased joint callset for use as a haplotype resource in phasing and imputation pipelines. This jointly called reference panel will serve as a key resource to support research of diverse ancestry populations.
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Affiliation(s)
- Zan Koenig
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary T. Yohannes
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lethukuthula L. Nkambule
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Julia K. Goodrich
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heesu Ally Kim
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael W. Wilson
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stephanie P. Hao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Nareh Sahakian
- Broad Genomics, The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark A. Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yunfei Lyu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Heidi L. Rehm
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin M. Neale
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael E. Talkowski
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Mark J. Daly
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Harrison Brand
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Konrad J. Karczewski
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Elizabeth G. Atkinson
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alicia R. Martin
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
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Kipkemoi P, Kim HA, Christ B, O'Heir E, Allen J, Austin-Tse C, Baxter S, Brand H, Bryant S, Buser N, de Menil V, Eastman E, Murugasen S, Galvin A, Kombe M, Ngombo A, Mkubwa B, Mwangi P, Kipkoech C, Lovgren A, MacArthur DG, Melly B, Mwangasha K, Martin A, Nkambule LL, Sanchis-Juan A, Singer-Berk M, Talkowski ME, VanNoy G, van der Merwe C, Newton C, O'Donnell-Luria A, Abubakar A, Donald KA, Robinson EB. Phenotype and genetic analysis of data collected within the first year of NeuroDev. Neuron 2023; 111:2800-2810.e5. [PMID: 37463579 DOI: 10.1016/j.neuron.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/13/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023]
Abstract
Genetic association studies have made significant contributions to our understanding of the etiology of neurodevelopmental disorders (NDDs). However, these studies rarely focused on the African continent. The NeuroDev Project aims to address this diversity gap through detailed phenotypic and genetic characterization of children with NDDs from Kenya and South Africa. We present results from NeuroDev's first year of data collection, including phenotype data from 206 cases and clinical genetic analyses of 99 parent-child trios. Most cases met criteria for global developmental delay/intellectual disability (GDD/ID, 80.3%). Approximately half of the children with GDD/ID also met criteria for autism. Analysis of exome-sequencing data identified a pathogenic or likely pathogenic variant in 13 (17%) of the 75 cases from South Africa and 9 (38%) of the 24 cases from Kenya. Data from the trio pilot are publicly available, and the NeuroDev Project will continue to develop resources for the global genetics community.
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Affiliation(s)
- Patricia Kipkemoi
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya; Complex Trait Genetics Department, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Heesu Ally Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bjorn Christ
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa
| | - Emily O'Heir
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jake Allen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Austin-Tse
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Harrison Brand
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Sam Bryant
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nick Buser
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Victoria de Menil
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Emma Eastman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa
| | - Serini Murugasen
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa
| | - Alice Galvin
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martha Kombe
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Alfred Ngombo
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Beatrice Mkubwa
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Paul Mwangi
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Collins Kipkoech
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Alysia Lovgren
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Brigitte Melly
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa
| | - Katini Mwangasha
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Alicia Martin
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lethukuthula L Nkambule
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alba Sanchis-Juan
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | | | - Michael E Talkowski
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Grace VanNoy
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Charles Newton
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, London, UK; Institute of Human Development, Aga Khan University, Nairobi, Kenya
| | - Anne O'Donnell-Luria
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Amina Abubakar
- Neuroscience Unit, KEMRI-Wellcome Trust, Center for Geographic Medicine Research Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, London, UK; Institute of Human Development, Aga Khan University, Nairobi, Kenya.
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, 4th Floor ICH Building, Rondebosch, South Africa; Neuroscience Institute, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, South Africa.
| | - Elise B Robinson
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
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3
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Majara L, Kalungi A, Koen N, Tsuo K, Wang Y, Gupta R, Nkambule LL, Zar H, Stein DJ, Kinyanda E, Atkinson EG, Martin AR. Low and differential polygenic score generalizability among African populations due largely to genetic diversity. HGG Adv 2023; 4:100184. [PMID: 36873096 PMCID: PMC9982687 DOI: 10.1016/j.xhgg.2023.100184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/04/2023] [Indexed: 02/15/2023] Open
Abstract
African populations are vastly underrepresented in genetic studies but have the most genetic variation and face wide-ranging environmental exposures globally. Because systematic evaluations of genetic prediction had not yet been conducted in ancestries that span African diversity, we calculated polygenic risk scores (PRSs) in simulations across Africa and in empirical data from South Africa, Uganda, and the United Kingdom to better understand the generalizability of genetic studies. PRS accuracy improves with ancestry-matched discovery cohorts more than from ancestry-mismatched studies. Within ancestrally and ethnically diverse South African individuals, we find that PRS accuracy is low for all traits but varies across groups. Differences in African ancestries contribute more to variability in PRS accuracy than other large cohort differences considered between individuals in the United Kingdom versus Uganda. We computed PRS in African ancestry populations using existing European-only versus ancestrally diverse genetic studies; the increased diversity produced the largest accuracy gains for hemoglobin concentration and white blood cell count, reflecting large-effect ancestry-enriched variants in genes known to influence sickle cell anemia and the allergic response, respectively. Differences in PRS accuracy across African ancestries originating from diverse regions are as large as across out-of-Africa continental ancestries, requiring commensurate nuance.
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Affiliation(s)
- Lerato Majara
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Allan Kalungi
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Department of Psychiatry, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Mental Health Project, Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) & London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Nastassja Koen
- Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER), Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Kristin Tsuo
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rahul Gupta
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Lethukuthula L. Nkambule
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heather Zar
- Department of Paediatrics and Child Health, Red Cross Children’s Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J. Stein
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, Cape Town, South Africa
| | - Eugene Kinyanda
- Mental Health Project, Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) & London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Elizabeth G. Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alicia R. Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Tsuo K, Zhou W, Wang Y, Kanai M, Namba S, Gupta R, Majara L, Nkambule LL, Morisaki T, Okada Y, Neale BM, Daly MJ, Martin AR. Multi-ancestry meta-analysis of asthma identifies novel associations and highlights the value of increased power and diversity. Cell Genom 2022; 2:100212. [PMID: 36778051 PMCID: PMC9903683 DOI: 10.1016/j.xgen.2022.100212] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 09/01/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
Abstract
Asthma is a complex disease that varies widely in prevalence across populations. The extent to which genetic variation contributes to these disparities is unclear, as the genetics underlying asthma have been investigated primarily in populations of European descent. As part of the Global Biobank Meta-analysis Initiative, we conducted a large-scale genome-wide association study of asthma (153,763 cases and 1,647,022 controls) via meta-analysis across 22 biobanks spanning multiple ancestries. We discovered 179 asthma-associated loci, 49 of which were not previously reported. Despite the wide range in asthma prevalence among biobanks, we found largely consistent genetic effects across biobanks and ancestries. The meta-analysis also improved polygenic risk prediction in non-European populations compared with previous studies. Additionally, we found considerable genetic overlap between age-of-onset subtypes and between asthma and comorbid diseases. Our work underscores the multi-factorial nature of asthma development and offers insight into its shared genetic architecture.
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Affiliation(s)
- Kristin Tsuo
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
| | - Wei Zhou
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
| | - Ying Wang
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Rahul Gupta
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Lerato Majara
- Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lethukuthula L. Nkambule
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
| | - Takayuki Morisaki
- Division of Molecular Pathology, The Institute of Medical Science, The University of Tokyo, Minatu-ku, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita 565-0871, Japan
| | - Benjamin M. Neale
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
| | - Global Biobank Meta-analysis Initiative
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Molecular Pathology, The Institute of Medical Science, The University of Tokyo, Minatu-ku, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita 565-0871, Japan
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Alicia R. Martin
- Analytic and Translational Genetics Unit, 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 MIT and Harvard, Cambridge, MA, USA
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