ArticlebioRxiv : the preprint server for biology2024
A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner.
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92 authors.
Toni A BoltzStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-0226-7924
Benjamin B ChuDepartment of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.ORCID 0000-0001-8342-2361
Calwing LiaoStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-6169-7137
Julia M SealockStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-9346-3498
Robert YeStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0009-0007-4947-9672
Lerato MajaraStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-9171-3115
Jack M FuProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-4152-5471
Susan ServiceCenter for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
Lingyu ZhanDepartment of Psychiatry, Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
Sarah E MedlandQIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.ORCID 0000-0003-1382-380X
Sinéad B ChapmanStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-9454-2737
Simone RubinacciProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-7725-4813
Matthew DeFeliceBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0009-0007-2481-8842
Jonna L GrimsbyBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-2304-7656
Tamrat AbebeDepartment of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.ORCID 0000-0002-6100-9303
Melkam AlemayehuDepartment of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
Fred K AshabaDepartment of Immunology & Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.
Elizabeth G AtkinsonDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.ORCID 0000-0002-6308-776X
Tim BigdeliInstitute for Genomics in Health, The State University of New York, Brooklyn, NY, USA.ORCID 0000-0003-2215-5946
Amanda B BradwayBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Harrison BrandProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Lori B ChibnikStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-6293-806X
Abebaw FekaduDepartment of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
Michael GatzenBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-5390-0705
Bizu GelayeStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-7934-548X
Stella GichuruDepartment of Mental Health, Moi Teaching and Referral Hospital, Eldoret, Kenya.
Marissa L GildeaBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Toni C HillBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Hailiang HuangStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-1461-5762
Kalyn M HubbardBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Wilfred E InjeraDepartment of Medical Laboratory Sciences, School of Health Sciences, Alupe University, Busia, Kenya.ORCID 0000-0001-8027-0585
Roxanne JamesDepartment of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa.
Moses JolobaSchool of Biomedical Sciences, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda.ORCID 0000-0002-0334-9983
Christopher KachulisBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-2095-7419
Phillip R KalmbachBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Rogers KamulegeyaSchool of Biomedical Sciences, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda.ORCID 0000-0001-7972-3647
Gabriel KigenDepartment of Pharmacology and Toxicology, Moi University School of Medicine, Eldoret, Kenya.ORCID 0000-0002-5047-4066
Soyeon KimStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Nastassja KoenDepartment of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa.
Edith K KwobahDepartment of Mental Health, Moi Teaching and Referral Hospital, Eldoret, Kenya.ORCID 0000-0002-1754-2127
Joseph KyebuzibwaDepartment of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda.ORCID 0000-0003-1416-245X
Seungmo LeeDepartment of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.
Niall J LennonBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-2874-7371
Penelope A LindQIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.ORCID 0000-0002-3887-2598
Esteban A Lopera-MayaCenter for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.ORCID 0000-0001-5862-3938
Johnstone MakaleEpidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya.ORCID 0000-0002-3670-7521
Serghei MangulDepartment of Quantitative and Computational Biology, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA.ORCID 0000-0003-4770-3443
Justin McMahonStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-6388-1429
Pierre MowlemAmpath Laboratories, Moi University School of Medicine, Eldoret, Kenya.
Henry MusinguziDepartment of Immunology & Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.
Rehema M MwemaNeurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast,, Kilifi, Kenya.
Noeline NakasujjaDepartment of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda.ORCID 0000-0002-8163-4376
Carter P NewmanStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-1565-9276
Lethukuthula L NkambuleStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Conor R O'NeilBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Ana Maria OlivaresStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-7325-9211
Catherine M OlsenQIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
Linnet OngeriCentre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya.ORCID 0000-0003-2330-6144
Sophie J ParsaStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Adele PretoriusDepartment of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa.
Raj RamesarSA MRC Unit on Risk & Resilience in Mental Disorders, University of Cape Town and Neuroscience Institute, Cape Town, South Africa.
Faye L ReaganBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Chiara SabattiDepartment of Biomedical Data Sciences, Stanford University, Stanford, CA, USA.ORCID 0000-0001-5829-9058
Jacquelyn A SchneiderBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Welelta ShiferawDepartment of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.ORCID 0000-0002-8927-0861
Anne StevensonStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-7890-3291
Erik StrickerDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.ORCID 0000-0003-2112-2202
Rocky E StroudStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-4246-7093
Jessie TangBroad Clinical Labs (BCL), Broad Institute of MIT and Harvard, Cambridge, MA, USA.
David WhitemanQIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.ORCID 0000-0003-2563-9559
Mary T YohannesStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Mingrui YuStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Kai YuanStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-8460-6581
NeuroGAP-Psychosis
Dickens AkenaDepartment of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda.ORCID 0000-0002-8886-4553
Lukoye AtwoliDepartment of Mental Health and Behavioural Sciences, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya.ORCID 0000-0001-7710-9723
Symon M KariukiNeurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya.ORCID 0000-0002-3934-5132
Karestan C KoenenStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-2978-7655
Charles R J C NewtonNeurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast,, Kilifi, Kenya.ORCID 0000-0002-6999-5507
Dan J SteinSA MRC Unit on Risk & Resilience in Mental Disorders, University of Cape Town and Neuroscience Institute, Cape Town, South Africa.ORCID 0000-0001-7218-7810
Solomon TeferraDepartment of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.ORCID 0000-0003-0405-1705
Zukiswa ZingelaExecutive Dean's Office, Faculty of Health Sciences, Nelson Mandela University, Gqebera, South Africa.ORCID 0000-0002-3425-1145
Carlos N PatoRutgers University, New Brunswick, NJ, USA.
Michele T PatoRutgers University, New Brunswick, NJ, USA.ORCID 0000-0002-4589-7398
Carlos Lopez-JaramilloDepartment of Psychiatry, University of Antioquia, University of Antioquia, Medellín, Antioquia, Colombia.ORCID 0000-0002-1875-1369
Nelson FreimerBD2: Breakthrough Discoveries for thriving with Bipolar Disorder, Santa Monica, CA, USA.
Roel A OphoffCenter for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.ORCID 0000-0002-8287-6457
Loes M Olde LoohuisCenter for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.ORCID 0000-0002-3327-7837
Michael E TalkowskiStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-2889-0992
Benjamin M NealeStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-1513-6077
Daniel P HowriganStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-7721-4838
Alicia R MartinStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-0241-3522
Funding
POSTDOCTORAL TRAINING IN MEDICAL INFORMATION SCIENCEST15LM007033 · NLM · STANFORD UNIVERSITY · PI SYLVIA KATINA PLEVRITIS · 1985 to 2026
$25.5M1/4 Powering Genetic Discovery for Severe Mental Illness in Latin American and African AncestriesU01MH125047 · NIMH · BROAD INSTITUTE, INC. · PI MARTIN, ALICIA, NEALE, BENJAMIN MICHAEL · 2020 to 2024
$11.5MClinical Diagnostic Sequencing of Structural VariationR01HD081256 · NICHD · MASSACHUSETTS GENERAL HOSPITAL · PI TALKOWSKI, MICHAEL E · 2015 to 2025
$7.2MLatino Ancestry Genomic Psychiatry CohortR01MH123451 · NIMH · SUNY DOWNSTATE MEDICAL CENTER · PI BIGDELI, TIM BERNARD, FANOUS, AYMAN H · 2020 to 2025
$7.1MJoint genomic and statistical analyses of schizophrenia and bipolar to decipher genetic susceptibilityR01MH115676 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Roel A Ophoff, Bogdan Pasaniuc · 2018 to 2026
$5.9MGenetics of Severe Mental IllnessR01MH113078 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BEARDEN, CARRIE E, FREIMER, NELSON B. · 2017 to 2021
$5.8M4/4 Powering Genetic Discovery for Severe Mental Illness in Latin American and African AncestriesU01MH125042 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FREIMER, NELSON B., LOPEZ JARAMILLO, CARLOS · 2020 to 2024
$5.3M2/4 Powering Genetic Discovery for Severe Mental Illness in Latin American and African AncestriesU01MH125045 · NIMH · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI KOENEN, KARESTAN C · 2020 to 2024
$3.1MEmpowering gene discovery and accelerating clinical translation for diverse admixed populationsR01HG012869 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI Elizabeth Grace Atkinson · 2023 to 2026
$3.1MPsychosis Genetics Research in Africa: Building Capacity by Investing in PeopleR01MH120642 · NIMH · BROAD INSTITUTE, INC. · PI AKENA, DICKENS HOWARD, CHIBNIK, LORI BETH · 2019 to 2023
$3.1MNeurodevelopment and Psychosis in the 22q11.2 Copy Number VariantsR37MH085953 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CARRIE E BEARDEN · 2023 to 2026
$2.9M3/4 Powering Genetic Discovery for Severe Mental Illness in Latin American andAfrican AncestriesU01MH125049 · NIMH · SUNY DOWNSTATE MEDICAL CENTER · PI MULLE, JENNIFER GLADYS, PATO, CARLOS N · 2020 to 2024
$2.0MNHGRI NIH HHS R01 HG012869NICHD NIH HHS R01 HD081256NIMH NIH HHS K01 MH137407NIMH NIH HHS R00 MH117229NIMH NIH HHS R01 MH113078NIMH NIH HHS R01 MH115676NIMH NIH HHS R01 MH120642NIMH NIH HHS R01 MH123451NIMH NIH HHS R37 MH085953NIMH NIH HHS U01 MH125042NIMH NIH HHS U01 MH125045NIMH NIH HHS U01 MH125047NIMH NIH HHS U01 MH125049NLM NIH HHS T15 LM007033
Abstract
We deployed the Blended Genome Exome (BGE), a DNA library blending approach that generates low pass whole genome (1-4× mean depth) and deep whole exome (30-40× mean depth) data in a single sequencing run. This technology is cost-effective, empowers most genomic discoveries possible with deep whole genome sequencing, and provides an unbiased method to capture the diversity of common SNP variation across the globe. To evaluate this new technology at scale, we applied BGE to sequence >53,000 samples from the Populations Underrepresented in Mental Illness Associations Studies (PUMAS) Project, which included participants across African, African American, and Latin American populations. We evaluated the accuracy of BGE imputed genotypes against raw genotype calls from the Illumina Global Screening Array. All PUMAS cohorts had
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