High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.

Female Genome, Human High-Throughput Nucleotide Sequencing / methods Humans INDEL Mutation Male Polymorphism, Single Nucleotide Whole Genome Sequencing
1000 Genomes Project INDEL SNV population genetics reference imputation panel structural variation trio sequencing whole-genome sequencing

Journal

Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066

Informations de publication

Date de publication:
01 09 2022
Historique:
received: 12 11 2021
revised: 21 06 2022
accepted: 03 08 2022
entrez: 2 9 2022
pubmed: 3 9 2022
medline: 9 9 2022
Statut: ppublish

Résumé

The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. The final, phase 3 release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS 1kGP resource, which now includes 602 complete trios, sequenced to a depth of 30X using Illumina. We performed single-nucleotide variant (SNV) and short insertion and deletion (INDEL) discovery and generated a comprehensive set of structural variants (SVs) by integrating multiple analytic methods through a machine learning model. We show gains in sensitivity and precision of variant calls compared to phase 3, especially among rare SNVs as well as INDELs and SVs spanning frequency spectrum. We also generated an improved reference imputation panel, making variants discovered here accessible for association studies.

Identifiants

DOI: 10.1016/j.cell.2022.08.004 PMID: 36055201 PMC: PMC9439720
pubmed: 36055201
pii: S0092-8674(22)00991-6
doi: 10.1016/j.cell.2022.08.004
pmc: PMC9439720
pii:
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

3426-3440.e19

Subventions

Organisme : NHGRI NIH HHS
ID : R01 HG002898
Pays : United States
Organisme : NICHD NIH HHS
ID : R03 HD099547
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM138212
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG008895
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG008901
Pays : United States
Organisme : NICHD NIH HHS
ID : R01 HD081256
Pays : United States
Organisme : NIMH NIH HHS
ID : R56 MH115957
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : U24 HG007497
Pays : United States
Organisme : NCI NIH HHS
ID : R21 CA259309
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH115957
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA261934
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG008853
Pays : United States

Investigateurs

Evan E Eichler (EE)
Jan O Korbel (JO)
Charles Lee (C)
Tobias Marschall (T)
Scott E Devine (SE)
William T Harvey (WT)
Weichen Zhou (W)
Ryan E Mills (RE)
Tobias Rausch (T)
Sushant Kumar (S)
Can Alkan (C)
Fereydoun Hormozdiari (F)
Zechen Chong (Z)
Yu Chen (Y)
Xiaofei Yang (X)
Jiadong Lin (J)
Mark B Gerstein (MB)
Ye Kai (Y)
Qihui Zhu (Q)
Feyza Yilmaz (F)
Chunlin Xiao (C)

Commentaires et corrections

Type : CommentIn

Informations de copyright

Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc. P.F. is an SAB member of Fabric Genomics, Inc., and Eagle Genomics, Ltd.

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Auteurs

Marta Byrska-Bishop (M)

New York Genome Center, New York, NY 10013, USA. Electronic address: mbyrska-bishop@nygenome.org.

Uday S Evani (US)

New York Genome Center, New York, NY 10013, USA.

Xuefang Zhao (X)

Program in Medical and Population Genetics, 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.

Anna O Basile (AO)

New York Genome Center, New York, NY 10013, USA.

Haley J Abel (HJ)

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.

Allison A Regier (AA)

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.

André Corvelo (A)

New York Genome Center, New York, NY 10013, USA.

Wayne E Clarke (WE)

New York Genome Center, New York, NY 10013, USA; Outlier Informatics Inc., Saskatoon, SK S7H 1L4, Canada.

Rajeeva Musunuri (R)

New York Genome Center, New York, NY 10013, USA.

Kshithija Nagulapalli (K)

New York Genome Center, New York, NY 10013, USA.

Susan Fairley (S)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Alexi Runnels (A)

New York Genome Center, New York, NY 10013, USA.

Lara Winterkorn (L)

New York Genome Center, New York, NY 10013, USA.

Ernesto Lowy (E)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Soren Germer (S)

New York Genome Center, New York, NY 10013, USA.

Harrison Brand (H)

Program in Medical and Population Genetics, 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; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Ira M Hall (IM)

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Genomic Health, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.

Michael E Talkowski (ME)

Program in Medical and Population Genetics, 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; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Giuseppe Narzisi (G)

New York Genome Center, New York, NY 10013, USA.

Michael C Zody (MC)

New York Genome Center, New York, NY 10013, USA. Electronic address: mczody@nygenome.org.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome humain › High-coverage whole-genome sequencing of the...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › High-coverage whole-genome sequencing of the...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › High-coverage whole-genome sequencing of the...
questionsmedicales.fr › Phénomènes génétiques › Mutagenèse › Mutation de type INDEL › High-coverage whole-genome sequencing of the...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › High-coverage whole-genome sequencing of the...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › High-coverage whole-genome sequencing of the...