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

Human Genome Structural Variation Consortium

doi:10.1016/j.cell.2022.08.004

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

Human Genome Structural Variation Consortium

电子与信息学部

New York Genome Center
Broad Institute
Massachusetts General Hospital
Washington University St. Louis
Outlier Informatics Inc.
European Molecular Biology Laboratory
Yale University

科研成果: 期刊稿件 › 文章 › 同行评审

614 引用（Scopus）

摘要

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.

源语言	英语
页（从-至）	3426-3440.e19
期刊	Cell
卷	185
期	18
DOI	https://doi.org/10.1016/j.cell.2022.08.004
出版状态	已出版 - 1 9月 2022

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10.1016/j.cell.2022.08.004

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title = "High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios",

abstract = "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.",

keywords = "1000 Genomes Project, INDEL, SNV, population genetics, reference imputation panel, structural variation, trio sequencing, whole-genome sequencing",

author = "\{Human Genome Structural Variation Consortium\} and Marta Byrska-Bishop and Evani, \{Uday S.\} and Xuefang Zhao and Basile, \{Anna O.\} and Abel, \{Haley J.\} and Regier, \{Allison A.\} and Andr{\'e} Corvelo and Clarke, \{Wayne E.\} and Rajeeva Musunuri and Kshithija Nagulapalli and Susan Fairley and Alexi Runnels and Lara Winterkorn and Ernesto Lowy and Eichler, \{Evan E.\} and Korbel, \{Jan O.\} and Charles Lee and Tobias Marschall and Devine, \{Scott E.\} and Harvey, \{William T.\} and Weichen Zhou and Mills, \{Ryan E.\} and Tobias Rausch and Sushant Kumar and Can Alkan and Fereydoun Hormozdiari and Zechen Chong and Yu Chen and Xiaofei Yang and Jiadong Lin and Gerstein, \{Mark B.\} and Ye Kai and Qihui Zhu and Feyza Yilmaz and Chunlin Xiao and \{Paul Flicek\}, Flicek and Soren Germer and Harrison Brand and Hall, \{Ira M.\} and Talkowski, \{Michael E.\} and Giuseppe Narzisi and Zody, \{Michael C.\}",

note = "Publisher Copyright: {\textcopyright} 2022 The Authors",

year = "2022",

month = sep,

day = "1",

doi = "10.1016/j.cell.2022.08.004",

language = "英语",

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T1 - High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

AU - Human Genome Structural Variation Consortium

AU - Byrska-Bishop, Marta

AU - Evani, Uday S.

AU - Zhao, Xuefang

AU - Basile, Anna O.

AU - Abel, Haley J.

AU - Regier, Allison A.

AU - Corvelo, André

AU - Clarke, Wayne E.

AU - Musunuri, Rajeeva

AU - Nagulapalli, Kshithija

AU - Fairley, Susan

AU - Runnels, Alexi

AU - Winterkorn, Lara

AU - Lowy, Ernesto

AU - Eichler, Evan E.

AU - Korbel, Jan O.

AU - Lee, Charles

AU - Marschall, Tobias

AU - Devine, Scott E.

AU - Harvey, William T.

AU - Zhou, Weichen

AU - Mills, Ryan E.

AU - Rausch, Tobias

AU - Kumar, Sushant

AU - Alkan, Can

AU - Hormozdiari, Fereydoun

AU - Chong, Zechen

AU - Chen, Yu

AU - Yang, Xiaofei

AU - Lin, Jiadong

AU - Gerstein, Mark B.

AU - Kai, Ye

AU - Zhu, Qihui

AU - Yilmaz, Feyza

AU - Xiao, Chunlin

AU - Paul Flicek, Flicek

AU - Germer, Soren

AU - Brand, Harrison

AU - Hall, Ira M.

AU - Talkowski, Michael E.

AU - Narzisi, Giuseppe

AU - Zody, Michael C.

PY - 2022/9/1

Y1 - 2022/9/1

N2 - 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.

AB - 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.

KW - 1000 Genomes Project

KW - INDEL

KW - SNV

KW - population genetics

KW - reference imputation panel

KW - structural variation

KW - trio sequencing

KW - whole-genome sequencing

UR - https://www.scopus.com/pages/publications/85136603644

U2 - 10.1016/j.cell.2022.08.004

DO - 10.1016/j.cell.2022.08.004

M3 - 文章

C2 - 36055201

AN - SCOPUS:85136603644

SN - 0092-8674

VL - 185

SP - 3426-3440.e19

JO - Cell

JF - Cell

IS - 18

ER -

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

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