ArticleCell2022
High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.
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Article in Cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 738 papers, 4 of them syntheses that pooled it.
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738citing papers in PubMed, 4 pooled it
80.2field-weighted citation impact, top 1% of its field
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738 citing papers in PubMed, 4 syntheses or guidelines pooled it, 977 citations in OpenAlex.
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678 more citing papers are in PubMed but not listed here.
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Authors and funding
22 authors at 5 institutions in 2 countries.
Marta Byrska-BishopNew York Genome Center, New York, NY 10013, USA. Electronic address: mbyrska-bishop@nygenome.org.
Uday S EvaniNew York Genome Center, New York, NY 10013, USA.
Xuefang ZhaoProgram 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 BasileNew York Genome Center, New York, NY 10013, USA.
Haley J AbelMcDonnell 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 RegierMcDonnell 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 CorveloNew York Genome Center, New York, NY 10013, USA.
Wayne E ClarkeNew York Genome Center, New York, NY 10013, USA; Outlier Informatics Inc., Saskatoon, SK S7H 1L4, Canada.
Rajeeva MusunuriNew York Genome Center, New York, NY 10013, USA.
Kshithija NagulapalliNew York Genome Center, New York, NY 10013, USA.
Susan FairleyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Alexi RunnelsNew York Genome Center, New York, NY 10013, USA.
Lara WinterkornNew York Genome Center, New York, NY 10013, USA.
Ernesto LowyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Human Genome Structural Variation Consortium
Paul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Soren GermerNew York Genome Center, New York, NY 10013, USA.
Harrison BrandProgram 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 HallMcDonnell 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 TalkowskiProgram 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 NarzisiNew York Genome Center, New York, NY 10013, USA.
Michael C ZodyNew York Genome Center, New York, NY 10013, USA. Electronic address: mczody@nygenome.org.
New York Genome Center · USBroad Institute · USEuropean Bioinformatics Institute · GBJames S. McDonnell Foundation · USWashington University in St. Louis · US
Funding
Center for Common Disease GeneticsUM1HG008895 · NHGRI · BROAD INSTITUTE, INC. · PI DALY, MARK JOSEPH, GABRIEL, STACEY · 2016 to 2020
$111.2MSupplement Proposal: Accelerated Genome Aggregation and Joint Variant Calling EffortUM1HG008853 · NHGRI · WASHINGTON UNIVERSITY · PI HALL, IRA M, MILBRANDT, JEFFREY D · 2016 to 2020
$76.2MNew York Center for Collaborative Research In Common Disease Genomics: Genome Aggregation and Joint Variant Calling for CCDG Freeze2UM1HG008901 · NHGRI · NEW YORK GENOME CENTER · PI MANIATIS, THOMAS P, WIGLER, MICHAEL H · 2016 to 2020
$56.6MIdentifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human GenomesU24HG007497 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Evan Eichler, Jan Oliver Korbel · 2019 to 2026
$17.2MClinical Diagnostic Sequencing of Structural VariationR01HD081256 · NICHD · MASSACHUSETTS GENERAL HOSPITAL · PI TALKOWSKI, MICHAEL E · 2015 to 2025
$7.2MScalable tool and comprehensive maps to interpret structural variation across the neuropsychiatric spectrumR01MH115957 · NIMH · BROAD INSTITUTE, INC. · PI TALKOWSKI, MICHAEL E · 2019 to 2025
$5.4MNatural Genetic Variation in the Human GenomeR01HG002898 · NHGRI · UNIVERSITY OF MARYLAND BALTIMORE · PI DEVINE, SCOTT E · 2004 to 2019
$3.7MStructural variation analysis with and without a reference genomeR35GM138212 · NIGMS · UNIVERSITY OF VIRGINIA · PI Zechen Chong · 2020 to 2026
$2.6MMobile element mutagenesis as a driver of human cancersR01CA261934 · NCI · UNIVERSITY OF MARYLAND BALTIMORE · PI Scott E Devine · 2022 to 2026
$1.7MScalable tools and comprehensive maps to interpret structural variation across the neuropsychiatric spectrumR56MH115957 · NIMH · BROAD INSTITUTE, INC. · PI TALKOWSKI, MICHAEL E · 2018 to 2018
$870kL1 element mutagenesis as a driver of epithelial cancers in African AmericansR21CA259309 · NCI · UNIVERSITY OF MARYLAND BALTIMORE · PI DEVINE, SCOTT E · 2022 to 2023
$394kExploring the genetic architecture of structural birth defectsR03HD099547 · NICHD · MASSACHUSETTS GENERAL HOSPITAL · PI TALKOWSKI, MICHAEL E · 2019 to 2020
$336kNCI NIH HHS R01 CA261934NCI NIH HHS R21 CA259309NHGRI NIH HHS R01 HG002898NHGRI NIH HHS U24 HG007497NHGRI NIH HHS UM1 HG008853NHGRI NIH HHS UM1 HG008895NHGRI NIH HHS UM1 HG008901NICHD NIH HHS R01 HD081256NICHD NIH HHS R03 HD099547NIGMS NIH HHS R35 GM138212NIMH NIH HHS R01 MH115957NIMH NIH HHS R56 MH115957Wellcome Trust
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.
Indexed as
Genome, HumanWhole Genome SequencingFemaleHigh-Throughput Nucleotide SequencingHumansINDEL MutationMalePolymorphism, Single Nucleotide1000 Genomes ProjectINDELpopulation geneticsreference imputation panelSNVstructural variationtrio sequencingwhole-genome sequencing
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