Extent to which array genotyping and imputation with large reference panels approximate deep whole-genome sequencing.

Gene Frequency / genetics Genome-Wide Association Study Genotype High-Throughput Nucleotide Sequencing Humans Polymorphism, Single Nucleotide / genetics Whole Genome Sequencing
genotype imputation genotyping array whole-genome sequencing

Journal

American journal of human genetics
ISSN: 1537-6605
Titre abrégé: Am J Hum Genet
Pays: United States
ID NLM: 0370475

Informations de publication

Date de publication:
01 09 2022
Historique:
received: 06 03 2022
accepted: 20 07 2022
pubmed: 19 8 2022
medline: 9 9 2022
entrez: 18 8 2022
Statut: ppublish

Résumé

Understanding the genetic basis of human diseases and traits is dependent on the identification and accurate genotyping of genetic variants. Deep whole-genome sequencing (WGS), the gold standard technology for SNP and indel identification and genotyping, remains very expensive for most large studies. Here, we quantify the extent to which array genotyping followed by genotype imputation can approximate WGS in studies of individuals of African, Hispanic/Latino, and European ancestry in the US and of Finnish ancestry in Finland (a population isolate). For each study, we performed genotype imputation by using the genetic variants present on the Illumina Core, OmniExpress, MEGA, and Omni 2.5M arrays with the 1000G, HRC, and TOPMed imputation reference panels. Using the Omni 2.5M array and the TOPMed panel, ≥90% of bi-allelic single-nucleotide variants (SNVs) are well imputed (r

Identifiants

DOI: 10.1016/j.ajhg.2022.07.012 PMID: 35981533 PMC: PMC9502057
pubmed: 35981533
pii: S0002-9297(22)00316-0
doi: 10.1016/j.ajhg.2022.07.012
pmc: PMC9502057
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

1653-1666

Subventions

Organisme : NIMH NIH HHS
ID : R01 MH104964
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH123451
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG000040
Pays : United States

Informations de copyright

Copyright © 2022 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests E.E.K. has received speaker honorarium from Regeneron, 23&Me, and Illumina and sits on the advisory board for Encompass Bio and Galateo Bio.

Références

Hum Mol Genet. 2018 May 1;27(9):1664-1674
pubmed: 29481666
Am J Psychiatry. 2013 Jan;170(1):102-10
pubmed: 23288387
Annu Rev Genomics Hum Genet. 2018 Aug 31;19:73-96
pubmed: 29799802
Cell. 2021 Apr 15;184(8):2068-2083.e11
pubmed: 33861964
Brief Bioinform. 2015 Jul;16(4):549-62
pubmed: 25246238
Eur J Hum Genet. 2015 Jul;23(7):975-83
pubmed: 25293720
Annu Rev Genomics Hum Genet. 2009;10:387-406
pubmed: 19715440
Am J Hum Genet. 1998 Dec;63(6):1839-51
pubmed: 9837836
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Hum Genomics. 2021 Jun 7;15(1):34
pubmed: 34099068
Nat Genet. 2006 Oct;38(10):1166-72
pubmed: 16998491
Genome Res. 2009 Sep;19(9):1655-64
pubmed: 19648217
Science. 2012 Jul 6;337(6090):64-9
pubmed: 22604720
Bioinformatics. 2010 Nov 15;26(22):2867-73
pubmed: 20926424
J Thromb Haemost. 2022 Sep;20(9):2022-2034
pubmed: 35770352
Schizophr Res. 2015 Apr;163(1-3):9-16
pubmed: 25454799
Am J Hum Genet. 2013 Aug 8;93(2):278-88
pubmed: 23910464
Nat Genet. 2016 Oct;48(10):1279-83
pubmed: 27548312
Nature. 2019 Jun;570(7759):71-76
pubmed: 31118516
Mol Psychiatry. 2009 Aug;14(8):755-63
pubmed: 19488044
Proc Natl Acad Sci U S A. 2010 May 11;107 Suppl 2:8954-61
pubmed: 20445096
Nature. 2015 Oct 1;526(7571):82-90
pubmed: 26367797
Science. 2008 Feb 22;319(5866):1100-4
pubmed: 18292342
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Nat Genet. 2015 May;47(5):435-44
pubmed: 25807286
Nat Genet. 2016 Oct;48(10):1284-1287
pubmed: 27571263
Gigascience. 2015 Feb 25;4:7
pubmed: 25722852
Genome Res. 2015 Jun;25(6):918-25
pubmed: 25883319
Mol Psychiatry. 2008 Jun;13(6):558-69
pubmed: 18317468
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6
pubmed: 14681465
Eur J Hum Genet. 2021 Nov;29(11):1611-1624
pubmed: 34140649
Genome Med. 2021 Aug 26;13(1):136
pubmed: 34446064
Curr Med Chem. 2018 Jan 30;25(3):404-432
pubmed: 28721829
Nat Genet. 2015 Nov;47(11):1272-1281
pubmed: 26366554
G3 (Bethesda). 2018 Oct 3;8(10):3255-3267
pubmed: 30131328
Annu Rev Genomics Hum Genet. 2018 Aug 31;19:97-112
pubmed: 29801418
HGG Adv. 2022 Jan 11;3(2):100090
pubmed: 35128485
J Lipid Res. 2017 Mar;58(3):481-493
pubmed: 28119442
Bioinformatics. 2017 Jul 01;33(13):2056-2058
pubmed: 28200055
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
Am J Med Genet B Neuropsychiatr Genet. 2013 Jun;162B(4):306-12
pubmed: 23650244
PLoS Genet. 2019 Dec 23;15(12):e1008500
pubmed: 31869403
Nature. 2020 Oct;586(7831):749-756
pubmed: 33087929
Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16139-44
pubmed: 24043777
Mol Psychiatry. 2020 Oct;25(10):2455-2467
pubmed: 31591465
Nature. 2021 Feb;590(7845):290-299
pubmed: 33568819
Eur J Hum Genet. 2017 Jun;25(7):869-876
pubmed: 28401899
Nat Rev Genet. 2019 Aug;20(8):467-484
pubmed: 31068683
Am J Hum Genet. 2012 Nov 2;91(5):794-808
pubmed: 23103231
Nat Rev Genet. 2013 Oct;14(10):681-91
pubmed: 23999272
Eur J Hum Genet. 2014 Nov;22(11):1321-6
pubmed: 24896149

Auteurs

Sarah C Hanks (SC)

Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.

Lukas Forer (L)

Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.

Sebastian Schönherr (S)

Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.

Jonathon LeFaive (J)

Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.

Taylor Martins (T)

Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.

Ryan Welch (R)

Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.

Sarah A Gagliano Taliun (SA)

Department of Medicine and Department of Neurosciences, Université de Montréal, Montreal, QC, Canada; Research Centre, Montreal Heart Institute, Montreal, QC, Canada.

David Braff (D)

Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.

Jill M Johnsen (JM)

Research Institute, Bloodworks, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA.

Eimear E Kenny (EE)

Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Barbara A Konkle (BA)

Department of Medicine, University of Washington, Seattle, WA, USA.

Markku Laakso (M)

Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland.

Ruth F J Loos (RFJ)

Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Steven McCarroll (S)

Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.

Carlos Pato (C)

Departments of Psychiatry, Rutgers University, Robert Wood Johnson Medical School and New Jersey Medical School, New Brunswick, NJ, USA.

Michele T Pato (MT)

Departments of Psychiatry, Rutgers University, Robert Wood Johnson Medical School and New Jersey Medical School, New Brunswick, NJ, USA.

Albert V Smith (AV)

Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.

Michael Boehnke (M)

Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.

Laura J Scott (LJ)

Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.

Christian Fuchsberger (C)

Institute for Biomedicine (Affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy. Electronic address: cfuchsberger@eurac.edu.

Articles similaires

Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.

Yue Zhang, Meifang Song, Deying Tang et al.
1.00
Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female

Evaluation of Low-Value Services Across Major Medicare Advantage Insurers and Traditional Medicare.

Ciara Duggan, Adam L Beckman, Ishani Ganguli et al.
1.00
Humans United States Aged Cross-Sectional Studies Medicare Part C

Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Fréquence d'allèle › Extent to which array genotyping and...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › Extent to which array genotyping and...
questionsmedicales.fr › Phénomènes génétiques › Génotype › Extent to which array genotyping and...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Extent to which array genotyping and...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Extent to which array genotyping and...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › Extent to which array genotyping and...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › Extent to which array genotyping and...