A deep population reference panel of tandem repeat variation.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
23 10 2023
23 10 2023
Historique:
received:
10
03
2023
accepted:
05
10
2023
medline:
27
10
2023
pubmed:
24
10
2023
entrez:
23
10
2023
Statut:
epublish
Résumé
Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.
Identifiants
pubmed: 37872149
doi: 10.1038/s41467-023-42278-3
pii: 10.1038/s41467-023-42278-3
pmc: PMC10593948
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
6711Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2023. Springer Nature Limited.
Références
Eur J Hum Genet. 2013 Oct;21(10):1120-7
pubmed: 23463025
Nat Commun. 2023 Oct 23;14(1):6711
pubmed: 37872149
Nature. 2022 Apr;604(7906):437-446
pubmed: 35444317
Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17095-100
pubmed: 19805156
Nat Commun. 2018 Oct 23;9(1):4397
pubmed: 30353011
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
Nat Methods. 2017 Jun;14(6):590-592
pubmed: 28436466
Genome Res. 2014 Nov;24(11):1894-904
pubmed: 25135957
Acta Neurol Scand. 2003 Oct;108(4):281-6
pubmed: 12956863
BMJ Open. 2017 Mar 31;7(3):e010711
pubmed: 28363916
Am J Hum Genet. 2019 Jul 3;105(1):151-165
pubmed: 31230722
Nature. 2021 Jan;589(7841):246-250
pubmed: 33442040
Am J Hum Genet. 2007 Nov;81(5):1084-97
pubmed: 17924348
Nat Rev Genet. 2018 May;19(5):286-298
pubmed: 29398703
Forensic Sci Int. 2002 Aug 28;128(3):196-201
pubmed: 12175966
Genome Res. 2017 Nov;27(11):1895-1903
pubmed: 28887402
Cell. 2022 Sep 1;185(18):3426-3440.e19
pubmed: 36055201
Nature. 2023 May;617(7960):312-324
pubmed: 37165242
Science. 2022 Apr;376(6588):44-53
pubmed: 35357919
Mol Biol Evol. 2011 Jan;28(1):303-12
pubmed: 20675409
Nucleic Acids Res. 2019 Sep 5;47(15):e90
pubmed: 31194863
Nat Biotechnol. 2000 Feb;18(2):233-4
pubmed: 10657137
Psychiatr Genet. 2016 Aug;26(4):156-65
pubmed: 27270050
Bioinform Adv. 2023 Apr 26;3(1):vbad058
pubmed: 37168281
Nat Commun. 2022 Dec 12;13(1):7682
pubmed: 36509785
Nature. 2022 Jul 20;:
pubmed: 35859127
Nature. 1997 Apr 24;386(6627):847-51
pubmed: 9126745
Nephrol Dial Transplant. 1999 Dec;14(12):2898-902
pubmed: 10570094
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6
pubmed: 14681465
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
pubmed: 9862982
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
Neurobiol Dis. 1999 Oct;6(5):424-32
pubmed: 10527808
Nature. 2022 Jul;607(7920):732-740
pubmed: 35859178
Bioinformatics. 2021 May 5;37(5):731-733
pubmed: 32805020
Nat Genet. 2019 Nov;51(11):1652-1659
pubmed: 31676866
Am J Hum Genet. 2021 Oct 7;108(10):1880-1890
pubmed: 34478634
Nucleic Acids Res. 2010 Sep;38(16):e164
pubmed: 20601685
Science. 2021 Sep 24;373(6562):1499-1505
pubmed: 34554798
Nature. 2016 Oct 13;538(7624):201-206
pubmed: 27654912
Genome Res. 2018 Nov;28(11):1709-1719
pubmed: 30352806
Mol Biol Rep. 2011 Feb;38(2):1341-6
pubmed: 20635151
Springerplus. 2015 Sep 30;4:566
pubmed: 26543701
Clin Genet. 2007 Nov;72(5):448-53
pubmed: 17877752
Am J Med Genet B Neuropsychiatr Genet. 2004 Jan 1;124B(1):15-9
pubmed: 14681907
Nat Protoc. 2012 Feb 16;7(3):500-7
pubmed: 22343431
Neurosci Lett. 2007 Dec 11;429(1):28-32
pubmed: 17961920
Nature. 2013 Sep 26;501(7468):506-11
pubmed: 24037378
Genome Res. 2002 Jun;12(6):996-1006
pubmed: 12045153
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Nat Genet. 2016 Jan;48(1):22-9
pubmed: 26642241
Nat Genet. 2012 Oct;44(10):1161-5
pubmed: 22922873
Nature. 2020 Oct;586(7831):741-748
pubmed: 33116287
Nat Med. 2009 Nov;15(11):1281-8
pubmed: 19881492
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
J Hum Genet. 2008;53(2):127-135
pubmed: 18157708
Hum Mutat. 2012 Aug;33(8):1302-9
pubmed: 22573514
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Hum Mol Genet. 1993 Aug;2(8):1123-8
pubmed: 8401493
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
J Comput Biol. 2000 Feb-Apr;7(1-2):203-14
pubmed: 10890397
Nature. 2001 Feb 15;409(6822):860-921
pubmed: 11237011
Genome Biol. 2018 Aug 21;19(1):121
pubmed: 30129428
Int J Mol Sci. 2021 Feb 08;22(4):
pubmed: 33567536
Nat Genet. 2006 Aug;38(8):904-9
pubmed: 16862161
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
J Med Genet. 1995 Sep;32(9):701-5
pubmed: 8544189
Bioinformatics. 2017 Dec 15;33(24):4041-4048
pubmed: 27591079
Nucleic Acids Res. 2016 May 5;44(8):3750-62
pubmed: 27060133
Genome Biol. 2020 Apr 28;21(1):102
pubmed: 32345345
Sci Data. 2020 Sep 8;7(1):294
pubmed: 32901039
Nat Commun. 2021 Apr 6;12(1):2075
pubmed: 33824302
J Mol Diagn. 2018 Nov;20(6):871-882
pubmed: 30138726
Clin Chem. 2010 Mar;56(3):399-408
pubmed: 20056738
Cardiovasc J Afr. 2007 May-Jun;18(3):175-9
pubmed: 17612750