A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2020
2020
Historique:
received:
02
03
2020
accepted:
31
07
2020
entrez:
11
9
2020
pubmed:
12
9
2020
medline:
22
10
2020
Statut:
epublish
Résumé
The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n = 1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n = 300) (ACpop) from Västerbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Västerbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Västerbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden.
Identifiants
pubmed: 32915809
doi: 10.1371/journal.pone.0237721
pii: PONE-D-20-06062
pmc: PMC7485808
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0237721Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
PLoS One. 2011 Feb 09;6(2):e16747
pubmed: 21347369
Science. 2012 Jul 6;337(6090):100-4
pubmed: 22604722
Ann Hum Genet. 2005 Sep;69(Pt 5):549-58
pubmed: 16138913
Gigascience. 2015 Feb 25;4:7
pubmed: 25722852
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
Bioinformatics. 2014 Jul 1;30(13):1940-1
pubmed: 24632498
Int J Circumpolar Health. 2008 Feb;67(1):27-42
pubmed: 18468257
Eur J Hum Genet. 2017 Nov;25(11):1253-1260
pubmed: 28832569
Eur J Hum Genet. 2011 May;19(5):583-7
pubmed: 21364699
Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33
pubmed: 25431634
Sci Rep. 2015 Dec 02;5:17453
pubmed: 26625947
Nat Methods. 2011 Dec 04;9(2):179-81
pubmed: 22138821
Eur J Hum Genet. 2017 Jun;25(7):869-876
pubmed: 28401899
G3 (Bethesda). 2011 Nov;1(6):457-70
pubmed: 22384356
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Hum Genet. 2012 Dec;131(12):1877-88
pubmed: 22886559
Genome Res. 2010 Oct;20(10):1344-51
pubmed: 20810666
Nat Commun. 2015 Aug 21;6:8018
pubmed: 26292667
Hereditas. 2007 Nov;144(5):171-80
pubmed: 18031350
Nat Genet. 2014 Aug;46(8):818-25
pubmed: 24974849
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Nat Genet. 2012 Jul 22;44(8):955-9
pubmed: 22820512
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Nat Genet. 2015 May;47(5):435-44
pubmed: 25807286
Nature. 2010 Sep 2;467(7311):52-8
pubmed: 20811451
Bioinformatics. 2016 Jan 15;32(2):292-4
pubmed: 26428292
PLoS One. 2011;6(8):e22547
pubmed: 21829632
Nature. 2016 Aug 17;536(7616):285-91
pubmed: 27535533
PLoS Genet. 2009 Jun;5(6):e1000529
pubmed: 19543373
Science. 2012 May 11;336(6082):740-3
pubmed: 22582263
Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-8
pubmed: 21730125
Nat Genet. 2011 May;43(5):491-8
pubmed: 21478889
PLoS One. 2019 Mar 27;14(3):e0213350
pubmed: 30917156
Nat Commun. 2010 Nov 30;1:131
pubmed: 21119644
Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894
pubmed: 30371827
Glob Health Action. 2012 Dec 17;5:1-9
pubmed: 23528041
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
Nat Genet. 2014 Mar;46(3):310-5
pubmed: 24487276
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Eur J Hum Genet. 2006 Aug;14(8):963-70
pubmed: 16724001
Stat Appl Genet Mol Biol. 2013 Aug;12(4):433-48
pubmed: 23934608
Nat Genet. 2005 Jan;37(1):90-5
pubmed: 15608637
Bioinformatics. 2010 Nov 15;26(22):2867-73
pubmed: 20926424
Nat Methods. 2013 Jan;10(1):5-6
pubmed: 23269371
Nature. 2013 Jan 10;493(7431):216-20
pubmed: 23201682