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Eur J Hum Genet. 2014 Oct;22(10):1190-200. doi: 10.1038/ejhg.2014.1. Epub 2014 Feb 19.

Using ancestry-informative markers to identify fine structure across 15 populations of European origin.

Collaborators (219)

Boraska V, Franklin CS, Floyd JA, Thornton LM, Huckins LM, Southam L, Rayner NW, Tachmazidou I, Klump KL, Treasure J, Lewis CM, Schmidt U, Tozzi F, Kiezebrink K, Hebebrand J, Gorwood P, Adan RA, Kas MJ, Avaro AF, Santonastaso P, Fernández-Aranda F, Gratacos M, Rybakowski F, Dmitrzak-Weglarz M, Kaprio J, Keski-Rahkonen A, Raevuori A, Van Furth EF, Slof-Op T Landt MC, Hudson JI, Reichborn-Kjennerud T, Knudsen GP, Monteleone P, Kaplan AS, Karwautz A, Hakonarson H, Berrettini WH, Guo Y, Li D, Schork NJ, Komaki G, Ando T, Inoko H, Esko T, Fischer K, Männik K, Metspalu A, Baker JH, Cone RD, Dackor J, DeSocio JE, Hilliard CE, O'Toole JK, Pantel J, Szatkiewicz JP, Taico C, Zerwas S, Trace SE, Davis OS, Helder S, Bühren K, Burghardt R, de Zwaan M, Egberts K, Ehrlich S, Herpertz-Dahlmann B, Herzog W, Imgart H, Scherag A, Scherag S, Zipfel S, Boni C, Ramoz N, Versini A, Brandys MK, Danner UN, de Kove C, Hendriks J, Koeleman BP, Ophoff RA, Strengman E, van Elburg AA, Bruson A, Clementi M, Degortes D, Forzan M, Tenconi E, Docampo E, Escaramís G, Jiménez-Murcia S, Lissowska J, Rajewski A, Szeszenia-Dabrowska N, Slopien A, Hauser J, Karhunen L, Meulenbelt I, Slagboom PE, Tortorella A, Maj M, Dedoussis G, Dikeos D, Gonidakis F, Tziouvas K, Tsitsika A, Papezova H, Slachtova L, Martaskova D, Kennedy JL, Levitan RD, Yilmaz Z, Huemer J, Koubek D, Merl E, Wagner G, Lichtenstein P, Breen G, Cohen-Woods S, Farmer A, McGuffin P, Cichon S, Giegling I, Herms S, Rujescu D, Schreiber S, Wichmann HE, Dina C, Sladek R, Gambaro G, Soranzo N, Julia A, Marsal S, Rabionet RA, Gaborieau V, Dick DM, Palotie A, Ripatti S, Widén E, Andreassen OA, Espeseth T, Lundervold A, Reinvang I, Steen VM, Hellard SL, Mattingsda M, Ntalla I, Bencko V, Foretova L, Janout V, Navratilova M, Gallinger S, Pinto D, Scherer SW, Aschauer H, Carlberg L, Schosser A, Alfredsson L, Ding B, Klareskog L, Padyukov L, Finan C, Kalsi G, Roberts M, Logan DW, Peltonen L, Ritchie GR, Courtet P, Guillame S, Jaussent I, Barrett JC, Estivill X, Hinney A, Sullivan PF, Collier DA, Zeggini E, Bulik CM, Anderson CA, Barrett JC, Floyd JA, Franklin CS, McGinnis R, Soranzo N, Zeggini E, Sambrook J, Stephens J, Ouwehand WH, McArdle WL, Ring SM, Strachan DP, Alexander G, Bulik CM, Collier DA, Conlon PJ, Dominiczak A, Duncanson A, Hill A, Langford C, Lord G, Maxwell AP, Morgan L, Peltonen L, Sandford RN, Sheerin N, Soranzo N, Vannberg FO, Barrett JC, Genotyping DN, Blackburn H, Chen WM, Edkins S, Gillman M, Gray E, Hunt SE, Langford C, Nengut-Gumuscu S, Potter S, Rich SS, Simpkin D, Whittaker P.

Author information

1
The Wellcome Trust Sanger Institute (WTSI), Hinxton, UK.
2
1] The Wellcome Trust Sanger Institute (WTSI), Hinxton, UK [2] University of Split School of Medicine, Split, Croatia.
3
University of North Carolina, Chapel Hill, NC, USA.
4
King's College, London, UK.

Abstract

The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5%; we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia.

PMID:
24549058
PMCID:
PMC4169539
DOI:
10.1038/ejhg.2014.1
[Indexed for MEDLINE]
Free PMC Article

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