Analysis and application of European genetic substructure using 300 K SNP information.

Chao Tian, Robert M. Plenge, Michael Ransom, Annette Lee, Pablo Villoslada, Carlo Selmi, Lars Klareskog, Ann E. Pulver, Lihong Qi, Peter K. Gregersen, Michael F. Seldin

Research output: Contribution to journalArticle

171 Citations (Scopus)

Abstract

European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans.

Original languageEnglish
JournalPLoS Genetics
Volume4
Issue number1
DOIs
Publication statusPublished - Jan 2008

Fingerprint

Genome-Wide Association Study
Population Genetics
ancestry
Single Nucleotide Polymorphism
population genetics
genome
Principal Component Analysis
Rheumatoid Arthritis
rheumatoid arthritis
Population
Genes
gene
analysis
genes
testing
Datasets

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Analysis and application of European genetic substructure using 300 K SNP information. / Tian, Chao; Plenge, Robert M.; Ransom, Michael; Lee, Annette; Villoslada, Pablo; Selmi, Carlo; Klareskog, Lars; Pulver, Ann E.; Qi, Lihong; Gregersen, Peter K.; Seldin, Michael F.

In: PLoS Genetics, Vol. 4, No. 1, 01.2008.

Research output: Contribution to journalArticle

Tian, C, Plenge, RM, Ransom, M, Lee, A, Villoslada, P, Selmi, C, Klareskog, L, Pulver, AE, Qi, L, Gregersen, PK & Seldin, MF 2008, 'Analysis and application of European genetic substructure using 300 K SNP information.', PLoS Genetics, vol. 4, no. 1. https://doi.org/10.1371/journal.pgen.0040004
Tian, Chao ; Plenge, Robert M. ; Ransom, Michael ; Lee, Annette ; Villoslada, Pablo ; Selmi, Carlo ; Klareskog, Lars ; Pulver, Ann E. ; Qi, Lihong ; Gregersen, Peter K. ; Seldin, Michael F. / Analysis and application of European genetic substructure using 300 K SNP information. In: PLoS Genetics. 2008 ; Vol. 4, No. 1.
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