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 journalArticlepeer-review

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 (US)
Pages (from-to)29-39
Number of pages11
JournalPLoS genetics
Volume4
Issue number1
DOIs
StatePublished - Jan 2008

ASJC Scopus subject areas

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

Fingerprint Dive into the research topics of 'Analysis and application of European genetic substructure using 300 K SNP information'. Together they form a unique fingerprint.

Cite this