Measuring European Population Stratification with Microarray Genotype Data

Abstract

A proper understanding of population genetic stratification--differences in individual ancestry within a population--is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of approximately 10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'Etude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.

Population differences in the International Multi‐Centre ADHD Gene Project

“…In general, most investigations into LD differences find that Northern Europeans can be grouped together for the purposes of generating and applying tag SNPs [Mueller et al, 2005;Gonzalez-Neira et al, 2006;de Bakker et al, 2006]. Southern Europeans and Israelis tend to form a different population cluster [Bauchet et al, 2007]. Our results are largely consistent with these observations in the context of genes implicated is psychiatric disorders.…”

“…The Northern European populations may still hold population differences at a finer level which are not picked up, given the sample size and subset of all genome variation genotyped in our analysis. As indicated by Bauchet et al Southeastern and Jewish populations ought not be grouped together with Northern European populations as there are significant differences [Bauchet et al, 2007]. BE: Ghent, Belgium; CH: Zurich, Switzerland; DE1: Essen, Germany; DE2: Goettingen, Germany; EN: London, England; ES: Valencia, Spain; IL1: Jerusalem, Israel; IL2: Tel Aviv, Israel; IR: Dublin, Ireland; NL1: Amsterdam, the Netherlands; NL2: Nijmegen, the Netherlands.The cells at the cross of the same population, refer to the number of tests that are nominally significant when excluding that population from the analysis (e.g.…”

“…Baucet and colleagues explore the population structure of Europeans as compared to the CEPH and Coriell samples. Broadly, Europe splits into two main sets, a northern (Polish, Irish, English, Germans, and some Italians) and a southeastern (Greeks, Armenians, Jews, and some Italians) [Bauchet et al, 2007]. Finally, Evans and Cardon compared the recombination rates across a region in chromosome 20 in the CEPH and a UK sample.…”

Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants

“…Contemporary Jewish communities have been genetically analyzed both from population genetics and medical perspectives by means of uniparental and recombining markers, [10][11][12][13][14][15][16][17] and more recently also through genome-wide approaches. [18][19][20][21][22][23] However, only a few reports have been published on Sephardic and crypto-Jewish descendants.…”

Receptor systems controlling natural killer cell function are genetically stratified in Europe

“…The presence of multiple genetic gradients from genes and single nucleotide polymorphisms have been established in recent times, which broadly distinguish northern from southern Europeans. [35][36][37] In this study, KIR gene and ligand frequencies were determined in two Irish populations and are compared with data reported for other European and Middle Eastern populations. Characterization of KIR and HLA diversity in the Irish population is of particular importance to this type of analysis, as genetic gradients increasing or decreasing into northwestern Europe often peak on this island.…”