The quest for genes associated with diseases is widely recognized as an essential task in the effort to investigate the genetic basis of complex human disorders and traits. A basic stage in association studies is the careful choice of the model population, with preference to closed groups having little population substructure. Here, we show evidence for significant geographic substructure (P=0.017) of the maternal lineage represented by mitochondrial DNA variation in one of the most commonly studied populations, the Ashkenazi Jews. Most of the substructure effect stems from differential representation of haplogroups K and H. Our results underline the essentiality of adjusting data of population genetic variation for substructure during the design of association studies, even in apparently closed populations.
Ashkenazi Jews, considered to be an isolated population that has undergone a recent bottleneck,1, 2, 3, 4 constitute a model population for the search of disease-causing mutations and disease-susceptibility genes. One of the most commonly used arguments for choosing Ashkenazi Jews for such studies is the lack of population substructure.5 Nevertheless, differential distribution of disease-causing-mutations among Ashkenazi Jews of Eastern European versus Central European ancestry suggests genetic drift and may thus imply possible population substructures among Ashkenazi Jews.6 This consideration is particularly crucial when association studies are performed with the common disease variant approach, as the prevalence of the disease-associated variant may vary among populations owing to genetic drift.4 Indeed, during an association study on type II diabetes mellitus and its complications recently conducted by our group, we found a significant difference in the distribution of linked sets of mitochondrial DNA (mtDNA) common variants (haplogroups) in Ashkenazi Jews of different geographic origins (Feder et al., 2007, submitted). This observation, along with the frequent use of mtDNA as a target for association studies, led us to assess, using mtDNA, population substructure in the maternal lineage of Ashkenazi Jews.
A cohort of 300 healthy unrelated subjects of Ashkenazi Jewish origin, who previously served as control subjects in association studies at the Hebrew University, was analyzed in a hierarchical manner for mtDNA haplogroups, starting from haplogroups K and H, reported to be the most prevalent in Ashkenazi Jews, followed by the less prevalent types.1, 7 To increase the sample size, we added to the analysis previously published data for mtDNA haplogroup distribution in 565 unrelated subjects of the Ashkenazi Jewish origin.7 Among these 865 subjects, 704 were with known maternal geographic origin. Classification of these subjects according to maternal geographic origin gave three subpopulations that were considered sufficiently large for further analysis: that originating from Russia and the Ukraine (combined into one group due to geographical proximity, 'RU'), that from Poland, and that from Romania. This division into subpopulations resulted in a total of 446 subjects included in the study (Table 1). To avoid comparisons of haplogroups for which sample sizes were small, we grouped some haplogroups together according to phylogenetic considerations, that is, N1 with I, and W with X. Haplogroups M and Pre-HV (as well as haplogroup L in Table 2) were considered together with 'others' (Table 1). We used the R C test of independence to compare the haplogroup distribution among the three different Jewish communities.8 To determine which of the haplogroups made the largest contribution to the overall heterogeneity, we performed an unplanned test.8 The statistical analyses were performed using Systat 9.0 (Systat Software, Inc., CA, USA), and results were considered statistically significant if <0.05.