Sunday, January 07, 2007

Differences in gene expression between Asians and Europeans   posted by p-ter @ 1/07/2007 04:43:00 PM

Different populations have different traits-- the distributions of hair color, skin color, behavior, etc., all vary between groups, and some of this variation is certainly genetic in origin. This much is clear. But how does genetics cause these population-level differences?

A new paper in Nature Genetics (see the news story here) is a start towards answering this question-- the authors find a huge percentage of genes have different levels of expression in Europeans and Asians, and that these expression differences are due to common genetic variation. In addition, clustering by expression profile led to almost perfect clusters according to ethnicity (those are the two clusters--Europeans and Asians--in the picture) Here's the abstract:
Variation in DNA sequence contributes to individual differences in quantitative traits, but in humans the specific sequence variants are known for very few traits. We characterized variation in gene expression in cells from individuals belonging to three major population groups. This quantitative phenotype differs significantly between European-derived and Asian-derived populations for 1,097 of 4,197 genes tested. For the phenotypes with the strongest evidence of cis determinants, most of the variation is due to allele frequency differences at cis-linked regulators. The results show that specific genetic variation among populations contributes appreciably to differences in gene expression phenotypes. Populations differ in prevalence of many complex genetic diseases, such as diabetes and cardiovascular disease. As some of these are probably influenced by the level of gene expression, our results suggest that allele frequency differences at regulatory polymorphisms also account for some population differences in prevalence of complex diseases.
1. This provides a neat mechanism for ethic differences-- a number differentially expressed genes act in a network to give various phenotypes-- be they diseases, skin colors, behaviors, or anything else with a genetic component.

2. It's also possible that different regulatory networks have evolved in the two populations:
In addition to the variation analyzed above, some variation in expression phenotypes between populations can probably be attributed to different regulatory mechanisms. For four phenotypes, we found significant cis association in the CHB+JPT [Asian] sample but not in the CEU [European] sample.

3. The elephant in the room: The authors used cell lines from the HapMap for these studies. Besides the European and Asian samples, there's another population in the HapMap which was not included in this paper-- that of an African population from Nigeria. If a full quarter of genes have different expression profiles in Europeans and Asians, then this African population is likely to be even more different. The authors of this study certainly have the African cell lines and have probably done the expression analysis. So where's the data?