October 14, 2010

Some population structured SNPs and also one epigenetic factor

Another more complex, yet still interesting, paper related with population structure in this last issue of PLoS ONE is:

Jingyu Liu et al., Identification of Genetic and Epigenetic Marks Involved in Population Structure. PLoS ONE 2010. Open Access

They have detected some SNPs, mostly related to appearance, that seem to weight specially high in population structure at global levels. Interestingly they have also located an epigenetic marker that weights somewhat in the European+African vs. East Asian+Native American axis.

The most relevant population structure SNPs are by this order:
  1. Rs16891982, strongly related to the West Eurasian type of depigmentation (SLC45A2), and logically structured along the West Eurasian-Others axis in an almost true/false type of structure, excepting admixed populations.
  2. Rs535878, not yet reported at SNPedia. It is structured along the Native American vs. African American+East Asian axis, with West Eurasians and admixed populations being intermediate (but closer to Native Americans). So Native Americans (and West Eurasians to some extent) seem to have the derived allele.
  3. Rs13013484, again not reported in SNPedia yet. The structure runs between African Americans and East Asians. With other populations being intermediate (but except Latinos all closer to African Americans). So East Asians (specially) have the derived allele. However notice that the East Asian sample of just one individual is somewhat inconclusive.
There are more SNPs pondered (see table 1) with factor ranking 22nd being 48 methylation sites in 44 genes of 18 chromosomes, affecting specially West Eurasians and Native Americans in opposite senses. In particular the PM20D1 methylated site seems to have some weak but significant selective pressure among West Eurasians (and admixed populations) - see fig.2B.

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