Sunday, September 09, 2012

Spatial structure of SNP distributions

The figure above is taken from A model-based approach for analysis of spatial structure in genetic data (Nature Genetics). The paper develops a novel method for extracting geographical origin from SNP data. (However, the panels I display show the results of standard PCA analysis.) An interesting aspect of the method in the paper is that it allows to identify specific genes with a large spatial gradient in allele frequency, which could be a signal for selection. Here is the distribution of scores on this gradient measure (e.g., LCT controls lactose tolerance). Someone should look up the SPA scores of height-associated alleles from GIANT. (Table 4 in the Supplement lists the top 0.1% of SNPs by SPA score.) Click images for larger versions.

1 comment:

ben_g said...

Has someone over produced a graphic which puts human variation in perspective with primate variation? I've heard the numbers, but it would be pretty enlightening to see a PC map with human populations + other species to get a visual idea of how different/similar we are

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