![]() ![]() There are also a number of divergent Yoruba, Luhya and African-American haplotypes distinct from the main global cluster. ![]() The European and American haplotypes tend to cluster more closely relative to Asian and African haplotypes. In the 1000G network, most haplotypes from Europeans, Asians, and Americans cluster as a closely related set. To examine the distribution of genetic variation in the FOXP2 area from a haplotype perspective, we created median-joining haplotype networks for the ROI for the 1000G dataset and Sanger sequencing data, as well as for the entire FOXP2 region in the HGDP genomes ( Figures 3A, 3B, and S3A). It is thus unlikely to randomly detect this many polymorphisms (seven in HGDP six in 1000G) clustered together at such a highly conserved locus ( Table 2). We underscore that the ROI remains a statistical outlier when we partition the data in multiple ways ( Figures 2, S1H, and S1I). The ROI is thus also an outlier considering the frequency of conserved SNPs in the window ( Figures S1H and S1I). We find that the number of observed constrained SNPs in the ROI is statistically significantly larger than the genic background for windows of the same size. After removing singletons to minimize bias resulting from sequencing error, the average GERP score for SNPs in the ROI is 4.677 in the HGDP dataset and 4.828 in 1000G, both highly significant compared to the background distribution averages of −0.070 and −0.474 (p 3), again requiring allele count to be greater than 1 to reduce inflation by sequencing error. To assess whether detecting so many extremely high-scoring GERP SNPs in a region of this size was exceptional, we calculated the average GERP score for SNPs located in contiguous, partially overlapping windows with same base pair width as the ROI throughout the genic regions of the autosomes ( STAR Methods). ![]()
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