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Thread: F-series SNPs from 1000 Genomes Project

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    F-series SNPs from 1000 Genomes Project

    Chuan-Chao Wang, Hui Li, Discovery of Phylogenetic Relevant Y-chromosome Variants in 1000 Genomes Project Data, arXiv:1310.6590v1
    http://arxiv.org/abs/1310.6590

    Abstract:

    Current Y chromosome research is limited in the poor resolution of Y chromosome phylogenetic tree. Entirely sequenced Y chromosomes in numerous human individuals have only recently become available by the advent of next-generation sequencing technology. The 1000 Genomes Project has sequenced Y chromosomes from more than 1000 males. Here, we analyzed 1000 Genomes Project Y chromosome data of 1269 individuals and discovered about 25,000 phylogenetic relevant SNPs. Those new markers are useful in the phylogeny of Y chromosome and will lead to an increased phylogenetic resolution for many Y chromosome studies.
    They have given the newly discovered SNPs F-numbers (F for Fudan University.)

    Extract:
    During the last ten years, a robust genealogical tree of human Y chromosomes based on about three thousand stable SNPs has been built, permitting inference of human population demographic history. However, current Y chromosome research is still limited in the poor resolution for some specific Y chromosome branches, such as haplogroup C-M130, D-M174, N-M231, O-M175, H-M69, and L-M11. Despite the huge population of those haplogroups, there have been fewer markers defined in those haplogroups than in haplogroups R and E. For instance, three Y-SNP markers, 002611, M134 and M117, represent about 260 million people in East Asia, but downstream markers are far from enough to reveal informative genetic substructures of those populations.
    Last edited by Jean M; 10-26-2013 at 08:55 PM.

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    They have set up a website with a new Y tree: http://comonca.org.cn/Y_tree/

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