How many SNPs should be used for the human phylogeny of highly related ethnicities? : a case of pan Asian 63 ethnicities

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Title
How many SNPs should be used for the human phylogeny of highly related ethnicities? : a case of pan Asian 63 ethnicities
Author(s)
H Ghang; Y Han; S Jeong; J Bhak; S Lee; T H Kim; C Kim; S Kim; F Al-Mulla; C H Youn; Hyang Sook Yoo; HUGO Pan-Asian SNP Consortium
Bibliographic Citation
Genomics & Informatics, vol. 9, no. 4, pp. 181-188
Publication Year
2011
Abstract
In planning a model-based phylogenic study for highly related ethnic data, the SNP marker number is an important factor to determine for relationship inferences. Genotype frequency data, utilizing a sub sampling method, from 63 Pan Asian ethnic groups was used for determining the minimum SNP number required to establish such relationships. Bootstrap random sub-samplings were done from 5.6K PASNPi SNP data. DA distance was calculated and neighbour-joining trees were drawn with every re-sampling data set. Consensus trees were made with the same 100 sub-samples and bootstrap proportions were calculated. The tree consistency to the one obtained from the whole marker set, improved with increasing marker numbers. The bootstrap proportions became reliable when more than 7,000 SNPs were used at a time. Within highly related ethnic groups, the minimum SNPs number for a robust neighbor-joining tree inference was about 7,000 for a 95% bootstrap support.
Keyword
neighbour-joiningphylogenyminimum SNPethnic group
ISSN
I000-0158
Publisher
Korea Soc-Assoc-Inst
DOI
http://dx.doi.org/10.5808/GI.2011.9.4.181
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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