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http://dx.doi.org/10.5808/GI.2011.9.4.181

How Many SNPs Should Be Used for the Human Phylogeny of Highly Related Ethnicities? A Case of Pan Asian 63 Ethnicities  

Ghang, Ho-Young (Department of Electrical Engineering, Korea Advanced Institute of Science and Technology)
Han, Young-Joo (Department of Electrical Engineering, Korea Advanced Institute of Science and Technology)
Jeong, Sang-Jin (Department of Electrical Engineering, Korea Advanced Institute of Science and Technology)
Bhak, Jong (Theragen Bio Institute, Theragen Etex Co. Ltd.)
Lee, Sung-Hoon (Theragen Bio Institute, Theragen Etex Co. Ltd.)
Kim, Tae-Hyung (Theragen Bio Institute, Theragen Etex Co. Ltd.)
Kim, Chul-Hong (Theragen Bio Institute, Theragen Etex Co. Ltd.)
Kim, Sang-Soo (Department of Bioinformatics & Life Sciences, Soongsil University)
Al-Mulla, Fahd (Department of Pathology, University of Kuwait)
Youn, Chan-Hyun (Department of Electrical Engineering, Korea Advanced Institute of Science and Technology)
Yoo, Hyang-Sook (Korea Research Institute of Bioscience and Biotechnology (KRIBB))
The HUGO Pan-Asian SNP Consortium, The HUGO Pan-Asian SNP Consortium (The HUGO Pan-Asian SNP Consortium)
Publication Information
Genomics & Informatics / v.9, no.4, 2011 , pp. 181-188 More about this Journal
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.
Keywords
neighbour-joining; phylogeny; minimum SNP; ethnic group;
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