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

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 r...

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Published inGenomics & informatics Vol. 9; no. 4; pp. 181 - 188
Main Authors Ghang, Ho-Young, Han, Young-Joo, Jeong, Sang-Jin, Bhak, Jong, Lee, Sung-Hoon, Kim, Tae-Hyung, Kim, Chul-Hong, Kim, Sang-Soo, Al-Mulla, Fahd, Youn, Chan-Hyun, Yoo, Hyang-Sook, The HUGO Pan-Asian SNP Consortium, The HUGO Pan-Asian SNP Consortium
Format Journal Article
LanguageEnglish
Published 한국유전체학회 31.12.2011
Subjects
자연과학일반
Online AccessGet full text
ISSN1598-866X
2234-0742
DOI10.5808/GI.2011.9.4.181

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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. KCI Citation Count: 0
AbstractList 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. KCI Citation Count: 0
Author Kim, Sang-Soo
Kim, Chul-Hong
Ghang, Ho-Young
Youn, Chan-Hyun
Bhak, Jong
The HUGO Pan-Asian SNP Consortium, The HUGO Pan-Asian SNP Consortium
Han, Young-Joo
Kim, Tae-Hyung
Lee, Sung-Hoon
Yoo, Hyang-Sook
Jeong, Sang-Jin
Al-Mulla, Fahd
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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
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