Unbalanced sample size effect on genome-wide population differentiation studies
作者： Kyunghee Han , Kyee Zu Kim , Jung Mi Oh , In Wha Kim , Kyungim Kim
DOI: 10.1504/IJDMB.2012.049303
关键词: Homogeneity (statistics) 、 Genome-wide association study 、 Sample size determination 、 Biology 、 Fixation index 、 Bayes estimator 、 Econometrics 、 Population 、 Genetic distance 、 International HapMap Project 、 Statistics
摘要: The fixation index (F(ST)) is one of the most widely used measurements genetic distance between populations. data set from international HapMap project has been served as a reference for population differentiation studies. F(ST) commonly in order to compare sample with data. In this study, however, we show that use without consideration sizes may mislead result. particular, first demonstrate suffers imbalance through simulation studies and analysis large scale Korean genome-wide association Then, propose modified version which shown be more robust size. addition, chi-square test homogeneity perform similarly F(ST).
sci-hub.se 参考文章(15)
N. Ryman, P. E. Jorde, Statistical power when testing for genetic differentiation. Molecular Ecology. ,vol. 10, pp. 2361- 2373 ,(2001) , 10.1046/J.0962-1083.2001.01345.X
Joshua M Akey, Ge Zhang, Kun Zhang, Li Jin, Mark D Shriver, Interrogating a High-Density SNP Map for Signatures of Natural Selection Genome Research. ,vol. 12, pp. 1805- 1814 ,(2002) , 10.1101/GR.631202
Jonathan Marchini, Lon R Cardon, Michael S Phillips, Peter Donnelly, None, The effects of human population structure on large genetic association studies. Nature Genetics. ,vol. 36, pp. 512- 517 ,(2004) , 10.1038/NG1337
M. Nei, Analysis of Gene Diversity in Subdivided Populations Proceedings of the National Academy of Sciences of the United States of America. ,vol. 70, pp. 3321- 3323 ,(1973) , 10.1073/PNAS.70.12.3321
Ki-Chan Lee, Sang-Soo Kim, A Scheme for Filtering SNPs Imputed in 8,842 Korean Individuals Based on the International HapMap Project Data Genomics & Informatics. ,vol. 7, pp. 136- 140 ,(2009) , 10.5808/GI.2009.7.2.136
B. S. Weir, C. Clark Cockerham, ESTIMATING F
-STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE Evolution. ,vol. 38, pp. 1358- 1370 ,(1984) , 10.1111/J.1558-5646.1984.TB05657.X
Mikako Mori, Ryo Yamada, Kyoko Kobayashi, Reimi Kawaida, Kazuhiko Yamamoto, Ethnic differences in allele frequency of autoimmune-disease-associated SNPs Journal of Human Genetics. ,vol. 50, pp. 264- 266 ,(2005) , 10.1007/S10038-005-0246-8
P Deloukas, D Bentley, The HapMap project and its application to genetic studies of drug response. Pharmacogenomics Journal. ,vol. 4, pp. 88- 90 ,(2004) , 10.1038/SJ.TPJ.6500226
TIH Project, None, The International HapMap Project Nature. ,vol. 426, pp. 789- 796 ,(2003) , 10.1038/NATURE02168
Luis B Barreiro, Guillaume Laval, Hélène Quach, Etienne Patin, Lluís Quintana-Murci, Natural selection has driven population differentiation in modern humans Nature Genetics. ,vol. 40, pp. 340- 345 ,(2008) , 10.1038/NG.78