Unbalanced sample size effect on genome-wide population differentiation studies
by Kyunghee Han; Kyee-Zu Kim; Jung Mi Oh; In-Wha Kim; Kyungim Kim; Taesung Park
International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 6, No. 5, 2012

Abstract: The fixation index (F_ST) is one of the most widely used measurements of genetic distance between populations. The data set from the international HapMap project has been served as a reference data set for population differentiation studies. F_ST is commonly used in order to compare the sample data with HapMap data. In this study, however, we show that the use of F_ST without consideration of sample sizes may mislead the result. In particular, we first demonstrate that F_ST suffers from imbalance of sample sizes through simulation studies and through the analysis of a large scale Korean genome-wide association data. Then, we propose a modified version of F_ST which is shown to be more robust to imbalance of sample size. In addition, the chi-square test commonly used for homogeneity test is shown to perform similarly to the modified version of F_ST.

Online publication date: Wed, 17-Dec-2014

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