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New Perspective on GWAS: East Asian Populations from the Viewpoint of Selection Pressure and Linear Algebra with AI

Masayuki Kanazaw

Genome Wide Association Studies (GWAS) are useful for comparing the characteristics of different human population groups. However, genomes can change rapidly over time when there is a strong selection pressure, such as a pandemic. The genetic information related to the immune system is thought to be very sensitive to such diseases. Therefore, it may be necessary to conduct not only the standard whole-genome GWAS but also a more detailed, chromosome-focused GWAS.

In this study, we compared chromosomes of immune system genes to those that are not thought to be related to the immune system, and analyzed GWAS results for SNPs in each chromosome to examine the differences. In order to keep the sample conditions as identical as possible, we limited the comparisons and the analyses to a few groups for which population movements were easy to interpret, and we also made sure the sample sizes were as close as possible. We selected a population of 403 East Asian people, consisting of 104 Japanese People in Tokyo (JPT), 103 Han Chinese People in Beijing (CHB) and 105 in Southern China (CHS), and 91 Korean People (KOR). PCA and Manhattan plot were used to analyze and compare the results.

Japanese, Chinese, and Korean populations formed distinctly different groups, with major differences observed. Validity of PCA and Manhattan plot was also discussed using Mahalanobis distance and AI.