We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive pregnancy testing (NIPT). We use these data to characterize the population genetic structure of China, and to investigate genetic associations with maternal and infectious traits. We discover that the present day distribution of alleles is a function of both ancient migration and recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and a variant near EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piRNA processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and population genetic analyses.
Liu, Siyang and Huang, Shujia and Chen, Fang and Zhao, Lijian and Yuan, Yuying and Francis, Stephen Starko and Fang, Lin and Li, Zilong and Lin, Long and Liu, Rong and Zhang, Yong and Xu, Huixin and Li, Shengkang and Zhou, Yuwen and Liu, Qiang and Walters, Robin G. and Lin, Kuang and Ju, Jia and Korneliussen, Thorfinn and Yang, Melinda A. and Fu, Qiaomei and Zhou, Lijun and Krogh, Anders and Zhang, Hongyun and Wang, Wei and Chen, Zhengming and Yin, Ye and Yang, Huanming and Yang, Huanming and Mao, Mao and Shendure, Jay and Wang, Jian and Albrechtsen, Anders and Jin, Xin and Nielsen, Rasmus and Xu, Xun, Low Pass Genomes of 141,431 Chinese Reveal Patterns of Viral Infection, Novel Phenotypic Associations, and the Genetic History of China (2018). Available at SSRN: https://ssrn.com/abstract=3188420 or http://dx.doi.org/10.2139/ssrn.3188420
This version of the paper has not been formally peer reviewed.
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