Low Pass Genomes of 141,431 Chinese Reveal Patterns of Viral Infection, Novel Phenotypic Associations, and the Genetic History of China

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.