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A comprehensive map of genetic variation in the world’s largest ethnic group - Han Chinese

View ORCID ProfileCharleston W. K. Chiang, Serghei Mangul, Christopher R. Robles, Warren W. Kretzschmar, View ORCID ProfileNa Cai, View ORCID ProfileKenneth S. Kendler, Sriram Sankararam, Jonathan Flint
doi: https://doi.org/10.1101/162982
Charleston W. K. Chiang
1Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, USA
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  • ORCID record for Charleston W. K. Chiang
Serghei Mangul
2Department of Computer Science, University of California Los Angeles, Los Angeles, California, USA
3Institute for Quantitative and Computational Bioscience, University of California Los Angeles, Los Angeles, California, USA
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Christopher R. Robles
4Department of Human enetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
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Warren W. Kretzschmar
5Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Na Cai
6Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
7European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Kenneth S. Kendler
8VirginiaInstitute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
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Sriram Sankararam
2Department of Computer Science, University of California Los Angeles, Los Angeles, California, USA
4Department of Human enetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
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Jonathan Flint
1Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, USA
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Abstract

As are most non-European populations around the globe, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our dataset. Individuals from our study come from 19 out of 22 provinces across China, allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identify previously unrecognized population structure along the East-West axis of China and report unique signals of admixture across geographical space, such as European influences among the Northwestern provinces of China. Finally, we identified a number of highly differentiated loci, indicative of local adaptation in the Han Chinese. In particular, we detected extreme differentiation among the Han Chinese at MTHFR, ADH7, and FADS loci, suggesting that these loci may not be specifically selected in Tibetan and Inuit populations as previously suggested. On the other hand, we find that Neandertal ancestry does not vary significantly across the provinces, consistent with admixture prior to the dispersal of modern Han Chinese. Furthermore, contrary to a previous report, Neandertal ancestry does not explain a significant amount of heritability in depression. Our findings provide the largest genetic data set so far made available for Han Chinese and provide insights into the history and population structure of the world’s largest ethnic group.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 13, 2017.
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A comprehensive map of genetic variation in the world’s largest ethnic group - Han Chinese
Charleston W. K. Chiang, Serghei Mangul, Christopher R. Robles, Warren W. Kretzschmar, Na Cai, Kenneth S. Kendler, Sriram Sankararam, Jonathan Flint
bioRxiv 162982; doi: https://doi.org/10.1101/162982
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A comprehensive map of genetic variation in the world’s largest ethnic group - Han Chinese
Charleston W. K. Chiang, Serghei Mangul, Christopher R. Robles, Warren W. Kretzschmar, Na Cai, Kenneth S. Kendler, Sriram Sankararam, Jonathan Flint
bioRxiv 162982; doi: https://doi.org/10.1101/162982

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