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Wong, Karen H. Y.; Ma, Walfred; Wei, Chun-Yu; Yeh, Erh-Chan; Lin, Wan-Jia; Wang, Elin H. F.; Su, Jen-Ping; Hsieh, Feng-Jen; Kao, Hsiao-Jung; Chen, Hsiao-Huei; Chow, Stephen K.; Young, Eleanor; Chu, Catherine; Poon, Annie; Yang, Chi-Fan; Lin, Dar-Shong; Hu, Yu-Feng; Wu, Jer-Yuarn; Lee, Ni-Chung; Hwu, Wuh-Liang; Boffelli, Dario; Martin, David; Xiao, Ming; Kwok, Pui-Yan
Nature communications, 10/2020, Letnik: 11, Številka: 1Journal Article
Abstract The current human reference genome is predominantly derived from a single individual and it does not adequately reflect human genetic diversity. Here, we analyze 338 high-quality human assemblies of genetically divergent human populations to identify missing sequences in the human reference genome with breakpoint resolution. We identify 127,727 recurrent non-reference unique insertions spanning 18,048,877 bp, some of which disrupt exons and known regulatory elements. To improve genome annotations, we linearly integrate these sequences into the chromosomal assemblies and construct a Human Diversity Reference. Leveraging this reference, an average of 402,573 previously unmapped reads can be recovered for a given genome sequenced to ~40X coverage. Transcriptomic diversity among these non-reference sequences can also be directly assessed. We successfully map tens of thousands of previously discarded RNA-Seq reads to this reference and identify transcription evidence in 4781 gene loci, underlining the importance of these non-reference sequences in functional genomics. Our extensive datasets are important advances toward a comprehensive reference representation of global human genetic diversity.
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
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in: SICRIS
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