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Journal article
Towards a reference genome that captures global genetic diversity
Nature communications, v 11(1), pp 5482-5482
30 Oct 2020
PMID: 33127893
Featured in Collection : UN Sustainable Development Goals @ Drexel
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.
The human reference genome does not fully reflect human genetic diversity. Here, the authors analyse 338 human genome assemblies from diverse populations to identify missing sequences, define non-reference unique insertions and construct a Human Diversity Reference.
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Details
- Title
- Towards a reference genome that captures global genetic diversity
- Creators
- Karen H. Y. Wong - Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.Walfred Ma - Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.Chun-Yu Wei - Taipei, TaiwanErh-Chan Yeh - Institute of Biomedical Sciences, Academia SinicaWan-Jia Lin - Institute of Biomedical Sciences, Academia SinicaElin H. F. Wang - Institute of Biomedical Sciences, Academia SinicaJen-Ping Su - Institute of Biomedical Sciences, Academia SinicaFeng-Jen Hsieh - Institute of Biomedical Sciences, Academia SinicaHsiao-Jung Kao - Institute of Biomedical Sciences, Academia SinicaHsiao-Huei Chen - Institute of Biomedical Sciences, Academia SinicaStephen K. Chow - Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.Eleanor Young - Drexel UniversityCatherine Chu - University of California, San FranciscoAnnie Poon - University of California, San FranciscoChi-Fan Yang - Institute of Biomedical Sciences, Academia SinicaDar-Shong Lin - Mackay Medical CollegeYu-Feng Hu - Taipei Veterans General HospitalJer-Yuarn Wu - Institute of Biomedical Sciences, Academia SinicaNi-Chung Lee - National Taiwan University HospitalWuh-Liang Hwu - National Taiwan University HospitalDario Boffelli - Children's Hospital Oakland Research InstituteDavid Martin - Oakland, CA 94609 USAMing Xiao - Drexel UniversityPui-Yan Kwok - University of California, San Francisco
- Publication Details
- Nature communications, v 11(1), pp 5482-5482
- Publisher
- Nature Publishing Group UK
- Grant note
- R01 HG005946 / ;
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000588063600005
- Scopus ID
- 2-s2.0-85094651296
- Other Identifier
- 991019167947504721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Genetics & Heredity