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De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations

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  • Karen H. Y. Wong

    (University of California, San Francisco)

  • Michal Levy-Sakin

    (University of California, San Francisco)

  • Pui-Yan Kwok

    (University of California, San Francisco
    University of California, San Francisco
    University of California, San Francisco)

Abstract

The human reference genome is used extensively in modern biological research. However, a single consensus representation is inadequate to provide a universal reference structure because it is a haplotype among many in the human population. Using 10× Genomics (10×G) “Linked-Read” technology, we perform whole genome sequencing (WGS) and de novo assembly on 17 individuals across five populations. We identify 1842 breakpoint-resolved non-reference unique insertions (NUIs) that, in aggregate, add up to 2.1 Mb of so far undescribed genomic content. Among these, 64% are considered ancestral to humans since they are found in non-human primate genomes. Furthermore, 37% of the NUIs can be found in the human transcriptome and 14% likely arose from Alu-recombination-mediated deletion. Our results underline the need of a set of human reference genomes that includes a comprehensive list of alternative haplotypes to depict the complete spectrum of genetic diversity across populations.

Suggested Citation

  • Karen H. Y. Wong & Michal Levy-Sakin & Pui-Yan Kwok, 2018. "De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05513-w
    DOI: 10.1038/s41467-018-05513-w
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