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Nat Commun. 2018 Aug 2;9(1):3040. doi: 10.1038/s41467-018-05513-w.

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

Author information

1
Cardiovascular Research Institute, University of California, San Francisco, San Francisco, 94158, CA, USA.
2
Cardiovascular Research Institute, University of California, San Francisco, San Francisco, 94158, CA, USA. pui.kwok@ucsf.edu.
3
Institute for Human Genetics, University of California, San Francisco, San Francisco, 94143, CA, USA. pui.kwok@ucsf.edu.
4
Department of Dermatology, University of California, San Francisco, San Francisco, 94115, CA, USA. pui.kwok@ucsf.edu.

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.

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