De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations.
De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations.
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DOI：
10.1038/s41467-018-05513-w
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发表时间：
2018-08-02
影响因子：
16.6
通讯作者：
Kwok PY
中科院分区：
文献类型：
--
作者：
Wong KHY;Levy-Sakin M;Kwok PY
人类参考基因组在现代生物学研究中被广泛使用。然而，一个单一的共识代表是不足以提供一个普遍的参考结构，因为它是一个单倍型在许多人的人口。使用10× Genomics（10×G）“Linked-Read”技术，我们对五个种群的17个个体进行全基因组测序（WGS）和从头组装。我们确定了1842个断点解析的非参考独特插入（NUI），总的来说，加起来有2.1 Mb的迄今为止未描述的基因组内容。其中，64%被认为是人类的祖先，因为它们是在非人类灵长类动物基因组中发现的。此外，37%的NUI可以在人类转录组中找到，14%可能来自于DNA重组介导的缺失。我们的研究结果强调了需要一套人类参考基因组，其中包括一个全面的替代单倍型列表，以描绘整个人群的遗传多样性谱。大多数人类参考基因组组装体表示为单一共有单倍型。在这里，Wong等人分析了17个不同的、单倍型解析的基因组的从头组装，以深入了解遗传多样性的结构，并编制了一份跨种群的替代单倍型列表。
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. The majority of the human reference genome assembly is represented as a single consensus haplotype. Here, Wong et al. analyze de novo assemblies of 17 diverse, haplotype-resolved genomes to gain insights into the structure of genetic diversity and compile a list of alternative haplotypes across populations.
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