数字农科院2.0

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

文献类型： 外文期刊

作者： Peng Jia;Lianhua Dong;Xiaofei Yang;Bo Wang;Stephen J. Bush;Tingjie Wang;Jiadong Lin;Songbo Wang;Xixi Zhao;Tun Xu;Yizhuo Che;Ningxin Dang;Luyao Ren;Yujing Zhang;Xia Wang;Fan Liang;Yang Wang;Jue Ruan;Han Xia;Yuanting Zheng;Leming Shi;Yi Lv;Jing Wang;Kai Ye

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期刊名称： Genome Biology

ISSN： 1474-7596

年卷期： 2023 年 24 卷 1 期

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收录情况： SCIE（2023版）

摘要： Background: Recent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and expand the scope of variant benchmarking datasets. Herein, we sequence a Chinese Quartet, comprising two monozygotic twin daughters and their biological parents, using four short and long sequencing platforms (Illumina, BGI, PacBio, and Oxford Nanopore Technology). Results: The long reads from the monozygotic twin daughters are phased into paternal and maternal haplotypes using the parent–child genetic map and for each haplotype. We also use long reads to generate haplotype-resolved whole-genome assemblies with completeness and continuity exceeding that of GRCh38. Using this Quartet, we comprehensively catalogue the human variant landscape, generating a dataset of 3,962,453 SNVs, 886,648 indels (< 50 bp), 9726 large deletions (≥ 50 bp), 15,600 large insertions (≥ 50 bp), 40 inversions, 31 complex structural variants, and 68 de novo mutations which are shared between the monozygotic twin daughters. Variants underrepresented in previous benchmarks owing to their complexity—including those located at long repeat regions, complex structural variants, and de novo mutations—are systematically examined in this study. Conclusions: In summary, this study provides high-quality haplotype-resolved assemblies and a comprehensive set of benchmarking resources for two Chinese monozygotic twin samples which, relative to existing benchmarks, offers expanded genomic coverage and insight into complex variant categories.

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