Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

文献类型： 外文期刊

第一作者： Jia, Peng

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

作者机构：

期刊名称：GENOME BIOLOGY （ 影响因子：12.3； 五年影响因子：17.4 ）

ISSN： 1474-760X

年卷期： 2023 年 24 卷 1 期

页码：

收录情况： SCI

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.

分类号：

  • 相关文献
作者其他论文 更多>>

微信小程序