{Reference Type}: Journal Article
{Title}: Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet.
{Author}: Jia P;Dong L;Yang X;Wang B;Bush SJ;Wang T;Lin J;Wang S;Zhao X;Xu T;Che Y;Dang N;Ren L;Zhang Y;Wang X;Liang F;Wang Y;Ruan J;Xia H;Zheng Y;Shi L;Lv Y;Wang J;Ye K;
{Journal}: Genome Biol
{Volume}: 24
{Issue}: 1
{Year}: 2023 12 4
暂无{DOI}: 10.1186/s13059-023-03116-3
{Abstract}: 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).<BR>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.<BR>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.