ArticleGenome biology2023
Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- A Telomere-to-telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet.Genomics, proteomics & bioinformatics · 2025Article
- Protein-level batch-effect correction enhances robustness in MS-based proteomics.Nature communications · 2025Article
- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 2025Review
- De novo and somatic structural variant discovery with SVision-pro.Nature biotechnology · 2025Article
- Reference Materials for Improving Reliability of Multiomics Profiling.Phenomics (Cham, Switzerland) · 2024Review
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials.Nature biotechnology · 2024Article
- Reliable biological and multi-omics research through biometrology.Analytical and bioanalytical chemistry · 2024Review
- Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet.Genome biology · 2023Article
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance.Genome biology · 2023Article
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Authors and funding
24 authors.
Funding
Abstract
backgroundRecent 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).
resultsThe 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.
conclusionsIn 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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