ArticleNature communications2023
Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- 3D chromatin architecture-related genes orchestrate LUAD evolution and therapy resistance: insights from integrative machine learning and spatial single-cell mapping.Functional & integrative genomics · 2026Article
- Loss of multilevel 3D genome organization during breast cancer progression.Genome research · 2026Article
- An integrated platform for concurrent structural and single-nucleotide variants improves copy-number detection and reveals pathogenic alleles in undiagnosed Mendelian families.Genome medicine · 2025Article
- ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling.Nature communications · 2025Article
- TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis.Genome biology · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake.Molecular biology and evolution · 2025Article
- Genome assembly resources of genitourinary cancers for chromosomal aberration at the single nucleotide level.Scientific data · 2025Article
- GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs.BMC bioinformatics · 2025Article
- TopoQual polishes circular consensus sequencing data and accurately predicts quality scores.BMC bioinformatics · 2025Article
- Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping.Scientific reports · 2024Article
- Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.Genome research · 2024Article
- Unravelling a KMT2A::ARHGEF12 fusion within chromoanagenesis in acute myeloid leukemia using Optical Genome Mapping.Annals of hematology · 2024Article
- Review
- An elevated rate of whole-genome duplications in cancers from Black patients.Nature communications · 2024Article
- Genome assembly in the telomere-to-telomere era.Nature reviews. Genetics · 2024Review
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cancer genomes are highly complex and heterogeneous. The standard short-read sequencing and analytical methods are unable to provide the complete and precise base-level structural variant landscape of cancer genomes. In this work, we apply high-resolution long accurate HiFi and long-range Hi-C sequencing to the melanoma COLO829 cancer line. Also, we develop an efficient graph-based approach that processes these data types for chromosome-scale haplotype-resolved reconstruction to characterise the cancer precise structural variant landscape. Our method produces high-quality phased scaffolds on the chromosome level on three healthy samples and the COLO829 cancer line in less than half a day even in the absence of trio information, outperforming existing state-of-the-art methods. In the COLO829 cancer cell line, here we show that our method identifies and characterises precise somatic structural variant calls in important repeat elements that were missed in short-read-based call sets. Our method also finds the precise chromosome-level structural variant (germline and somatic) landscape with 19,956 insertions, 14,846 deletions, 421 duplications, 52 inversions and 498 translocations at the base resolution. Our simple pstools approach should facilitate better personalised diagnosis and disease management, including predicting therapeutic responses.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.