ArticleGenome research2020
Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 19 citations in OpenAlex.
- Proof-of-concept study for the detection of somatic structural variant driver alterations using HiFi long-read sequencing in a pediatric leukemia cohort.NPJ genomic medicine · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability.Nature communications · 2025Article
- CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.bioRxiv : the preprint server for biology · 2024Article
- Most large structural variants in cancer genomes can be detected without long reads.Nature genetics · 2023Article
- Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures.Cell genomics · 2023Article
- Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies.Genome biology · 2022Article
- Computational analysis of cancer genome sequencing data.Nature reviews. Genetics · 2022Review
- Integrative reconstruction of cancer genome karyotypes using InfoGenomeR.Nature communications · 2021Article
- Computational methods for chromosome-scale haplotype reconstruction.Genome biology · 2021Review
- Application of long-read sequencing to the detection of structural variants in human cancer genomes.Computational and structural biotechnology journal · 2021Review
- Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing.Genome research · 2020Article
- Recovering rearranged cancer chromosomes from karyotype graphs.BMC bioinformatics · 2019Article
- Algorithmic approaches to clonal reconstruction in heterogeneous cell populations.Quantitative biology (Beijing, China) · 2019Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Many cancer genomes are extensively rearranged with aberrant chromosomal karyotypes. Deriving these karyotypes from high-throughput DNA sequencing of bulk tumor samples is complicated because most tumors are a heterogeneous mixture of normal cells and subpopulations of cancer cells, or clones, that harbor distinct somatic mutations. We introduce a new algorithm, Reconstructing Cancer Karyotypes (RCK), to reconstruct haplotype-specific karyotypes of one or more rearranged cancer genomes from DNA sequencing data from a bulk tumor sample. RCK leverages evolutionary constraints on the somatic mutational process in cancer to reduce ambiguity in the deconvolution of admixed sequencing data into multiple haplotype-specific cancer karyotypes. RCK models mixtures containing an arbitrary number of derived genomes and allows the incorporation of information both from short-read and long-read DNA sequencing technologies. We compare RCK to existing approaches on 17 primary and metastatic prostate cancer samples. We find that RCK infers cancer karyotypes that better explain the DNA sequencing data and conform to a reasonable evolutionary model. RCK's reconstructions of clone- and haplotype-specific karyotypes will aid further studies of the role of intra-tumor heterogeneity in cancer development and response to treatment. RCK is freely available as open source software.
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