ArticleCell systems2016
Allele-Specific Quantification of Structural Variations in Cancer Genomes.
Article in Cell systems, 2016. 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed.
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- 3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression.Nature communications · 2024Article
- Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing.Nucleic acids research · 2023Article
- Helsmoortel-van der Aa syndrome in a Chinese pediatric patient due toFrontiers in pediatrics · 2023Article
- Computational analysis of cancer genome sequencing data.Nature reviews. Genetics · 2022Review
- Computational Approaches for the Investigation of Intra-tumor Heterogeneity and Clonal Evolution from Bulk Sequencing Data in Precision Oncology Applications.Advances in experimental medicine and biology · 2022Review
- Integrative reconstruction of cancer genome karyotypes using InfoGenomeR.Nature communications · 2021Article
- Article
- Accurate and efficient detection of gene fusions from RNA sequencing data.Genome research · 2021Article
- Assessing the contribution of tumor mutational phenotypes to cancer progression risk.PLoS computational biology · 2021Article
- SPIN reveals genome-wide landscape of nuclear compartmentalization.Genome biology · 2021Article
- Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.PLoS computational biology · 2020Article
- Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.Cell · 2020Article
- Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples.Genome research · 2020Article
- Copy number evolution with weighted aberrations in cancer.Bioinformatics (Oxford, England) · 2020Article
- Meltos: multi-sample tumor phylogeny reconstruction for structural variants.Bioinformatics (Oxford, England) · 2020Article
- Inferring structural variant cancer cell fraction.Nature communications · 2020Article
- A new era of long-read sequencing for cancer genomics.Journal of human genetics · 2020Review
- RBV: Read balance validator, a tool for prioritising copy number variations in germline conditions.Scientific reports · 2019Article
- Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.Nature communications · 2019Article
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Authors and funding
4 authors.
Funding
Abstract
Aneuploidy and structural variations (SVs) generate cancer genomes containing a mixture of rearranged genomic segments with extensive somatic copy number alterations. However, existing methods can identify either SVs or allele-specific copy number alterations but not both simultaneously, which provides a limited view of cancer genome structure. Here, we introduce Weaver, an algorithm for the quantification and analysis of allele-specific copy numbers of SVs. Weaver uses a Markov random field to estimate joint probabilities of allele-specific copy numbers of SVs and their inter-connectivity based on paired-end whole-genome sequencing data. Weaver also predicts the timing of SVs relative to chromosome amplifications. We demonstrate the accuracy of Weaver using simulations and findings from whole-genome optical mapping. We apply Weaver to generate allele-specific copy numbers of SVs for MCF-7 and HeLa cell lines and identify recurrent SV patterns in 44 TCGA ovarian cancer whole-genome sequencing datasets. Our approach provides a more complete assessment of the complex genomic architectures inherent to many cancer genomes.
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