ArticleNucleic acids research2017
Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- Experimental method for haplotype phasing across the entire length of chromosome 21 in trisomy 21 cells using a chromosome elimination technique.Journal of human genetics · 2022Article
- Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.Blood advances · 2022Article
- Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62.Scientific reports · 2022Article
- Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer.Nature biotechnology · 2021Article
- Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8.Genome medicine · 2021Article
- Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology.NPJ precision oncology · 2021Review
- Application of long-read sequencing to the detection of structural variants in human cancer genomes.Computational and structural biotechnology journal · 2021Review
- Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.PLoS computational biology · 2020Article
- MRLR: unraveling high-resolution meiotic recombination by linked reads.Bioinformatics (Oxford, England) · 2020Article
- Programmed DNA elimination of germline development genes in songbirds.Nature communications · 2019Article
- Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2.Nucleic acids research · 2019Article
- Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562.Genome research · 2019Article
- Tumour heterogeneity and metastasis at single-cell resolution.Nature cell biology · 2018Review
- SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.GigaScience · 2018Article
- Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer.Genome research · 2018Article
- Identification of large rearrangements in cancer genomes with barcode linked reads.Nucleic acids research · 2018Article
- Current Strategies of Polyploid Plant Genome Sequence Assembly.Frontiers in plant science · 2018Review
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8 authors.
Funding
Abstract
Genomic instability is a frequently occurring feature of cancer that involves large-scale structural alterations. These somatic changes in chromosome structure include duplication of entire chromosome arms and aneuploidy where chromosomes are duplicated beyond normal diploid content. However, the accurate determination of aneuploidy events in cancer genomes is a challenge. Recent advances in sequencing technology allow the characterization of haplotypes that extend megabases along the human genome using high molecular weight (HMW) DNA. For this study, we employed a library preparation method in which sequence reads have barcodes linked to single HMW DNA molecules. Barcode-linked reads are used to generate extended haplotypes on the order of megabases. We developed a method that leverages haplotypes to identify chromosomal segmental alterations in cancer and uses this information to join haplotypes together, thus extending the range of phased variants. With this approach, we identified mega-haplotypes that encompass entire chromosome arms. We characterized the chromosomal arm changes and aneuploidy events in a manner that offers similar information as a traditional karyotype but with the benefit of DNA sequence resolution. We applied this approach to characterize aneuploidy and chromosomal alterations from a series of primary colorectal cancers.
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