ArticleOncotarget2017
Next generation mapping reveals novel large genomic rearrangements in prostate cancer.
Article in Oncotarget, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Combination of Long-Read Sequencing and Hi-C Technology to Identify Chromoanagenesis Events in Cancer.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.Molecular biology and evolution · 2024Article
- Detection of Genomic Structural Variations Associated with Drug Sensitivity and Resistance in Acute Leukemia.Cancers · 2024Article
- Optical genome mapping identifies clinically relevant genomic rearrangements in prostate cancer biopsy sample.Cancer cell international · 2022Article
- Extrachromosomal DNA in Cancer.Annual review of genomics and human genetics · 2022Review
- Genetic Testing and Its Clinical Application in Prostate Cancer Management: Consensus Statements from the Hong Kong Urological Association and Hong Kong Society of Uro-Oncology.Frontiers in oncology · 2022Article
- Towards improved genetic diagnosis of human differences of sex development.Nature reviews. Genetics · 2021Review
- Next-generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping.American journal of human genetics · 2021Article
- Whole-genome optical mapping of bone-marrow myeloma cells reveals association of extramedullary multiple myeloma with chromosome 1 abnormalities.Scientific reports · 2021Article
- ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data.Genome medicine · 2021Article
- Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping.Journal of personalized medicine · 2021Article
- nanotatoR: a tool for enhanced annotation of genomic structural variants.BMC genomics · 2021Article
- Integrated analysis of optical mapping and whole-genome sequencing reveals intratumoral genetic heterogeneity in metastatic lung squamous cell carcinoma.Translational lung cancer research · 2020Article
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
- Overview of research on fusion genes in prostate cancer.Translational cancer research · 2020Review
- Identification of a likely pathogenic structural variation in theNPJ genomic medicine · 2020Article
- Translating genomics to the clinical diagnosis of disorders/differences of sex development.Current topics in developmental biology · 2019Review
- Genome-Based Classification and Therapy of Prostate Cancer.Diagnostics (Basel, Switzerland) · 2018Review
- Article
- New technologies to uncover the molecular basis of disorders of sex development.Molecular and cellular endocrinology · 2018Review
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS. In this study, we sought to determine the feasibility of using the Irys (Bionano Genomics Inc.) nanochannel NGM technology to generate whole genome maps of a primary prostate tumor and matched blood from a Gleason score 7 (4 + 3), ETS-fusion negative prostate cancer patient. With an effective mapped coverage of 35X and sequence coverage of 60X, and an estimated 43% tumor purity, we identified 85 large somatic structural rearrangements and 6,172 smaller somatic variants, respectively. The vast majority of the large SVs (89%), of which 73% are insertions, were not detectable ab initio using high-coverage short-read NGS. However, guided manual inspection of single NGS reads and de novo assembled scaffolds of NGM-derived candidate regions allowed for confirmation of 94% of these large SVs, with over a third impacting genes with oncogenic potential. From this single-patient study, the first cancer study to integrate NGS and NGM data, we hypothesise that there exists a novel spectrum of large genomic rearrangements in prostate cancer, that these large genomic rearrangements are likely early events in tumorigenesis, and they have potential to enhance taxonomy.
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