ArticleGenome research2018
Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 57 citations in OpenAlex.
- Review
- Scaling for African Inclusion in High-Throughput Whole Cancer Genome Bioinformatic Workflows.Cancers · 2025Review
- The Emergence of Nanofluidics for Single-Biomolecule Manipulation and Sensing.Analytical chemistry · 2025Review
- Case Report: Optical genome mapping enables identification of complex balanced chromosomal rearrangements.Frontiers in genetics · 2025Article
- Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements.Nature reviews. Genetics · 2024Review
- Detection of Genomic Structural Variations Associated with Drug Sensitivity and Resistance in Acute Leukemia.Cancers · 2024Article
- Cytogenetics Is a Science, Not a Technique! Why Optical Genome Mapping Is So Important to Clinical Genetic Laboratories.Cancers · 2023Article
- A survey of algorithms for the detection of genomic structural variants from long-read sequencing data.Nature methods · 2023Review
- Article
- Mate Pair Sequencing: Next-Generation Sequencing for Structural Variant Detection.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research.Life (Basel, Switzerland) · 2022Review
- Optical genome mapping identifies clinically relevant genomic rearrangements in prostate cancer biopsy sample.Cancer cell international · 2022Article
- The Clinical Utility of Optical Genome Mapping for the Assessment of Genomic Aberrations in Acute Lymphoblastic Leukemia.Cancers · 2021Article
- Whole-genome optical mapping of bone-marrow myeloma cells reveals association of extramedullary multiple myeloma with chromosome 1 abnormalities.Scientific reports · 2021Article
- Re-examination of two diatom reference genomes using long-read sequencing.BMC genomics · 2021Article
- FaNDOM: Fast nested distance-based seeding of optical maps.Patterns (New York, N.Y.) · 2021Article
- Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.Human genetics · 2021Article
- Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale.Essays in biochemistry · 2021Article
- DNA Manipulation and Single-Molecule Imaging.Molecules (Basel, Switzerland) · 2021Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic rearrangements are common in cancer, with demonstrated links to disease progression and treatment response. These rearrangements can be complex, resulting in fusions of multiple chromosomal fragments and generation of derivative chromosomes. Although methods exist for detecting individual fusions, they are generally unable to reconstruct complex chained events. To overcome these limitations, we adopted a new optical mapping approach, allowing megabase-length genome maps to be reconstructed and rearranged genomes to be visualized without loss of integrity. Whole-genome mapping (Bionano Genomics) of a well-studied highly rearranged liposarcoma cell line resulted in 3338 assembled consensus genome maps, including 72 fusion maps. These fusion maps represent 112.3 Mb of highly rearranged genomic regions, illuminating the complex architecture of chained fusions, including content, order, orientation, and size. Spanning the junction of 147 chromosomal translocations, we found a total of 28 Mb of interspersed sequences that could not be aligned to the reference genome. Traversing these interspersed sequences using short-read sequencing breakpoint calls, we were able to identify and place 399 sequencing fragments within the optical mapping gaps, thus illustrating the complementary nature of optical mapping and short-read sequencing. We demonstrate that optical mapping provides a powerful new approach for capturing a higher level of complex genomic architecture, creating a scaffold for renewed interpretation of sequencing data of particular relevance to human cancer.
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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 OpenQuestion graph.