ArticleJournal of personalized medicine2021
Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping.
Article in Journal of personalized medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 37 citations in OpenAlex.
- Evaluation of the efficacy of optical genome mapping in prenatal diagnosis: a retrospective cohort study.Journal of translational medicine · 2026Article
- Optical genome mapping as a diagnostic tool for unsolved balanced translocations in couples with adverse pregnancy outcomes: a case series.European journal of medical research · 2026Article
- Optical genome mapping as a high-resolution tool for uncovering cytogenetic complex and cryptic alterations in a cohort of patients with MDS and AML.NPJ precision oncology · 2026Article
- Article
- Genomic innovations in cancer prevention, diagnosis, prognosis and precision therapeutics.Frontiers in genetics · 2026Review
- Review
- Interlaboratory evaluation of high molecular weight DNA extraction methods for long-read sequencing and structural variant analysis.BMC genomics · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Exploring the Potential of Optical Genome Mapping in the Diagnosis and Prognosis of Soft Tissue and Bone Tumors.International journal of molecular sciences · 2025Article
- Optical genome mapping to decipher the chromosomal aberrations in families seeking for preconception genetic counseling.Scientific reports · 2025Article
- Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection.Journal of personalized medicine · 2024Article
- Identification of complex and cryptic chromosomal rearrangements by optical genome mapping.Molecular cytogenetics · 2023Article
- Optical genome mapping in acute myeloid leukemia: a multicenter evaluation.Blood advances · 2023Article
- From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research.Life (Basel, Switzerland) · 2022Review
- Reclassification ofGenes · 2022Article
- Optical genome mapping identifies clinically relevant genomic rearrangements in prostate cancer biopsy sample.Cancer cell international · 2022Article
- Human Papillomavirus Integration Strictly Correlates with Global Genome Instability in Head and Neck Cancer.Molecular cancer research : MCR · 2022Article
- Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing.Scientific reports · 2021Article
- Next-generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping.American journal of human genetics · 2021Article
- Multicolor Whole-Genome Mapping in Nanochannels for Genetic Analysis.Analytical chemistry · 2021Article
Corrections and comments
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Authors and funding
15 authors at 2 institutions in 1 country.
Funding
Abstract
Genomic structural variants comprise a significant fraction of somatic mutations driving cancer onset and progression. However, such variants are not readily revealed by standard next-generation sequencing. Optical genome mapping (OGM) surpasses short-read sequencing in detecting large (>500 bp) and complex structural variants (SVs) but requires isolation of ultra-high-molecular-weight DNA from the tissue of interest. We have successfully applied a protocol involving a paramagnetic nanobind disc to a wide range of solid tumors. Using as little as 6.5 mg of input tumor tissue, we show successful extraction of high-molecular-weight genomic DNA that provides a high genomic map rate and effective coverage by optical mapping. We demonstrate the system's utility in identifying somatic SVs affecting functional and cancer-related genes for each sample. Duplicate/triplicate analysis of select samples shows intra-sample reliability but also intra-sample heterogeneity. We also demonstrate that simply filtering SVs based on a GRCh38 human control database provides high positive and negative predictive values for true somatic variants. Our results indicate that the solid tissue DNA extraction protocol, OGM and SV analysis can be applied to a wide variety of solid tumors to capture SVs across the entire genome with functional importance in cancer prognosis and treatment.
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Registered trials
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.