ArticleBMC genomics2013
Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis.
Article in BMC genomics, 2013. 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, 34 citations in OpenAlex.
- Developing an insert to protect large DNA molecules during cell lysis.BioTechniques · 2025Article
- Concentration of lambda concatemers using a 3D printed device.Electrophoresis · 2023Article
- Combination of trio-based whole exome sequencing and optical genome mapping reveals a cryptic balanced translocation that causes unbalanced chromosomal rearrangements in a family with multiple anomalies.Frontiers in genetics · 2023Article
- Enzyme-free optical DNA mapping of the human genome using competitive binding.Nucleic acids research · 2019Article
- Determining if DNA Stained with a Cyanine Dye Can Be Digested with Restriction Enzymes.Journal of visualized experiments : JoVE · 2018Article
- Electrostatic confinement and manipulation of DNA molecules for genome analysis.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps.Genome biology · 2017Article
- Allele-Specific Quantification of Structural Variations in Cancer Genomes.Cell systems · 2016Article
- Maligner: a fast ordered restriction map aligner.Bioinformatics (Oxford, England) · 2016Article
- Article
- OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.GigaScience · 2016Article
- Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates.PLoS genetics · 2015Article
- Chromosomal defects track tumor subpopulations and change in progression in oligodendroglioma.Convergent science physical oncology · 2015Article
- Single-molecule analysis reveals widespread structural variation in multiple myeloma.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Image processing for optical mapping.GigaScience · 2015Review
- Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line.GigaScience · 2015Article
- Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry.Nucleic acids research · 2014Article
- Computational methods for optical mapping.GigaScience · 2014Review
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundSolid tumors present a panoply of genomic alterations, from single base changes to the gain or loss of entire chromosomes. Although aberrations at the two extremes of this spectrum are readily defined, comprehensive discernment of the complex and disperse mutational spectrum of cancer genomes remains a significant challenge for current genome analysis platforms. In this context, high throughput, single molecule platforms like Optical Mapping offer a unique perspective.
resultsUsing measurements from large ensembles of individual DNA molecules, we have discovered genomic structural alterations in the solid tumor oligodendroglioma. Over a thousand structural variants were identified in each tumor sample, without any prior hypotheses, and often in genomic regions deemed intractable by other technologies. These findings were then validated by comprehensive comparisons to variants reported in external and internal databases, and by selected experimental corroborations. Alterations range in size from under 5 kb to hundreds of kilobases, and comprise insertions, deletions, inversions and compound events. Candidate mutations were scored at sub-genic resolution and unambiguously reveal structural details at aberrant loci.
conclusionsThe Optical Mapping system provides a rich description of the complex genomes of solid tumors, including sequence level aberrations, structural alterations and copy number variants that power generation of functional hypotheses for oligodendroglioma genetics.
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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.