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Discover New and Meaningful Structural Variants With Optical Genome Mapping

Structural variants (SVs) are a hallmark of cancer, yet next-generation sequencing (NGS) methods fail to detect all classes and sizes of SVs, missing a significant amount of information critical to understanding cancer biology.1-4 Studies have shown that both short-read and long-read sequencing technologies miss a significant portion of SVs detected by optical genome mapping (OGM).1,2

Combine NGS with OGM to unlock a broader spectrum of genetic variants, generate a more complete cancer genome profile, and discover new actionable biomarkers.

  • Generate true comprehensive cancer profiles by supplementing small variant data obtained from NGS with high-resolution, genome-wide SV data from OGM
  • Detect, in a single assay, all classes of SVs equal or larger than 500bp, including rare events down to 5% allele fraction
  • Reveal SVs commonly missed by sequencing methods3
  • OGM has been proven to find multiple pathogenic SVs mapped to cancer genes that could lead to new therapy investigations across more than ten solid tumor types1,4,5

 

  • OGM workflow steps are like molecular workflows and can easily be implemented for a streamlined, sample-to-answer solution
  • See how our automated OGM workflow enables low hands-on time and scalability for easy in-house implementation
  • Simplify analysis of all small variant and SV results with Bionano software solutions for easier identification of pathogenic alterations, annotation, interpretation, and reporting

 

Case Studies

Explore these cancer genomic case studies and learn how OGM uncovers SVs that short- and long-read sequencing can’t reliably identify.
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“OGM found clinically relevant variants in breast cancer samples, which were missed by exome sequencing.”

Dr. Tuomo Mantere
University of Oulu, Finland

“OGM revealed important translocations, in Ewing sarcoma samples, that could be useful as a prognostic marker for patients with poor clinical outcome.”

Dr. Juan Diaz Martin
Instituto de Biomedicina de Sevilla (IBiS) Sevilla, Spain

DATA EXAMPLES

Study with Multiple Tumor Types Reveals SVs That Would Not Be Readily Identified by Targeted Gene Panels Generally Used to Assess Tumor Genomes:

  • Several SVs were detected in known cancer genes, offering the opportunity for studies with targeted therapies or immunotherapies
  • In many cases, the cancer genes altered by SVs were not previously associated with the cancer type observed in the study.5

 

By combining WGS and optical mapping, researchers could reconstruct the structure of complex SVs at large scale and single-base resolution in a subgroup of hepatocellular carcinoma with cyclin-induced replication stress.1

 

OGM Solved Cancer Predisposition Mystery in a Pediatric ATRT Case

Previous analysis using Sanger sequencing, NGS (whole exome and whole genome sequencing), and MLPA could not identify a causative variant.

OGM revealed a 2.7kb insertion in the ATRT gene.4 OGM analysis of germline DNA showing an SV call enclosing the insertion at the SMARCB1 locus.

 

Discover How OGM Benefits Clinical Research in Cancer

Utility of optical genome mapping for the chromosomal characterization of solid tumors.

Ravindra Kolhe, MD, PhD, FCAP

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Optical genome mapping reveals novel structural variants in pediatric brain tumors.

Miriam Bornhorst, MD

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Learn More About OGM

Read about what structural variations are and why they matter.

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See how OGM reveals structural variation in a way that has never been done before.

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Find the latest research in our Publications Library.

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Sign up to get the latest updates on Bionano solutions for solid tumor applications.

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RELATED MATERIALS

title Source Authors
Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia September 21, 2023

Brandes, Danielle; Yasin, Layal; Nebral, Karin; Ebler, Jana; Schinnerl, Dagmar; Picard, Daniel; Bergmann, Anke; Alam, Jubayer; Köhrer, Stefan; Haas, Oskar A.; Attarbaschi, Andishe; Marschall, Tobias; Stanulla, Martin; Borkhardt, Arndt; Brozou, Triantafyllia; Fischer, Ute; Wagener, Rabea
Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation June 12, 2023

Pille Hallast, Peter Ebert, Mark Loftus, Feyza Yilmaz, Peter A. Audano, Glennis A. Logsdon, Marc Jan Bonder, Weichen Zhou, Wolfram Hoeps, Kwondo Kim, Chong Li, Philip C Dishuck, David Porubsky, Fotios Tsetsos, Jee Young Kwon, Qihui Zhu, Katherine M. Munson, Patrick Hasenfeld, William T. Harvey, Alexandra P. Lewis, Jennifer Kordosky, Kendra Hoekzema, The Human Genome Structural Variation Consortium (HGSVC), Jan O. Korbel, Chris Tyler-Smith, Evan E. Eichler, Xinghua Shi, Christine R Beck, Tobias Marschall, Miriam K. Konkel, Charles Lee
Babesia duncani multi-omics identifies virulence factors and drug targets April 13, 2023

Pallavi Singh, Stefano Lonardi, Qihua Liang, Pratap Vydyam, Eleonora Khabirova, Tiffany Fang, Shalev Gihaz, Jose Thekkiniath, Muhammad Munshi, Steven Abel, Loic Ciampossin, Gayani Batugedara, Mohit Gupta, Xueqing Maggie Lu, Todd Lenz, Sakshar Chakravarty, Emmanuel Cornillot, Yangyang Hu, Wenxiu Ma, Luis Miguel Gonzalez, Sergio Sánchez, Karel Estrada, Alejandro Sánchez-Flores, Estrella Montero, Omar S. Harb, Karine G. Le Roch, Choukri Ben Mamoun
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Optical genome mapping offers a groundbreaking method for studying the human genome with […]

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Customer Testimonial: Ravi Kohle | Optical Genome Mapping Unveils Hidden Structural Variants.

For decades, the field of oncology has heavily relied on traditional investigative methods […]

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Reference(s)
  1. Bayard Q, Cordier P, Péneau C, et al. Structure, dynamics, and Impact of replication stress-induced structural variants in hepatocellular carcinoma. Cancer Res. 2022;82(8):1470-1481. doi:10.1158/0008-5472.CAN-21-3665
  2. Ebert P, Audano PA, Zhu Q, et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science. 2021;372(6537):eabf7117. doi:10.1126/science.abf7117
  3. Chaisson MJP, Sanders AD, Zhao X, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun. 2019;10(1):1784. Published 2019 Apr 16. doi:10.1038/s41467-018-08148-z
  4. Sabatella M, Mantere T, Waanders E, et al. Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors. J Pathol. 2021;255(2):202-211. doi:10.1002/path.5755
  5. Goldrich DY, LaBarge B, Chartrand S, et al. Identification of somatic structural variants in solid tumors by optical genome mapping. J Pers Med. 2021;11(2):142. Published 2021 Feb 18. doi:10.3390/jpm11020142