SAN DIEGO, Calif. — Bionano Genomics, Inc. (Nasdaq: BNGO) today announced the publication of a study in Cancers from The University of Texas MD Anderson Cancer Center showing how optical genome mapping (OGM) can address key limitations of targeted RNA-sequencing (RNA-seq) panels in detecting therapeutically-relevant gene rearrangements in acute leukemias. This peer-reviewed publication, entitled “Comparative Analysis of Targeted RNA-Seq and Optical Genome Mapping for Detecting Gene Rearrangements in Acute Leukemia,” is the first to describe the comparison of OGM and RNA-seq in cancer.
While RNA-seq panels are useful for detecting expressed variants, including chimeric transcripts, they have limitations. For example, when rearrangements lead to overexpression of a gene under a hijacked enhancer or when fusion transcripts are absent or poorly expressed, RNA-seq analysis may yield false-negative results. OGM complements RNA-seq with its ability to detect structural variants (SVs) at the DNA level that RNA-seq may fail to detect, including cryptic rearrangements, fusion genes, enhancer-hijackings, and large‐scale events more commonly identified with legacy cytogenetic techniques.
Summary of Key Findings
- A total of 234 gene rearrangements or fusions were detected by OGM and/or RNA-seq across 206 subjects (43.6%) in a cohort of 467 acute leukemia research subjects. This rate varied across different leukemia types, from 36.1% in acute myelogenous leukemia (AML) to 75% in T-cell acute lymphoblastic leukemia (T-ALL)
- 175 of the 234 gene rearrangements or fusions (74.7%) were detected by both OGM and the targeted RNA-seq panel
- OGM uniquely identified 37 events (15.8%) of varying complexity, whereas the RNA-seq panel uniquely identified 22 events (9.4%), mostly small gene insertions and intrachromosomal deletions
- Tier 1 aberrations, which are classified as those having well-established prognostic, diagnostic, or therapeutic relevance according to guidelines set by medical societies such as WHO, NCCN and ICC, were found by OGM and/or RNA-seq in 147 of the 467 subjects (31.5%)
- RNA-seq detected just 20.6% of the enhancer-hijacking events detected by OGM. Gene rearrangements or fusions in this class, such as MECOM, BCL11B and IGH rearrangements, can be important to reliably detect since they are known to be drivers of leukemogenesis
Overall, this study from The University of Texas MD Anderson Cancer Center showed that OGM can identify a higher proportion of clinically significant SVs compared to a 108-gene targeted RNA-seq panel. Using OGM and RNA-seq together on the same cohort would yield the most comprehensive result in acute leukemia cases.
“This study is a great representation of how the utility of OGM is continuing to expand,” said Erik Holmlin, PhD, president and CEO of Bionano. “With this comparison against RNA-seq, we believe OGM is growing its footprint in digital pathology where it is imperative to use tools that reveal the complete architecture of the cancer genome and capture cryptic events that other technologies miss. The combination of OGM and RNA-seq can deliver the most comprehensive analysis of genome to potentially impact disease classification, risk stratification, and therapeutic selection.”
The full research publication, Comparative Analysis of Targeted RNA-Seq and Optical Genome Mapping for Detecting Gene Rearrangements in Acute Leukemia, is available at: https://www.mdpi.com/2072-6694/17/21/3458.
About Bionano Genomics
Bionano is a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. The Company’s mission is to transform the way the world sees the genome through optical genome mapping (OGM) solutions, diagnostic services and software. The Company offers OGM solutions for applications across basic, translational and clinical research. The Company also offers an industry-leading, platform-agnostic genome analysis software solution, and nucleic acid extraction and purification solutions using proprietary isotachophoresis (ITP) technology. Through its Lineagen, Inc. d/b/a Bionano Laboratories business, the Company also offers OGM-based diagnostic testing services.
For more information, visit www.bionano.com or www.bionanolaboratories.com.
Bionano’s products are for research use only and not for use in diagnostic procedures.
Company Contact
Erik Holmlin, CEO
Bionano Genomics, Inc.
+1 (858) 888-7610
[email protected]
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Gilmartin Group
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