Study Finds the Combination of Optical Genome Mapping and Short-Read Sequencing Provides a Comprehensive Genome Analysis for Lung Cancer Samples and Enables the Discovery of New Biomarkers
Non-small cell lung carcinoma (NSCLC) is the leading cause of cancer-related death worldwide. Genomic structural variations (SVs), including large indels, inversions, duplications, and translocations, are essential causes of alterations in gene expression and are recognized as hallmarks in tumorigenesis. In this study, recurrently SV-disrupted genes were significantly enriched in cancer-related pathways highlighting the importance of OGM for detecting all classes of SVs. This study utilized short-read NGS and Bionano’s OGM to obtain high-technical-confidence somatic SVs to investigate candidate oncogenes in cancer patients. An essential role of high-technical-confidence somatic SVs guided the identification of two new oncogenes (TRIO and SESTD1) in NSCLC.
The authors of this study, Xia et al., claim that NGS and OGM are complementary techniques in oncogene discovery and translational research applications since all somatic variants from 1bp and above can be identified. In addition, the identification of SVs via NGS alone remains challenging because of the nature of the short reads generated by this method. The authors expect to be able to identify more high-technical-confidence SVs and determine more candidate oncogenes of NSCLC or other tumors by using this approach of combining NGS and OGM. The utilization of these two techniques would make them able to more comprehensively quantify the contribution of somatic SVs in cancer as compared to short-read NGS alone.
In addition, the authors confirmed that deletions and inversions have bidirectional influences on gene expression. The analysis by Xia et al., suggests that this bidirectional influence might be the result of independent effects of SVs and open peaks on gene expression. This finding reinforces the importance in being able to accurately detect inversions, which are difficult to detect with NGS but a strength of Bionano’s OGM technique on the Saphyr® system.
“We believe the combination of NGS and OGM is currently the most comprehensive and cost-effective analysis of the cancer genome,” commented
This publication is available at https://www.sciencedirect.com/science/article/pii/S2211124721011049
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Bionano is a genome analysis company providing tools and services based on its Saphyr® system to scientists and clinicians conducting genetic research and patient testing; it also provides diagnostic testing for those with autism spectrum disorder (ASD) and other neurodevelopmental disabilities through its
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Source: Bionano Genomics