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32. Clinical utility and feasibility of adopting optical genome mapping for chromosomal characterization of solid tumors

Cancer Genetics 2022
Sahajpal NS, et al.

Nikhil Sahajpal, Ashis Mondal, Sudha Ananth, Colin Williams, Alex Hastie, Alka Chuabey, Amyn Rojiani, Ravindra Kolhe Bionano’s optical genome mapping (OGM) technology is an emerging alternative to karyotyping, FISH and chromosomal microarray (CMA) for the characterization of chromosomal abnormalities. Recent reports have demonstrated the clinical utility of OGM in heme malignancies and constitutional cases. The present study was aimed at evaluating the clinical performance and feasibility of adopting OGM for chromosomal characterization of solid tumors. This study evaluated solid tumor (n=15) cases previously characterized by CMA. The samples were blinded for OGM analyses and clinically relevant SVs and CNVs were reported using in-built filteration criterias and phenotype specific target list. OGM data was not only 100% concordant with CMA in identifying previously characterized SVs, but identified additional clinically relevant abberations and demonstrated a higher resolution and sensitivity to accurately define SVs w.r.t size and location. The following variant types were validated: deletions, duplications, and CNVs, with additional insertions, inversion, and translocations identified with OGM. OGM identified several clinically relevant SVs: t(3;19) disrupting the DNMT1 gene in a case of utrine cancer, a nested deletion impacting CDKN2A gene that resulted in an unbalanced t(1:9) in a case of glioblastoma, chromothrypsis of chromosome 8 identified in 2 additional cases of gliobastoma, which are beyond the detection capabilities of CMA. We contend that this approach of obtaining high-resolution genomic data at reduced cost can be incorporated in the laboratory workflow and will facilitate precise diagnosis and better prognostication of malignancies, which was not previously possible.

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