A Year in Review: Parallel Testing of Hematologic Malignancies using Optical Genome Mapping Compared to Conventional Cytogenetics.

The Cancer Cytogenetics Laboratory at the University Health Network (Toronto) started a pilot program nearly one year ago to test the feasibility of replacing karyotyping and FISH assays with Optical Genome Mapping as a front line test. Our goal was to test several different types of hematolgic malignancy and compare the results seen with Optical Genome Mapping (OGM) with conventional cytogenetics (CC). To that end, we tested more than 25 prospective samples referred for our Eosinophilic FISH panel (PDGFRA, PDGFRB and FGFR1 FISH), an additional five samples from the Princess Margaret Tissue Bank and the KG-1 Cell Line (known FGFR1 translocation) were used as positive controls. Our results showed that OGM was concordant to FISH and in some cases more clearly identified complex rearrangements not clearly delineated by FISH. We further tested greater than 40 samples with acute leukemia that showed high concordance between OGM and CC. Additional testing of cases with failed CC showed that OGM was able to generate a result in many cases where CC had failed. Further, OGM was able to identify previously unidentified translocations and structural variations of clinical significance. The era of precision medicine, especially in hematologic malignancies, demands that structural variation analysis be performed at high resolution, cost effectively and with a fast enough turn around time that clinical management decisions can be made. OGM has demonstrated its compatibility as a front line test in public health care setting.