Optical Mapping Uncovers Multiple Novel Genomic Structural Variants In Patient Leukemias

Leukemias are a diverse collection of hematopoietic cancers with limited chemotherapeutic treatment options. Patients unsuitable or unable for bone marrow transplantation have a dismal prognosis. Although previous studies have shown that there are only a limited number of potential driver mutations (3-8) per leukemia, there is an extensive heterogeneity of subtypes of disease. Using optical mapping with the Saphyr genome imaging system we confirm what other laboratories have found; that leukemias have additionally approximately 30-70 genomic structural variants per patient. This suggests that these SVs could ascribe the observed heterogeneity and could be responsible for individual pathogenesis of disease. Furthermore, we show that of many these SVs involve genes with functions associated with cellular processes relevant to cancer. Whilst known SVs, such asBCR-ABLtranslocations, are readily detected, multiple novel variants are also uncovered by Saphyr. Here we demonstrate the utility of this technique to uncover potential driver SV events and provide examples of such, some of which are associated with sensitivity and resistance to chemotherapeutics, including the standard of care drug Idarubicin (Idamycin). Finally, optical genome mapping shows 100% concordance with extant cytogenetic analyses, yet with a more streamlined methodology, a greater resolution, and higher sensitivity of detection.