Nikhil Sahajpal, Ashis K Mondal, Sudha Ananth, Vamsi Kota, Suzanne Hurley, Alka Chuabey, Alex Hastie, Amyn M Rojiani, Fariboz Rashid-Kolvear, Ravindra Kolhe
Fetal genetic testing by karyotype, FISH and chromosomal microarray analysis (CMA) using cultured amniocytes or chorionic villi (CVS) remain the standard diagnostic tests in pregnancies with suspected fetal anomalies. However, the complete cytogenetic profiling of amniocytes or CVS using these multiple technologies is time consuming, cost-prohibitive, and dependent on the limit of resolution of each technology. Herein, we present two complex amniocentesis cases performed on cultured amniocytes using the Bionano Saphry platform, demonstrating the ability of genome optical mapping (GOM) technology to better characterize and delineate structural variants (SVs) and copy number variations (CNV) originally identified by conventional techniques. In case 1, karyotype analysis identified a dicentric chr15, and a der(21) t(15;21) with the CMA demonstrating a copy number gain on chr15. GOM identified the previously characterized SVs and demonstrated a higher resolution to better define the breakpoints of the SVs and CNVs. GOM was concordant in identifying the dicentric chr15, copy number gain and der (21) t(15;21). Further, the SV events were better resolved by identifying an inversion and fusion on chr15 that explained events on chr15 with better accuracy. The der (21) was identified as a result of the translocation involving chr15 and 21. In case 2, karyotype analysis identified an extra dicentric chromosome 15 and a trisomy 21. CMA had previously detected the copy number gains on chr15 and trisomy 21 but unable to delineate the structural abnormality involving chr 15. GOM, in addition to identifying these events, identified a fold-back inversion on chr15 associated with the copy number gains and was able to accurately decipher the break points of the complex SV. These cases highlight the clinical utility of GOM in genomic characterization of SVs that are difficult to characterize and resolve by conventional techniques, and the potential to replace multiple technologies using this single assay.