11. Utilization of multimodality testing data to develop an optimal diagnostic algorithm for pediatric leukemia

Abstract

Chromosomal microarrays (CMA) and next generation sequencing (NGS) panels are increasingly used as a complement to karyotyping and FISH for diagnostic evaluation of oncology samples. To determine which combination of assays provides the highest diagnostic yield in pediatric leukemias, we tested 56 consecutive newly diagnosed AML (n = 16) and B-ALL (n = 40) cases by karyotyping, FISH, CMA and our OncoKidsSM NGS panel. OncoKidsSM is a DNA -and RNA-based ampliseq pediatric cancer panel designed to detect sequence variants and RNA fusions. In B-ALL, the FISH panel had the highest overall yield since it detects the most common alterations in pediatric patients, hyperdiploidy and ETV6-RUNX1 fusions. However, the highest overall detection of both primary drivers and secondary clinically significant variants was achieved by combined use of CMA and OncoKids. These assays detected all alterations identified by cytogenetics and FISH, but also revealed primary abnormalities in five cytogenetically normal cases. In AML, OncoKids had the highest yield for detection of both primary and secondary oncogenic mutations. All of the abnormal fusions revealed by karyotype and FISH were detected; we identified three fusions missed by conventional cytogenetics (NPM-MLF1, CBFA2T3-GLIS2 and KMT2A-MLLT3), and found clinically significant sequence changes in WT1, FLT3, NRAS, KRAS and TP53. Our preliminary data justifies using a FISH panel as the initial screening method in B-ALL, and suggests that OncoKids represents a superior alternative to karyotyping as the first line test in pediatric AML. Analysis of additional cases will allow our laboratory to develop and implement optimized genetic testing algorithms for pediatric leukemias.