Abstract
Myeloid and lymphoid malignancies consist of a heterogenous population of neoplasms, all of which contain distinct genomic alterations used for prognostic, diagnostic, and therapeutic intervention strategies. To clinically evaluate all hematological malignancies using a single test in our laboratory, we have developed a Next-Generation Sequencing assay (NGS) (the PanHeme Assay) that identifies clinically relevant SNV, INDEL (including FLT3-ITDs), CNV, and Fusion mutations known to be important across all myeloid and lymphoid cancers. The PanHeme Assay consists of 358 full coding DNA genes, 125 RNA-based fusions genes, as well as a genome-wide SNP backbone for calling chromosomal copy number changes. This comprehensive assay allows for a single automated laboratory and bioinformatics solution reducing sample-to-report turnaround time to <3 days.
Since the integration of this clinical assay, >4,000 unique patients with >6,000 unique tests have been performed leading to >46,000 NGS-based mutations identified. This large reservoir of data includes SNV, INDEL, FLT3-ITD, full chromosome, arm, and gene level gains and losses, as well as clinically relevant fusions, including IGH enhancer driven modifications across all hematological malignancies.
This large cohort of data has allowed us to focus on several intriguing questions related to hematological testing, progression, stratification of disease and monitoring. To this end we have focused on interpreting the role mutations associated with Clonal Hematopoiesis of Indeterminate Potential (CHIP) have as a reservoir of potential for cancer progression and relapse. Furthermore, we have investigated the concordance of mutation calling between blood and bone marrow biopsies taken within close proximity within the same patient to better understand the need for invasive BM biopsy procedures and how this can further relate to serial monitoring of disease at future timepoints. Beyond these evaluations we have also focused on the ability of this comprehensive assay, which contains classical mutational profiling as well as molecular cytogenomics capabilities, to show that using CNV and mutation calls derived from the PanHeme assay coupled to hematologic data accurately recapitulate IPSS-M risk stratification and predicts survival in MDS without the need of classical cytogenetics. The final investigation of this clinical data set was to assess the most prevalent mutations identified in AML outside of FLT3-ITDs and NPM1 mutations to help us to develop a comprehensive MRD panel which would cover a larger set of AML patients than current testing modalities. By investigating common mutations within this cohort we can create a small “hotspot” panel to concisely target recurrent mutations in AML patients for serial monitoring, which will be further developed into a clinical MRD assay within our lab.
The PanHeme assay has become absolutely necessary for prognostication, diagnosis, and therapy selection within our clinics due to its robust content and extremely fast turn-around time from sample-to-clinical reporting. Beyond this, the assay has also created a large data cohort which can be utilized to address key concepts in the myeloid and lymphoid diseases. This data set has become paramount and has opened up interesting channels around diagnosis, risk stratification, monitoring, and evolution of disease.
