Myeloma Genome Project Panel is a Comprehensive Targeted Genomics Panel for Molecular Profiling of Patients with Multiple Myeloma
Parvathi Sudha, Aarif Ahsan, Cody Ashby, Tasneem Kausar, Akhil Khera, Mohammad H. Kazeroun, Chih-Chao Hsu, Lin Wang, Evelyn Fitzsimons, Outi Salminen, Patrick Blaney, Magdalena Czader, Jonathan Williams, Mohammad I. Abu Zaid, Naser Ansari-Pour, Kwee L. Yong, Frits van Rhee, William E. Pierceall, Gareth J. Morgan, Erin Flynt, Sarah Gooding, Rafat Abonour, Karthik Ramasamy, Anjan Thakurta, Brian A. Walker
Abstract
PURPOSE: We designed a comprehensive multiple myeloma targeted sequencing panel to identify common genomic abnormalities in a single assay and validated it against known standards. EXPERIMENTAL DESIGN: The panel comprised 228 genes/exons for mutations, 6 regions for translocations, and 56 regions for copy number abnormalities (CNA). Toward panel validation, targeted sequencing was conducted on 233 patient samples and further validated using clinical FISH (translocations), multiplex ligation probe analysis (MLPA; CNAs), whole-genome sequencing (WGS; CNAs, mutations, translocations), or droplet digital PCR (ddPCR) of known standards (mutations). RESULTS: Canonical immunoglobulin heavy chain translocations were detected in 43.2% of patients by sequencing, and aligned with FISH except for 1 patient. CNAs determined by sequencing and MLPA for 22 regions were comparable in 103 samples and concordance between platforms was R2 = 0.969. Variant allele frequency (VAF) for 74 mutations were compared between sequencing and ddPCR with concordance of R2 = 0.9849. CONCLUSIONS: In summary, we have developed a targeted sequencing panel that is as robust or superior to FISH and WGS. This molecular panel is cost-effective, comprehensive, clinically actionable, and can be routinely deployed to assist risk stratification at diagnosis or posttreatment to guide sequencing of therapies.