94. Comparison of FISH to whole exome/whole transcriptome detection of relevant structural alterations in Multiple Myeloma

Abstract

In multiple myeloma and monoclonal gammopathies, single nucleotide variants (SNV), copy number variants (CNV) and IGH-rearrangements with prognostic/therapeutic relevance, are assessed by NGS, FISH, and karyotype. Recently, whole exome/transcriptome sequencing (WES/WTS) post CD138+-enrichment has been clinically implemented, thus we evaluated this approach to detect relevant alterations. Over 9 months, 160 aspirates were enriched including assessment of %CD138+ by flow cytometry post-enrichment. Extracted DNA/RNA were sent out for WES/WTS (20% tumor cellularity cut-off). Eighteen were insufficient where DNA yield correlated with WES/WTS success by Welch Two Sample t-test (p<0.001). Of 142 reported, post-enrichment %CD138 correlated with the detection of relevant SNV or CNV (n=97) (p<0.001), and after excluding those only displaying CHIP-associated SNVs (n=11) (p<0.00001). FISH was performed outside on similarly enriched CD138+ cells (collected during same procedure) for 122 cases. While the specificity was ?91%, the sensitivities of detection by WES of gain of 1q, 9, 11, 15 and loss of 1p, 13/13q14, 17p/17, were 70%, 79%, 76%, 79%, and 71%, 67%, 83% respectively. Lack of detection was primarily in cases with FISH-detected gain/loss <20%. For 10 cases with IGH-FGFR3 and 6 with IGH-MAF (by FISH), 9 had detectable IGH-NSD2 and 3 IGH-WWOX fusion transcripts respectively. Thus, WES/WTS is less sensitive than FISH for detection of CNV <20%, but affords the detection of additional relevant abnormalities (4p, 16q loss). Increasing the dataset will afford the establishment of cut-offs for DNA yield and %CD138+ to improve overall diagnostic yield, and for the level of CCND1 transcripts that correlate with IGH-CCND1 rearrangement.