Whole genome sequencing to identify novel, clinically relevant findings missed by standard of care for patients with myelodysplastic syndrome.

Abstract

6570 Background: Genomic analysis is critical for accurate diagnosis and risk stratification for patients with myeloid malignancies. Whole genome sequencing (WGS) has the ability to capture a breadth of alterations and has the potential to complement or replace current genomic profiling techniques. We sought to validate the molecular findings from Tempus xH, a WGS based assay, with standard of care [SOC] results from a major academic institution (MDACC). Methods: We retrospectively sequenced 43 patient samples from MDACC using the Tempus xH WGS assay. SOC data from cytogenetics (karyotype +/- FISH), 81-gene panel sequencing, and/or optical genome mapping OGM (n=10), was regarded as the source of truth. We performed a two-part study: an initial unblinded analysis (n=10) comparing WGS to SOC, followed by a blinded unbiased comparative review (n=33). Clinically relevant alterations were compared between the SOC and xH reportable range workflows. We excluded mutations with <= 10% VAF and filtered copy number alterations (CNAs) < 5Mb, and combined OGM and cytogenetics (10>= metaphases). Structural variants (SVs) were included if they overlapped orthogonal truth or were recurrent myeloid fusions. Results: In the unblinded analysis (n=10), WGS detected 53 clinically reported alterations, yielding 94% sensitivity. Single nucleotide variants (SNVs) had 100% sensitivity, and 18/20 CNA events and 6/7 SVs were detected. The single missed SV event was a derivative chromosome (chr), between chr1 and chr20, identified by cytogenetics with breakpoints over the masked centromere region of the WGS. However, WGS detected CNAs in chr arms of 1 and 20, signalling the event was captured yet not resolved as a derivative chr. Two copy losses on chr 19 (complete loss and p-arm) and an ASXL1 frameshift were detected by WGS but not by SOC. In the blinded study (n=33), WGS detected 143 events, including 124 true positives and no alterations from SOC went undetected by WGS demonstrating 100% sensitivity. WGS identified 24/24 of the CNAs detected by cytogenetics. Among all specimens, 21 novel, high confidence variants were identified in 11 specimens (39%) by WGS that were not detected by SOC; including 14 CNAs, two SNVs, and five SVs, including diagnostically and/or prognostically critical alterations: 2 MECOM rearrangements, 1 KMT2A -PTD, an 11MB deletion in chr 17p ( TP53 locus), and a focal RUNX1 deletion highlighting the potential clinical benefit of WGS. Conclusions: WGS accurately recapitulates results from targeted NGS panels, OGM and cytogenetics and advances our understanding of MDS biology. xH WGS uncovered a significant number of novel, clinically relevant and potentially targetable findings undetected by SOC. WGS provides a complementary view of the genome, identifying actionable and prognostic markers helping clinicians make more informed treatment decisions.