Whole-Genome Sequencing of Patients With Myelodysplastic Syndrome Uncovers Novel, Clinically Relevant Biomarkers Missed by Standard-of-Care Methods

Context
Genomic analysis is critical for accurate diagnosis and risk stratification in myeloid malignancies. While standard-of-care (SOC) workflows employ multiple tools, including next-generation sequencing (NGS) panels, cytogenetics, and optical genome mapping (OGM), whole-genome sequencing (WGS) consolidates these in a single assay.

 

Objective
We retrospectively evaluated whether a WGS-based assay could detect both SOC clinical and novel genomic alterations atMDACC.

 

Design
Fifty patient samples were sequenced using the Tempus xH WGS assay. SOC data consisting of karyotyping (±FISH), an 81-gene NGS panel, and/or OGM (n = 10) were the source of truth. Analysis focused on clinically relevant genomic alterations between the SOC and xH reportable range workflows. Exclusions included mutations with ≤10% variant allele frequency (VAF), copy number alterations (CNAs) <5 Mb, and karyotypes with <10 metaphases. Structural variants (SVs) were included if they overlapped with orthogonal truth or were recurrent myeloid fusions.

 

Main Outcome Measures
WGS sensitivity relative to SOC and cryptic findings detected by WGS.

 

Results
WGS identified an average of 5 clinically relevant genomic alterations per sample; overall sensitivity was 98% relative to SOC. Sensitivity was 100% for single-nucleotide variants (SNVs; n = 133), 95.6% for CNAs (65/68), and 90.9% for SVs (10/11). Notably, the WGS assay identified 34 novel, high-confidence variants (26 CNAs, 2 SNVs, and 6 SVs) across 20 specimens (40%) that were undetected by SOC. Retrospective clinical review determined that 14% (7/50) of patients had clinically significant novel findings, including three MECOM rearrangements, del(17p) involving the TP53 locus, KMT2A-PTD, high VAF (48%) ASXL1 mutation, and a large RUNX1 deletion in exon 8—all are associated with poor prognosis in myelodysplastic syndromes. Additional alterations identified by the Tempus xH WGS assay would have changed IPSS-M risk for three patients: high to very high (ASXL1 mutation), moderate-high to high (KMT2A-PTD), and low to moderate-low (MECOM rearrangement).

 

Conclusions
WGS demonstrated high concordance (98% sensitivity) with SOC workflows and detected cryptic clinically relevant alterations in 14% of patients. These data suggest that WGS can aid clinical decision-making by consolidating diagnostic workflows and identifying critical prognostic and therapeutic biomarkers that escape traditional testing limits. ASXL1: ASXL transcriptional regulator 1, FISH: fluorescence in situ hybridization, IPSS-M: Molecular International Prognostic Scoring System, KMT2A-PTD: lysine methyltransferase 2A gene partial tandem duplication, MDACC:MD Anderson Cancer Center, MECOM: myelodysplasia syndrome 1 and ecotropic viral integration site 1 complex locus, RUNX1: RUNX family transcription factor 1, TP53: tumor protein p53.