Comprehensive Workup of Myelodysplastic Syndromes: Comparing Targeted DNA Sequencing, Oligo/SNP Microarray and Higher Dimensional Flow Cytometry.
Authors: Slovak Marilyn L , Hsu Ya-Hsuan , Chen Hseuh-Hua , Wang Yongbao , Mowrey Philip N , Repetti Charles , Ho Albert K , Pan Qiulu , Bansal Ila , Jones Dan 
Published: October 2019

Abstract 2519

The myelodysplastic syndromes (MDS) comprise a heterogeneous group of clonal hematopoietic diseases characterized by ineffective hematopoiesis, cytopenias, and dysplasia in the erythroid, myeloid or megakaryocytic lineages. However, MDS can be difficult to recognize when blasts are not increased. Subtle phenotypic shifts in early MDS can be detected using higher-dimensional flow cytometry, by DNA mutation profiling, or by detection of a range of large and small genomic abnormalities by genome-wide SNP microarray. We compared the diagnostic potential of these 3 modalities in a group of 33 patients >50 years old referred for workup of cytopenia (17 blood, 16 bone marrow aspirate samples). Platforms compared were an oligo/SNP 2.6 million-probe microarray (Cytoscan HD, Affymetrix), a 161-amplicon targeted exome sequencing assay that includes TET2, ASXL1, EZH2, IDH1, IDH2, JAK2, KRAS, and NRAS (Ion Torrent protocol with PCR/product harvesting using Fluidigm Access Array), and flow cytometry using a 6-color, 22-marker panel and an 8-color, 26-marker panel (BD FACS Canto II). Nine patients had increased myeloblasts consistent with MDS (up to 20% in blood or 5%–20% in bone marrow)(Group 1), 23 had cytopenia(s) without increase in blasts (Group 2); an additional patient had a B-cell lymphoma. Group 1 patients all had aberrations detected by at least 1 of the 3 modalities (Table). In Group 2, 1 patient had unequivocal alterations by all 3 methods, 8 by 2 assays, and 6 by 1 assay; the other 9 patients had no unequivocal aberrations (Table). Copy-neutral loss of homozygosity (CN-LOH) of >10 Mb was the sole genomic aberration observed in 3 cases of cytopenia without an increase in blasts (affecting 5q, 7q and 20q), whereas others had losses/gains at chromosomal sites characteristic of MDS [i.e., partial 1q trisomy, del(5q), del(7q), +8, del(13q) and del(20q)].

Genes with mutations detected by sequencing Submicroscopic gene deletions or CN-LOH detected by array Flow cytometry abnormality Group 1: Cytopenia(s) with increased blasts (n=9) ASXL1 (2)  TET2 (1)  KRAS (1)  EZH2 (1)  JAK2 (1) BRAF (3)  EZH2 (3)  FLT3 (2)  TP53 (2)  RPS14 (2)  EPO (2)  ASXL1 (1)  ETV6 (1) Myeloid maturation (9/9)  CD56 expression (5/9) Group 2: Cytopenia(s) without increased blasts (n=24) TET2 (4)  ASXL1 (2)  KRAS (2)  IDH2 (1) BRAF (2)  EZH2 (2)  TET2 (2)  ASXL1 (1)  ETV6 (1)  RPS14 (1)  EPO (1)  TP53 (1) Myeloid maturation (9/24)  CD56 expression (1/24)

Among older MDS patients with cytopenias(s) but no increase in blasts, phenotypic and genomic profiling can frequently identify aberrations similar to those seen in higher-grade MDS. Locations of some submicroscopic deletions included loci commonly implicated in MDS pathogenesis. Detection of these aberrations in peripheral blood should facilitate the diagnosis of early MDS.

Disclosures:

No relevant conflicts of interest to declare.