Correlation between the Integrated MDS Flow Cytometry Score and Genomic Abnormalities - a Single Centre Analysis from King's College Hospital
Authors: Wood Henry , Jamieson Lauren , Manogaran Charles , Jones Katy , Kong Kar Lok , Goodwin Josephine , Best Steve , Mohamedali Azim , Kizilors Aytug , Lea Nicholas C , Thorn Zoe , Aldridge Frances , Barnea Slonim Liron , Hardefeldt Prudence , Hannah Guy , Kassam Shireen , Yallop Deborah , Kulasekararaj Austin G. 
Published: December 2024

Myelodysplastic syndromes (MDS) are diagnosed based on peripheral cytopenias, morphological dysplasia and recurrent genomic abnormalities. Gene variants are found in approximately 90% of cases and cytogenetic abnormalities in 50% (Arber et al, 2022). Genomic abnormalities are key to diagnosis and prognosis (Bernard et al, 2022).

The European Leukemia Net international MDS flow cytometry working group has recommended an integrated flow cytometry score (iFS) to support diagnosis of MDS (Oelshlaegel et al 2021; van de Loosdrecht et al, 2021). The score identifies three categories based on the number of MDS related changes: A (unlikely to be MDS), B (possible MDS), or C (consistent with MDS).

The iFS was adopted in the hematological malignancies diagnostic service at King's College Hospital from 2019. In order to understand the relationship between iFS and genomic abnormalities, we have assessed the results of these tests performed between 2019 and 2022.

An iFS category was assigned to 1734 samples during this period. In 1411 cases, results were available from a next generation sequencing myeloid gene panel (MGP; 1142 cases) and/or single nucleotide polymorphism array (SNP-A) karyotyping (974 cases) performed on the same sample or another within +/-14 days. Results of testing by both modalities were available for 705 cases.

Of the 1411 cases, 463 were assigned to iFS category A, 531 to category B, and 420 to category C. The availability of MGP and SNP-A results was evenly distributed between the iFS categories.

In cases for which both MGP and SNP-A were performed, normal results were seen in 64.5% of category A, 37.3% of category B and 18.0% of category C.

Variants of clinical significance were identified by the MGP in 540/1142 (47.3%) cases tested - 80/371 (21.6%) in category A, 201/427 (47.1%) in category B, and 259/344 (75.3%) in category C. Median number of genes with variants was 0 in categories A/B and 2 in category C (range 0-6 for all categories).

SNP-A abnormalities were identified in 349/974 (35.8%) cases tested - 62/308 (20.1%) in category A, 139/374 (37.2%) in category B, and 148/292 (50.7%) in category C.

From the diagnostic perspective, variants in SF3B1 were found in 6.6% of the whole cohort tested (category A: 5.9%, category B: 6.6%, category C: 7.3%), biallelic TP53 abnormalities in 3.2% (category A: 0%, category B: 0.7%, category C: 6.3%), -7 in 0.6% (category A: 0%, category B: 0%, category C: 2.1%), del(7q) in 1.6% (category A: 0.3%, category B: 1.3%, category C: 3.4%), and del(5q) in 1.8% (category A: 0.3%, category B: 1.6%, category C: 3.8%).

Additional results relevant to the molecular international prognostic scoring system (IPSS-M) include variants in FLT3 in 0.1% (category A: 0%, category B: 0%, category C: 0.3%), SF3B1 with isolated del(5q) in 0.1% (category A: 0%, category B: 0.4%, category C: 0%), NPM1 in 0.5% (category A: 0%, category B: 0.2%, category C: 1.5%), RUNX1 in 5.3% (category A: 1.1%, category B: 3.0%, category C: 12.5%), NRAS in 1.8% (category A: 0%, category B: 1.4%, category C: 4.4%), ETV6 in 0.4% (category A: 0%, category B: 0%, category C: 1.2%), IDH2 in 2.0% (category A: 0.8%, category B: 2.1%, category C: 3.2%), CBL in 2.1% (category A: 0.5%, category B: 0.7%, category C: 5.5%), EZH2 in 2.6% (category A: 0.3%, category B: 1.2%, category C: 7.0%), U2AF1 in 3.2% (category A: 0%, category B: 2.6%, category C: 7.6%), SRSF2 in 13.1% (category A: 2.4%, category B: 11.5%, category C: 26.7%), DNMT3A in 7.6% (category A: 4.9%, category B: 7.5%, category C: 10.8%), ASXL1 in 12.1% (category A: 3.5%, category B: 7.7%, category C: 26.7%), KRAS in 1.5% (category A: 0.5%, category B: 1.6%, category C: 2.3%), isolated SF3B1 in 6.3% (category A: 7.8%, category B: 7.4%, category C: 3.6%), one variant from the residual gene list in 9.0% (category A: 2.2%, category B: 8.0%, category C: 18.3%), and two variants in 0.6% (category A: 0%, category B: 0.2%, category C: 1.7%).

Our data show a clear association between MDS iFS and recurrent genomic abnormalities. Interestingly, many of these abnormalities are present throughout the iFS categories, but increase in frequency from A to C (notable exceptions include isolated variants in SF3B1 and -Y). The iFS may therefore identify a scale of clonal haematopoiesis. Further work is required to create a more comprehensive picture of genomic abnormalities in each iFS category and to correlate these with morphology, peripheral counts and patient outcomes.