CYTOGENOMIC PROFILING OF LARGE COHORT OF INDIAN MYELODYSPLASTIC SYNDROMES

Introduction: About 40% - 50% of Myelodysplastic syndromes (MDS) patients present with a normal karyotype whereas 50% - 60% of patients are of low risk, however, they tend to have worse outcomes and a higher chance of disease progression. Hence, we aim to study the genomic pathophysiology of disease and their association with overall survival in MDS. Methods: The study cohort included 200 MDS patients. The molecular cytogenetic and mutation profiling was carried out in all MDS patients. The patients were clinically followed up. The Kaplan-Meier survival and multivariate analysis was performed using GraphPad Prism 5.00 Results: The WHO 2016 classification revealed a high frequency of MDS – MLD (33%) followed by MDS – SLD (25%), MDS – EB-1/2 (24%). The chromosomal aberrations were identified in 35% of MDS patients by CK/FISH. The NGS identified gene mutations in 75% of the cohort. The survival analysis revealed that the mutations in TP53, JAK2/3, KRAS, NRAS, and ASXL1 are significantly (P < 0.05) associated with poor survival. SNP array analysis (n=77), revealed, patients with chromosome 2 aberrations have a poor prognosis. SNP array combined with NGS confirmed the biallelic loss of function of the TP53 gene (3/7), a clinically relevant biomarker and new genetic-based MDS entity i.e. MDS-biTP53 as per the new WHO classification 2022. The univariate and multivariate analysis suggested that genetic lesions (mutations/CNVs/LOH) with IPSS-R could be prognosticating markers in MDS patients. Conclusions: Our study strongly supports that the genome profiling by combined CGH+SNP array and NGS improves prognostication and hence personalized disease management

Three way translocation in a new variant of t(8;21) acute myeloid leukemia involving Xp22

The t(8;21)(q22;q22) is one of the most frequent chromosomal abnormality associated with acute myeloid leukemia (AML) M2 sub type. The additional chromosomal abnormalities including structural and numerical are frequently reported with the translocation, t (8;21)(q22;q22). We report a case of AML-M2 with t(X;8;21)(p22;q22;q22) associated with loss of Y chromosome. Using a dual color fluorescence in situ hybridization (FISH) analysis with ETO and AML1 probes, we demonstrated an ETO/AML1 fusion signal on the derivative chromosome 8 and one ETO signal on derivative Chromosome Xp22. The patient did not respond to therapy and follow-up of cytogenetics revealed same chromosome abnormality. Hence, this three way translocation involving X chromosome might be associated with poor prognosis

Three way translocation in a new variant of t(8;21) acute myeloid leukemia involving Xp22

The t(8;21)(q22;q22) is one of the most frequent chromosomal abnormality associated with acute myeloid leukemia (AML) M2 sub type. The additional chromosomal abnormalities including structural and numerical are frequently reported with the translocation, t (8;21)(q22;q22). We report a case of AML-M2 with t(X;8;21)(p22;q22;q22) associated with loss of Y chromosome. Using a dual color fluorescence in situ hybridization (FISH) analysis with ETO and AML1 probes, we demonstrated an ETO/AML1 fusion signal on the derivative chromosome 8 and one ETO signal on derivative Chromosome Xp22. The patient did not respond to therapy and follow-up of cytogenetics revealed same chromosome abnormality. Hence, this three way translocation involving X chromosome might be associated with poor prognosis

Supplementary Material for: Comprehensive study of chromosomal CNVs and genomic variations predicting overall survival in Myelodysplastic syndromes

Introduction: Myelodysplastic syndrome (MDS) is a heterogeneous disease characterized by cytopenia, marrow dysplasia and has a propensity to develop into acute myeloid leukemia (AML). The disease progression is majorly affected by genetic defects. However, about 40% - 50% of patients with MDS present with a normal karyotype and develop different courses of disease. Hence there remains a room to advance the biological understanding and to find molecular prognostic markers for cytogenetically normal (CN) MDS. Methods: We performed a high-resolution CGH + SNP array along with NGS of 77 primary diagnosed MDS patients and also they were clinically followed up. Results: Our study revealed 82 clinically significant genomic lesions (losses/gains) in 49% of MDS patients. CGH + SNP array reduced the proportion of normal karyotype by 30%. SNP array in combination with NGS confirmed the biallelic loss of function of the TP53 gene (2/6), which is a clinically relevant biomarker and new genetic-based MDS entity i.e. MDS-biTP53 as per the new WHO classification 2022. Genomic region 2p22.3 presented with frequent lesions and also with a more hazard ratio (2.7, 95% CI 0.37 – 21) when analyzed by Kaplan Meier survival analysis. Conclusion: CGH + SNP array changed the cytogenetic and IPSS-R risk group in 18% and 13% of patients respectively with an improved prediction of prognosis. This study emphasizes the cytogenetic heterogeneity of MDS and highlights that abnormality with chromosome 2 may have a diagnostic and prognostic impact