Karyotypic analysis provides useful diagnostic and prognostic information for many hematological malignancies.Single nucleotide polymorphism array(SNP-A)technique has gained more popularity due to its superb resolution than metaphase cytogenetics(MC)methods.Our study aimed at evaluating the value of SNP-A analysis on the diagnosis and prognosis of Chinese patients with myelodysplastic syndromes(MDS).416 cases were recruited from two medical centers in China.SNP-A analysis leaded to a significantly higher detection yield of chromosome abnormalities than MC methods.Notably,20 of 62 ICUS patients had abnormal detections by SNP-A,and 17 of 20 with abnormal SNP-A detections transformed to typical MDS with a median follow-up time at 11 months.Prognosis of the MDS patients with abnormal SNP-A detections was significantly worse than those without abnormal observations in overall survival(OS)(P=0.004)and progression free survival(PFS)(P=0.002).Furthermore,in the group of patients with low-risk MDS,the patients with SNP-A abnormalities showed significantly inferior survival than those without abnormal detections in OS(P=0.001)and PFS(P=0.008).SNP-A analysis can help significantly improve the diagnosis and better evaluate the prognosis of patients with MDS,and help better assess the risk of MDS transformation in patients with ICUS.