ALBERT

Description: Background: Metaphase cytogenetics (MC), which has an important diagnostic, prognostic and therapeutic roles in myelodysplastic syndrome (MDS), is widely used as cytogenetic analyzing tools. It can present entire cytogenetic information at one time, although with some limitations such as Hypocellularity, fewer mitotic cells, secondary myelofibrosis and technicians' subjectivity. Single nucleotide polymorphism(SNP)array based karyotyping ( SNP-A based karyotyping) is a novel diagnostic tool which can detect copy number variations with a high resolution. More importantly, SNP-based array has a unique advantage in detection of loss of heterozygosity, also referred as to uniparental disomy (UPD), which results from duplication of a paternal (unimaternal) or maternal (unipaternal) chromosomal region and concurrent loss of the other allele. However the technology is still relatively expensive, and balanced structural METHOD: We analyzed SNP-A results from 127 patients diagnosed of MDS or MDS related myeloid malignancies(including 6 MDS/MPN, 11 acute myeloid leukemia from MDS, and 110 MDS). 122 patients of them had both MC and SNP-A results. We compared the frequency and diagnostic sensitivity between the cytogenetic aberration findings by MC and genomic alteration findings by SNP-A. In addition, we investigated the novel or additional lesions detected by SNP-A which had not been found by MC, and find further information about the edges of SNP-A. We drew attention to the missing matters of SNP-A which mentioned in MC reports to integrate the limits of SNP-A. We also used multiple-factor analysis to find out the specific situation which MC are not inferior to SNP-A. RESULTS: There are 199 genomic alteration findings in 127 patients by SNP-A ( including 43 UPDs, 57 gain alterations, 86 loss alterations and 13 complicated alterations). The average length of genomic alterations found by SNP-A is 27795.71Kb, the longest one is GainMosaic(1) (248375kb), the shortest is a UPD found in 17q (41.88Kb). In the 122 patients who had both MC and SNP-A results, SNP-A turns to be more effective than MC in significant chromosomal defects(58.2% vs 36.9%,P