Utility of Oligonucleotide Array Comparative Genomic Hybridization to Identify Cryptic Copy Number Alterations in Myelodysplastic Syndromes

Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematological neoplasms characterized by peripheral cytopenias due to ineffective hematopoiesis and significant cytologic atypia in one or more of the myeloid lineages. There is a variable risk of progression to acute myeloid leukemia, which is dependent on the blast count and certain recurrent cytogenetic abnormalities. Cytogenetic characterization is important in both diagnosis and prognosis, but can be of limited value in lower-risk MDS subtypes because of the low frequency of karyotypic abnormalities detected by chromosome analysis. Recently, array comparative genomic hybridization (aCGH) has been shown to be an important technique in detecting gross and cryptic copy number changes in leukemias. However, there is little data on aCGH application in MDS. We used a custom design 105,000 probe oligonucleotide aCGH platform to analyze 44 bone marrows, in which a diagnosis of MDS was made to determine the clinical utility of oligonucleotide aCGH. All bone marrows were analyzed by morphology, flow cytometry, cytogenetics, and fluorescent in situ hybridization (FISH). Gender matched normal controls were used to assess copy number alterations in MDS samples. We classified significant gains and losses

• as a minimum of 10% deviation from the baseline of at least 10 contiguous oligonucleotide probes spanning at least 1 Mb and

• as not within a previously defined region of copy number polymorphism in the Database of Genomic Variants.

Array CGH was able to detect all cytogenetically identified imbalances present in more than 1 cell, but as expected did not detect any of the balanced translocations or inversions. Of the 24 cases that were cytogenetically normal, 9 (38%) had anomalies detected by aCGH. In 5 (25%) of the 20 cases with at least one cytogenetic abnormality detected previously by chromosome analysis, additional imbalances were identified by aCGH. Recurrent copy number losses detected by aCGH were observed in 13/44 (29.5%) of cases and included 5q21 in 5 cases, chromosome 7 in 2 cases, 12p13 in 3 cases, 13q21-31 in 3 cases, and 20q12-13 in 2 cases. Oligonucleotide aCGH was able to provide extremely high resolution of the boundaries of the gains and losses due to the high oligonucleotide probe density. In 14/44 cases (31.8%), oligonucleotide aCGH provided novel information not provided by conventional cytogenetics and FISH and can be used to precisely define recurrent gains and losses. Our data demonstrates the clinical applicability of oligonucleotide aCGH in the diagnosis of MDS in addition to conventional cytogenetics to detect new cryptic abnormalities which may provide novel targets for therapy.