Utilization of a SNP Microarray for the Detection and Delineation of Chromosomal Changes In CLL Patients: the Efficacy of Implementing New Technology to An Old Question

Abstract 2763

Chronic Lymphocytic leukemia is the most common form of adult-onset leukemia in the Western world and the preferred method of analysis is to utilize fluorescence in-situ hybridization (FISH) utilizing probes to detect deletions of 11q, 13q and 17p, as well as trisomy 12 and Cyclin D1/IGH fusion. This FISH panel analysis revealed a positive clone in approximately 64% of the samples sent in for analysis.

The promise of microarray analysis of CLL clones is the 100x resolution power compared to routine chromosome analysis (only partially effective in detecting clones in 3–5 day mitogen cultures) in identifying significant clonal genetic alterations or compared to the limited DNA probe targets utilized in routine FISH analysis. In order to validate microarray analysis and verify the utility for studying CLL, we have examined the DNA from112 patients, including those with either normal or abnormal results in chromosome analysis and/or FISH using the Affymetrix SNP 6.0 microarray.

The studies have yielded a number of interesting and important findings including: (1) Of the 20 normal cases; 1 abnormality was detected by the array analysis; (2) Of the cases with abnormalities detected by FISH, 49 of 92 (52.3%) had an additional finding that could be delineated by array. (3) Those with 1 abnormality, seen in less than 20% of nuclei, had a 33% chance of having a second array abnormality; those with an abnormality in more than 20% of the cells had ∼50% chance of having a second array abnormality; (4) If the single abnormality was a 11q−, 17p− or +12, the individual had a higher chance of having a second abnormality (60-80%), than if the abnormality was a 13q− (∼43% chance of having a second abnormality); (5) Twelve cases had 4 or more additional abnormalities and of these 12 cases 5 had a massive number (>10), most of which involved a deletion of 17p detected by FISH, consistent with the poor prognosis associated with P53 deletions; (6) Of the 49 cases that had additional abnormalities, there were a total of 184 abnormalities not detected by FISH. There are about 18 different alterations that have been seen in multiple patients, including deletions of P16, DCC, MYLB and duplication of MYC; (7) The 13q and 11q deletions were very heterogeneous with each deletion having a different proximal and distal breakpoint. Approximately 1/3 of the 13q deletions included Rb1and all included mir15/16; (8) The 17p deletions all included P53 and 11/12 were terminal deletions; (8) The value of a genotyping array was underscored by delineation of five cases (5.4%) with segmental UPD in the abnormal group. [UPD9q, UPD11q, UPD11q, UPD13q and UPD16q]. In three of these there was also a deletion within the chromosome involved in the UPD; (9) The array could detect every abnormality detected by FISH which was present in at least 16.5% of the cells and about half of the abnormalities present in 5–16.5% of the cells; (10) Based on our rate of detection and pattern of ascertainment, we estimate that only 2.1% of CLL clones will be missed because of low level disease, whereas 32% of cases will have additional abnormalities are detected. These studies clearly show the advantages of genotyping array analysis in the study and staging of patients with CLL.