QuickScan Reviews in Pathology, August 30 2009

Background: Among chromosomal deletions and gains that are prognostically significant in chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), unfavorable 17p deletions are the strongest predictor of outcome. Genetic abnormalities with lesser prognostic significance include del 11q 22.3, trisomy 12, del 13q14, and an additional locus as chromosome 13q34, all of which are routinely assayed by FISH. Comparative genomic hybridization (CGH) of labeled tumor DNA to microarrays, as opposed to metaphase spreads, provides increased resolution, sensitivity, and lab throughput. Objective: To evaluate high-density CGH arrays for characterizing genetic alterations in CLL/SLL. Methods: 100 samples of CLL, including 62 for a pilot study (56 bone marrow; 6 peripheral blood) and 38 subsequent sequential cases (26 bone marrow; 12 peripheral blood) were analyzed by FISH at 11q22.3, 12p11.1-q11, 13q14.3, 13q34, and 17p13.1. Isolated patient and control female DNA were digested and labeled with Cy5-dUTP or Cy3-dUTP, respectively, prior to hybridization to a customized 44,000-probe oligonucleotide array. The array represented human genomic DNA at a resolution of 50 to 75 kb, except for loci known to be abnormal in CLL, for which high density probe tiling produces a resolution of 5 to 11 kb. Results: In the pilot series, 56 cases had array CGH and FISH data for comparison. Among these, there was 93% concordance for del 11q22.3, 92% for trisomy 12, 78% concordance for del 13q14.3, 50% concordance for del LAMP1/13q34, and 72% concordance for del TP53/17p13.1. In the sequential series, among 36 cases with array CGH and FISH data for comparison, there was 89% concordance between array CGH and FISH. There were no false positives by array CGH. Overall, among the 100 samples, array CGH and FISH were 89% concordant. Most discordance (84%) occurred in specimens with <25% CLL cells, which appears to be a limit of array CGH sensitivity. Conclusions: Array based CGH appears to be slightly less sensitive than FISH for characterizing known genetic alterations in CLL but has the theoretical advantage of detecting random genetic abnormalities. Reviewer's Comments: Array based CGH detects only unbalanced genetic changes (chromosomal gain or loss). Balanced genetic changes that characterize many leukemias and lymphomas, such as reciprocal translocations and inversions, are not detected. Therefore, one can predict a role for array based CGH in evaluation of diseases such as myelodysplastic syndromes, but it is unlikely to replace FISH testing for many recurrent leukemias and lymphoma-associated changes. (Reviewer-Guy E. Nichols, MD).