Utilization of a SNP Microarray for Chronic Lymphocytic Leukemia: Efficacy, Informative Findings and Prognostic Capabilities

      Chronic lymphocytic leukemia is the most common form of adult-onset leukemia in the Western world. A total of 775 patients who were confirmed to have CLL were studied by microarray analysis which has the potential to identify significant genetic alterations that would remain uncharacterized not targeted by the DNA probes utilized in routine FISH analysis. FISH was negative in 21.2% of the patients but 55.4% of this FISH negative group had aberrations by array studies. Array abnormalities were detected in over 90% of the patients. The array revealed genome complexity in ~ 46% of the patients, compared to 9% by FISH analysis. The array analysis revealed genome complexity in 38% of 13q deletion patients suggesting a poorer outcome in this subgroup. Overall, it can be concluded from these studies that: (1) The array is clearly more effective in detecting abnormalities than FISH alone; (2) Although the array may be slightly less sensitive than FISH it could pick up abnormalities present in at least 10% of the cells; (3) The array delineated genome complexity ~90% of the time that FISH did not and was effective in subdividing 13q deletions into two groups; one with a much more likely chance of being an aggressive disease; (4) The array is effective in detecting anomalies such as CN-LOH (in 17.9% of patients) and chromothripsis (1.6%) that could not be delineated by FISH; (5) The whole genome array was effective in detecting a second disorder such as myelodysplasia that would not be seen by FISH.
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