Clinical Evaluation of a Custom Genome Wide 44K Oligoarray for Copy Number Changes in Acute Myeloid Leukemia

Oligonucleotide-based array CGH (aCGH) technique enables detection of submicroscopic copy number changes in cancer. This technique offers the flexibility to

1. increase robustness by selecting best performing probes

2. maximize the gene coverage while excluding repetitive sequences through a combination of bioinformatics and computation and

3. increased resolution that allows for detection of smaller region of change. We designed a high resolution (44,000 probes) custom array using an Agilent platform and specifically targeted ~500 genes implicated in leukemogenesis.

The disease gene regions have an average spatial resolution of ~1 oligo per 7.5 kb whereas the backbone regions have an average resolution of 1 oligo per 78 kb. A total of 13 samples from patients with AML have been studied to date. aCGH was performed in a blinded fashion and the results were compared to the results from routine cytogenetic analysis. A GAIN in copy number on the long arm of chromosome 8 at band 8q22.2 encompassing 2.05 Mb was observed in one of 7 cases with normal chromosome analysis. Of the remaining 6 cases, the results from aCGH were concordant with the abnormality detected by chromosome analysis in three although the size of the copy number change was determined with greater precision by aCGH. Additional copy number changes were observed in the remaining two cases. In one case, in addition to the deletion of 5q14q34 detected by cytogenetic analysis, a loss in copy number on the long arm of 17q at band 17q11.2 encompassing 1.8 Mb including the NF-1 gene was detected by aCGH. Two additional copy number changes in 3q26.1 and 8q24.1 were observed in another case in which monosomy 7 was observed cytogenetically. aCGH failed to detect a clone (2 cells) with a deletion on 5 from band 5p13q13 in one case. In total, 30% of the patients with chromosome analysis displayed an additional cryptic change by aCGH. Our results suggest that a subset of potentially significant genomic alteration may be missed by the conventional chromosome analysis. This pilot study demonstrates that aCGH offers high sensitivity and specificity for routine screening of copy number changes in acute myeloid leukemia.