Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis

Abstract

Background: Cytogenetic evaluation is a key component of the diagnosis and prognosis of chronic lymphocytic leukemia (CLL). We performed oligonucleotide-based comparative genomic hybridization microarray analysis on 34 samples with CLL and known abnormal karyotypes previously determined by cytogenetics and/or fluorescence in situ hybridization (FISH).

Results: Using a custom designed microarray that targets >1800 genes involved in hematologic disease and other malignancies, we identified additional cryptic aberrations and novel findings in 59% of cases. These included gains and losses of genes associated with cell cycle regulation, apoptosis and susceptibility loci on 3p21.31, 5q35.2q35.3, 10q23.31q23.33, 11q22.3, and 22q11.23.

Conclusions: Our results show that microarray analysis will detect known aberrations, including microscopic and cryptic alterations. In addition, novel genomic changes will be uncovered that may become important prognostic predictors or treatment targets for CLL in the future.

Figure 1

Microdeletions of 13q14.3 detected by microarray analysis. (A) Green bars represent deletion sizes for each case (based on UCSC 2006 hg18 assembly). Cases 3, 10 and 13 had biallelic deletions, represented by navy blue bars. Red boxes represent genes of interest in the interval. (B) Microarray results for case 3. Microarray analysis showed biallelic deletion of MIR15A/MIR16-1, DLEU2, and DLEU1 (shaded in dark blue) and monoallelic deletion of RB1 (shaded in light blue). Probes are ordered on the x-axis according to physical mapping positions, with the most proximal 13q probes on the left and the most distal 13q probes on the right. Values along the y-axis represent log₂ ratios of patient:control signal intensities. Results are visualized using Oncoglyphix (Signature Genomics).

Figure 2

Microarray results for six cases (cases 1, 3, 14, 20, 30 and 33) with a biallelic deletion at 22q11.23 of 49 to 56 kb that includes GSTT1. Probes are ordered on the x-axis according to physical mapping positions, with the most proximal 22q probes on the left and the most distal 22q probes on the right. Values along the y-axis represent log₂ ratios of patient:control signal intensities. Results are visualized using Oncoglyphix (Signature Genomics).

Figure 3

Novel aberrations by microarray. (A) Microarray results for case 11 showing a 3.6-Mb gain (shaded in pink) encompassing 5q35.2q35.3 that includes CDHR2, a tumor suppressor candidate. Probes are ordered on the x-axis according to physical mapping positions, with the most proximal 5q probes on the left and the most distal 5q probes on the right. (B) Microarray results for case 17 showing a 4.8-Mb deletion (shaded in blue) at 10q23.31q23.33 that includes MIR107 and FAS. Probes are ordered on the x-axis according to physical mapping positions, with the most proximal 10q probes on the left and the most distal 10q probes on the right. (C) Microarray results for cases 25 and 32 with deletions (shaded in blue) of 3p21.31 that include CDC25A. Case 25 has a 2.2-Mb deletion, and case 32 has a 3.1-Mb deletion. CDC25A is required for progression from G1 to S phase in the cell cycle. Probes are ordered on the x-axis according to physical mapping positions, with the most distal 3p probes on the left and the most proximal 3p probes on the right. For A–C, values along the y-axis represent log₂ ratios of patient:control signal intensities. Results are visualized using Oncoglyphix (Signature Genomics).