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

Kathryn A Kolquist,Caitlin Valentin,Steve Byerly,Sara Minier,Raymond R Tubbs,Theresa C Brown,Marilyn L Slovak,Roger A Schultz,Lisa D Mcdaniel,Nicholas J Neill,Trilochan Sahoo,Blake C Ballif,Lisa G Shaffer,Karl S Theil,James R Cook,S Annie Morton,Victoria Cawich

doi:10.1186/1755-8166-4-25

Abstract

BackgroundCytogenetic 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).ResultsUsing 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.ConclusionsOur 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.

Highlights

Cytogenetic evaluation is a key component of the diagnosis and prognosis of chronic lymphocytic leukemia (CLL)
In a novel approach as compared to these previous array studies, we developed a 135K-feature oligonucleotide-based microarray targeted to more than 1800 cancer genes and regions and evaluated 34 patients diagnosed with CLL to compare the performance of this array to that of chromosome analysis and fluorescence in situ hybridization (FISH)
We tested 34 samples, which had been previously assessed by routine chromosome analysis and/or FISH, on a CGH-based microarray designed for detecting copy gains and losses associated with leukemia and lymphoma

Summary

Introduction

Cytogenetic evaluation is a key component of the diagnosis and prognosis of chronic lymphocytic leukemia (CLL). The diagnosis of CLL is made using histopathology; flow cytometry with a typical pattern of coexpression of CD5, CD23, CD20(dim), and surface Ig (dim); and chromosomal abnormalities detected by fluorescence in situ hybridization (FISH) probes and karyotyping. Conventional cytogenetics with karyotyping requires the use of an immunostimulatory CpG-oligodinucleotide DSP 30 plus IL-2 cocktail to enhance the yield of detectable chromosome aberrations in CLL cells. This cell culturing process is costly, time consuming, and requires the clinical indication of CLL at sample submission. FISH has been used to detect specific prognostic chromosome markers in CLL using a panel of five to six probes. Most anomalies detected by cytogenetics in CLL are copy number gains and losses; translocations are rarely identified [2]

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Discussion

Conclusion