Customized Oligonucleotide Array-based Comparative Genomic Hybridization as a Clinical Assay for Genomic Profiling of Chronic Lymphocytic Leukemia

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Journal of Molecular Diagnostics, doi:10.2353/jmoldx.2009.080037

Customized Oligonucleotide Array-based Comparative Genomic Hybridization as a

Clinical Assay for Genomic Profiling of Chronic Lymphocytic Leukemia

Sargent*, Dan *, Lynne V. Abruzzo*, Hui Yao, Bonderover*,

Marissa Cisneros*, G. Wierda, J. Keating, and Rajyalakshmi

Luthra*@

From the Department of Hematopathology,* the Division of Quantitative Sciences,

and the Department of Leukemia, The University of Texas M. D. Cancer

Center, Houston, Texas

@ To whom correspondence should be addressed. E-mail: rluthra@... .

Abstract

Chromosome gains and losses used for risk stratification in chronic lymphocytic

leukemia (CLL) are commonly assessed by multiprobe fluorescence in situ

hybridization (FISH) studies. We designed and validated a customized

array-comparative genomic hybridization (aCGH) platform as a clinical assay for

CLL genomic profiling. A 60-mer, 44,000-probe oligonucleotide array with a 50-kb

average spatial resolution was augmented with high-density probe tiling at loci

that are frequently aberrant in CLL. Aberrations identified by aCGH were

compared with those identified by a FISH panel, including locus-specific probes

to ATM (11q22.3), the centromeric region of chromosome 12 (12p11.1-q11), D13S319

(13q14.3), LAMP1 (13q34), and TP53 (17p13.1). In 100 CLL samples, aCGH/FISH

concordance was seen for 89% of FISH-called aberrations at the ATM (n = 18),

D13S319 (n = 42), LAMP (n = 12), and TP53 (n = 22) loci and for chromosome 12 (n

= 14). Eighty-four percentage of FISH/aCGH discordant calls were in samples

either at or below the limit of aCGH sensitivity (10% to 25% FISH

aberration-containing cells). Therefore, aCGH profiling is a feasible routine

clinical test with comparable results to multiprobe FISH studies; however, it

may be less sensitive than FISH in cases with low-level aberrations. Further, a

customized array design can provide comprehensive genomic profiling with

additional accuracy in both identifying and defining the extent of small

aberrations at target loci.