Comparison of a quantitative PCR method with FISH for the assessment of the four aneuploidies commonly evaluated in CLL patients

Abstract

Four chromosomal defects associated with outcome are commonly evaluated by fluorescent in situ hybridization (FISH) in chronic lymphocytic leukemia (CLL), namely deletions of the 13q13-q14, 11q22 and 17p13 regions and trisomy 12. In this study, we compared a quantitative PCR method -quantitative multiplex PCR of short fluorescent fragment (QMPSF) -with FISH for the detection of these acquired aneuploidies in a series of 110 patients with Binet stage A CLL. Genes located in the deleted or gained regions were selected as target genes and amplified using a method based on the simultaneous amplification of short fluorescent genomic fragments under quantitative conditions. A chromosomal imbalance involving one or several of the four loci was detected by either method in 72 patients (65%). A chromosome 13 deletion was present in 61 patients (54%), a 11q22 deletion in nine (8%), a trisomy 12 in nine and a 17p deletion in one. FISH and QMPSF results were identical for 103 out of 110 patients and discrepancies could be explained in most cases. This study demonstrates that a quantitative multiplex PCR represents a cost-effective method that could replace FISH in CLL patients. However, although QMPSF is perfectly adapted to the detection of primary defects, care should be taken when searching for clonal evolutions present in a small proportion of tumor cells.

Recurrent genomic aberrations combined with deletions of various tumour suppressor genes may deregulate the G1/S transition in CD4+CD56+ haematodermic neoplasms and contribute to the aggressiveness of the disease

“…11 Briefly, QMPSF is a sensitive method for the detection of genomic deletions or duplications based on the simultaneous amplification of short genomic fragments using dye-labelled primers under quantitative conditions. PCR products were analysed on an ABI Prism310 genetic analyser in the fragment analysis mode, in which both peak heights and areas are proportional to the quantity of template present for each target sequence.…”

Detection of somatic quantitative genetic alterations by multiplex polymerase chain reaction for the prediction of outcome in diffuse large B-cell lymphomas

“…Using this approach, we demonstrated that TP53 and MDM2 somatic defects could be reliably detected when the proportion of tumoral cells was as low as 20%. 15 In addition, polymorphic gene copy number changes were excluded in some cases using matched non-tumoral DNA as control.…”

“…By contrast, quantitative multiplex polymerase chain reaction of short fluorescent fragments (QMPSF) is an inexpensive and sensitive method for the detection of genomic deletions or duplications based on the simultaneous amplification of short genomic fragments using dye-labeled primers under quantitative conditions. [13][14][15] Using this approach, we determined gain/loss frequencies of several targeted genes and built a biological score able to predict the outcome of DLBCL independently of the International Prognostic Index.…”

Diffuse large B-cell lymphomas with CDKN2A deletion have a distinct gene expression signature and a poor prognosis under R-CHOP treatment: a GELA study

“…11 We previously demonstrated its applicability to the analysis of various hematologic neoplasms, including chronic lymphocytic leukemia (CLL), DLBCL, mantle cell lymphoma (MCL), and CD4 ϩ CD56 ϩ hematodermic neoplasms. [12][13][14][15] We also assessed its prognostic relevance and its feasibility using formalin-fixed paraffin-embedded (FFPE) tissues in MCL. 13 Here, we assess the prognostic value of GCNA (TP53, CDKN2A, REL, BCL2, MYC, and RB1) detected by QMPSF in DLBCL, in a setting of clinical trials based on the use of R-CHOP or R-CHOPlike regimens.…”