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Open Access Research article

Large scale copy number variation (CNV) at 14q12 is associated with the presence of genomic abnormalities in neoplasia

Ilan Braude12, Bisera Vukovic23, Mona Prasad2, Paula Marrano2, Stefanie Turley3, Dwayne Barber12, Maria Zielenska14 and Jeremy A Squire12*

Author Affiliations

1 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada

2 The Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Ontario, Canada

3 Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada

4 Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada

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BMC Genomics 2006, 7:138  doi:10.1186/1471-2164-7-138

Published: 6 June 2006

Abstract

Background

Advances made in the area of microarray comparative genomic hybridization (aCGH) have enabled the interrogation of the entire genome at a previously unattainable resolution. This has lead to the discovery of a novel class of alternative entities called large-scale copy number variations (CNVs). These CNVs are often found in regions of closely linked sequence homology called duplicons that are thought to facilitate genomic rearrangements in some classes of neoplasia. Recently, it was proposed that duplicons located near the recurrent translocation break points on chromosomes 9 and 22 in chronic myeloid leukemia (CML) may facilitate this tumor-specific translocation. Furthermore, ~15–20% of CML patients also carry a microdeletion on the derivative 9 chromosome (der(9)) and these patients have a poor prognosis. It has been hypothesised that der(9) deletion patients have increased levels of chromosomal instability.

Results

In this study aCGH was performed and identified a CNV (RP11-125A5, hereafter called CNV14q12) that was present as a genomic gain or loss in 10% of control DNA samples derived from cytogenetically normal individuals. CNV14q12 was the same clone identified by Iafrate et al. as a CNV. Real-time polymerase chain reaction (Q-PCR) was used to determine the relative frequency of this CNV in DNA from a series of 16 CML patients (both with and without a der(9) deletion) together with DNA derived from 36 paediatric solid tumors in comparison to the incidence of CNV in control DNA. CNV14q12 was present in ~50% of both tumor and CML DNA, but was found in 72% of CML bearing a der(9) microdeletion. Chi square analysis found a statistically significant difference (p ≤ 0.001) between the incidence of this CNV in cancer and normal DNA and a slightly increased incidence in CML with deletions in comparison to those CML without a detectable deletion.

Conclusion

The increased incidence of CNV14q12 in tumor samples suggests that either acquired or inherited genomic variation of this new class of variation may be associated with onset or progression of neoplasia.