Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data.

Gaëlle Marenne 1, 2 Francisco Real 1, 3 Nathaniel Rothman 4 Benjamin Rodríguez-Santiago 1, 5 Luis Pérez-Jurado 1, 6, 7 Manolis Kogevinas 8, 9, 10, 11 Montse García-Closas 1 Debra Silverman 1 Stephen Chanock 1 Emmanuelle Génin 2 Núria Malats 1, *
* Auteur correspondant
1 CNIO - Spanish National Cancer Research Center
2 Variabilité Génétique et Maladies Humaines
3 Departament de Ciències Experimentals i de la Salut
4 Division of Cancer Epidemiology and Genetics
5 CIBERER - Centro de Investigación Biomédica en Red de Enfermedades Raras
6 Programa de Medicina Molecular i Genètica
7 GS - Department of Genome Sciences [Seattle]
8 IMIM-Hospital del Mar
9 CREAL - Center for Research in Environmental Epidemiology
10 CIBERESP - Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública
11 Epidemiology
Abstract : ABSTRACT: BACKGROUND: Structural variations such as copy number variants (CNV) influence the expression of different phenotypic traits. Algorithms to identify CNVs through SNP-array platforms are available. The ability to evaluate well-characterized CNVs such as GSTM1 (1p13.3) deletion provides an important opportunity to assess their performance. RESULTS: 773 cases and 759 controls from the SBC/EPICURO Study were genotyped in the GSTM1 region using TaqMan, Multiplex Ligation-dependent Probe Amplification (MLPA), and Illumina Infinium 1M SNP-array platforms. CNV callings provided by TaqMan and MLPA were highly concordant and replicated the association between GSTM1 and bladder cancer. This was not the case when CNVs were called using Illumina 1M data through available algorithms since no deletion was detected across the study samples. In contrast, when the Log R Ratio (LRR) was used as a continuous measure for the 5 probes contained in this locus, we were able to detect their association with bladder cancer using simple regression models or more sophisticated methods such as the ones implemented in the CNVtools package. CONCLUSIONS: This study highlights an important limitation in the CNV calling from SNP-array data in regions of common aberrations and suggests that there may be added advantage for using LRR as a continuous measure in association tests rather than relying on calling algorithms.
Keywords : Bladder cancer risk Glutathione S-transferase mu 1 (GSTM1) Copy number variation (CNV) SNP-array
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BMC Genomics, BioMed Central, 2012, 13 (1), pp.326. 〈10.1186/1471-2164-13-326〉
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Gaëlle Marenne, Francisco Real, Nathaniel Rothman, Benjamin Rodríguez-Santiago, Luis Pérez-Jurado, et al.. Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data.. BMC Genomics, BioMed Central, 2012, 13 (1), pp.326. 〈10.1186/1471-2164-13-326〉. 〈inserm-00724696〉

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