Open Access Methodology article

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

Gaëlle Marenne12, Francisco X Real13, Nathaniel Rothman4, Benjamin Rodríguez-Santiago35, Luis Pérez-Jurado3567, Manolis Kogevinas101189, Montse García-Closas4, Debra T Silverman4, Stephen J Chanock4, Emmanuelle Génin2 and Núria Malats1*

  • * Corresponding author: Núria Malats nmalats@cnio.es

  • † Equal contributors

Author Affiliations

1 Spanish National Cancer Research Center (CNIO), Madrid, E-28029, Spain

2 Inserm UMR-S946, Univ. Paris Diderot, Institut Universitaire d’Hématologie, Paris, F-75010, France

3 Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, E-08003, Spain

4 Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20852-4907, USA

5 Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, E-08003, Spain

6 Programa de Medicina Molecular i Genètica, Hospital Universitari Vall d’Hebron, Barcelona, E-08003, Spain

7 Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA

8 Municipal Institute of Medical Research (IMIM-Hospital del Mar), Barcelona, E-08003, Spain

9 Centre for Research in Environmental Epidemiology (CREAL), Barcelona, E-08003, Spain

10 Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, E-08003, Spain

11 National School of Public Health, Athens, G-11521, Greece

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BMC Genomics 2012, 13:326  doi:10.1186/1471-2164-13-326

Published: 20 July 2012

Additional files

Additional file 1:

Table S1. Details on the number of individuals genotyped by each of the three platforms. Number of callings available at GSTM1 are also provided. Table S2.GSTM1 CNV assessment conducted by each of the genotyping platforms. We applied the PennCNV algorithm to call the CNVs from the Illumina 1M array genotyping data. Figure S1. Venn diagrams describing the common individuals genotyped by the three platforms a) for the cases and controls, b) for cases only and c) for controls only.

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