Open Access Research article

A colorectal cancer genome-wide association study in a Spanish cohort identifies two variants associated with colorectal cancer risk at 1p33 and 8p12

Ceres Fernandez-Rozadilla1, Jean-Baptiste Cazier2, Ian P Tomlinson23, Luis G Carvajal-Carmona4, Claire Palles2, María J Lamas5, Montserrat Baiget6, Luis A López-Fernández7, Alejandro Brea-Fernández1, Anna Abulí89, Luis Bujanda10, Juan Clofent1112, Dolors Gonzalez13, Rosa Xicola14, Montserrat Andreu8, Xavier Bessa8, Rodrigo Jover15, Xavier Llor14, The EPICOLON Consortium, Víctor Moreno16, Antoni Castells9, Ángel Carracedo1, Sergi Castellvi-Bel9 and Clara Ruiz-Ponte1*

Author Affiliations

1 Galician Public Fundation of Genomic Medicine (FPGMX)-Grupo de Medicina Xenómica-Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer)-IDIS, Santiago de Compostela, 15706, Spain

2 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK

3 NIHR Comprehensive Biomedical Research Centre, University of Oxford, Oxford, OX3 7BN, UK

4 Department of Biochemistry and Molecular Medicine School of Medicine University of California, Davis, California, USA

5 Oncology Pharmacy Unit, Complejo Hospitalario Universitario of Santiago (CHUS), Santiago de Compostela, 15706, Spain

6 Genetics Department, Hospital de Santa Creu I Sant Pau, Barcelona, 08025, Spain

7 Pharmacogenetics & Pharmacogenomics Laboratory, Servicio de Farmacia, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón,, Madrid, 28007, Spain

8 Gastroenterology Department, Hospital del Mar, Barcelona, 08003, Spain

9 Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, 08036, Spain

10 Gastroenterology Department, Donostia Hospital, CIBERehd, University of the Basque Country, San Sebastián, 20014, Spain

11 Gastroenterology Department, Hospital do Meixoeiro, Vigo, 36214, Spain

12 Section of Digestive Diseases, Internal Medicine Department, Hospital Sagunto, Valencia, 46520, Spain

13 Servicio de Patologia Digestiva, Hospital Sant PAu, Barcelona, 08003, Spain

14 Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, IL, 60607, USA

15 Gastroenterology Department, Hospital General Universitario de Alicante, Alicante, 03010, Spain

16 Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Centre (IDIBELL), CIBERESP, Barcelona, 08907, Spain

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BMC Genomics 2013, 14:55  doi:10.1186/1471-2164-14-55

Published: 26 January 2013

Additional files

Additional file 1: Table S1:

Phase I and Phase II cohorts. Main features and sample distribution of the phases. Gender count, hospital of origin and age statistics for cases and controls are shown for each phase.Table S2. Associations by phenotype. Phenotype counts and association values for SNPs rs12080929 and rs11987193 and each of the clinical variables studied.Table S3. Associated loci and imputation regions. Location of the 24 associated loci and description of the regions that were imputed for finer mapping.

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Additional file 2: Figure S1:

Q-Q plots of p-value distribution. A: GAL ,B: REST; C: VAS; D:meta-analysis.

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Additional file 3: Figure S2:

Imputation plots for the 24 loci associated with CRC in EPICOLON. P-value plots for the imputed markers in the associated regions. Diamonds represents typed SNPs, squares depict imputed markers, the biggest diamond is the best-associated SNP in the region, irrespective of typed/imputed status; red grading represents LD relationships . X axis: Chromosome location , Y axis: observed (-logP); Z axis: Recombination rate (cM/Mb).

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Additional file 4:

Supplementary note. Members of the EPICOLON Consortium (Gastrointestinal Oncology Group of the Spanish Gastroenterological Association).

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