TY - JOUR
T1 - Genotype - Environment interactions in microsatellite stable/microsatellite instability-low colorectal cancer
T2 - Results from a genome-wide association study
AU - Figueiredo, Jane C.
AU - Lewinger, Juan Pablo
AU - Song, Chi
AU - Campbell, Peter T.
AU - Conti, David V.
AU - Edlund, Christopher K.
AU - Duggan, Dave J.
AU - Rangrej, Jagadish
AU - Lemire, Mathieu
AU - Hudson, Thomas
AU - Zanke, Brent
AU - Cotterchio, Michelle
AU - Gallinger, Steven
AU - Jenkins, Mark
AU - Hopper, John
AU - Haile, Robert
AU - Newcomb, Polly
AU - Potter, John
AU - Baron, John A.
AU - Le Marchand, Loic
AU - Casey, Graham
PY - 2011/5
Y1 - 2011/5
N2 - Background: Genome-wide association studies (GWAS) have led to the identification of a number of common susceptibility loci for colorectal cancer (CRC); however, none of these GWAS have considered gene - environment (G x E) interactions. Therefore, it is unclear whether current hits are modified by environmental exposures or whether there are additional hits whose effects are dependent on environmental exposures. Methods: We conducted a systematic search for G x E interactions using genome wide data from the Colon Cancer Family Registry that included 1,191 cases of microsatellite stable (MSS) or microsatellite instability - low (MSI-L) CRC and 999 controls genotyped using either the Illumina Human1M or Human1M-Duo BeadChip. We tested for interactions between genotypes and 14 environmental factors using 3 methods: a traditional case - control test, a case-only test, and the recently proposed 2-step method by Murcray and colleagues. All potentially significant findings were replicated in the ARCTIC Study. Results: No G x E interactions were identified that reached genome-wide significance by any of the 3 methods. When analyzing previously reported susceptibility loci, 7 significant G x E interactions were found at a 5% significance level. We investigated these 7 interactions in an independent sample and none of the interactions were replicated. Conclusions: Identifying G x E interactions will present challenges in a GWAS setting. Our power calculations illustrate the need for larger sample sizes; however, as CRC is a heterogeneous disease, a tradeoff between increasing sample size and heterogeneity needs to be considered. Impact: The results from this first genome-wide analysis of G x E in CRC identify several challenges, which may be addressed by large consortium efforts.
AB - Background: Genome-wide association studies (GWAS) have led to the identification of a number of common susceptibility loci for colorectal cancer (CRC); however, none of these GWAS have considered gene - environment (G x E) interactions. Therefore, it is unclear whether current hits are modified by environmental exposures or whether there are additional hits whose effects are dependent on environmental exposures. Methods: We conducted a systematic search for G x E interactions using genome wide data from the Colon Cancer Family Registry that included 1,191 cases of microsatellite stable (MSS) or microsatellite instability - low (MSI-L) CRC and 999 controls genotyped using either the Illumina Human1M or Human1M-Duo BeadChip. We tested for interactions between genotypes and 14 environmental factors using 3 methods: a traditional case - control test, a case-only test, and the recently proposed 2-step method by Murcray and colleagues. All potentially significant findings were replicated in the ARCTIC Study. Results: No G x E interactions were identified that reached genome-wide significance by any of the 3 methods. When analyzing previously reported susceptibility loci, 7 significant G x E interactions were found at a 5% significance level. We investigated these 7 interactions in an independent sample and none of the interactions were replicated. Conclusions: Identifying G x E interactions will present challenges in a GWAS setting. Our power calculations illustrate the need for larger sample sizes; however, as CRC is a heterogeneous disease, a tradeoff between increasing sample size and heterogeneity needs to be considered. Impact: The results from this first genome-wide analysis of G x E in CRC identify several challenges, which may be addressed by large consortium efforts.
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U2 - 10.1158/1055-9965.EPI-10-0675
DO - 10.1158/1055-9965.EPI-10-0675
M3 - Article
C2 - 21357381
AN - SCOPUS:79955780907
SN - 1055-9965
VL - 20
SP - 758
EP - 766
JO - Cancer Epidemiology Biomarkers and Prevention
JF - Cancer Epidemiology Biomarkers and Prevention
IS - 5
ER -