Introduction :

Colorectal cancer (CRC) is a tremendous public health issue in France where it is the third most common cancer and the second most fatal malignancy. The vast majority of CRC cases are sporadic forms due to both environmental and genetic factors. To date, the etiology of this fairly complex multifactorial disease has not been fully unravelled. Therefore, we conducted a case-control association study based on two cohorts of 1026 patients affected with sporadic CRC and 1118 controls. In the present work, we adapted a pangenomic strategy using SNP microarrays to identify predisposition loci for the disease.


We used the SNP-Map approach developed by Butcher et al. to study mild mental impairment in children. According to the age of the participants, we defined three pools of 240 individuals each within the patient and control cohorts: one representing patients under 60, one representing patients above 60, and another one representing controls above 65. Each pool was then divided in three subpools of 80 individuals, in order to test the reproductibility of our method.

The DNA concentration of all individual samples used for pool construction was determined by using the Picogreen dsDNA Quantitation Reagents (Molecular Probes, Eugene, OR). Then, we adjusted the concentration of all the samples to 10 ng/µl. To ensure an equal amplification efficiency of all the DNA samples used for the pools, we performed a quantitative real time PCR of the diluted DNA with a monomorphic TaqMan genotyping probe (5’ nuclease assay) designed in a housekeeping gene. We discarded the samples that did not amplify enough and we constituted the nine subpools of samples by adding equal DNA amounts.

In the next step, we hybridized the nine subpools on Affymetrix Genechip Mapping 250 K Array Nsp. We reproduced the procedure three times for each subpool, in order to test the repetability of our method. The genotypes generated this way were analyzed successively with softwares GCOS (Affymetrix), GTYPE (Affymetrix) and Merlin v1.0.1 (University of Michigan). To date, the genotypes results are still under analysis.

Conclusion :

We adapted a method already tested with success by Butcher et al., which should enable the prediction of potential susceptibility locus for sporadic CRC. Thereby, it may reduce the field of genetic investigation on sporadic CRC by pointing to novel candidate genes.

98th AACR Annual Meeting-- Apr 14-18, 2007; Los Angeles, CA