Genome-wide association study (GWAS) is a kind of method to detect all or most of the genes among different individuals in specific species and to understand the genetic variation between different individuals.
Many susceptibility genes and loci have been found in colorectal cancer using the GWAS method, but there are still many unknown susceptibility genes and loci that have not yet been discovered.
In order to search for new colorectal cancer susceptibility genes and loci, researchers detected 1023 cases of colorectal cancer and 1306 normal controls by using the GWAS method (Illumina second generation sequencing platform). From these samples, they found a SNP rs2238126 site that frequently mutated in cancer tissue. The site was located in the promoter region of a gene ETV6 on chromosome 12p13.2. They found that ETV6 gene is a tumor suppressor gene that over expression or interference of it in colorectal cancer cells can significantly inhibit and promote the proliferation of tumor cells.
They then used the sequenom massarray platform to validate in 855 cases of colorectal cancer samples and 1258 cases of normal control samples. This method could simultaneously detect dozens of SNP loci in a large number of samples. Compared with the second generation sequencing, it can significantly decrease the cost. Finally, they used the Taqman method to validate such site in 6340 cases of colorectal carcinoma samples and 8193 normal tissues.The results showed that the A/G mutation occurred frequently in colorectal cancer tissues.
Then they found that mutation at the level of the cell level will make the transcription of ETV6 decreased, resulting in decreased expression of the gene and promoting the malignant proliferation of cells. Results indicate that ETV6 may play an important regulatory capacity in colorectal cancer, and its rs2238126 site can be used as a potential diagnostic target and drug target.
Flow chart of sample screening: