Since SNPs can be gene markers, SNP profiles may help scientists to identify the full collection of genes that contribute to the development of complex diseases such as cancer. For example, scientists will examine the SNP profiles from many people, including colon cancer patients. Within the many different profiles they may discover a small subset of SNPs that are only present in colon cancer patients. This implies that this subset of SNPs is associated only with colon cancer. When this happens, the SNPs themselves may be considered markers for colon cancer genes.

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