SNP link to several cancers

An international collaboration has linked common single nucleotide polymorphisms (SNPs) on chromosome 5 to five different types of cancer while at the same time conferring protection against melanoma.

The team, led by Iceland’s deCODE genetics, looked at the TERT-CLPTM1L locus in the chromosome 5p15 region, which is frequently amplified in many types of cancer.

The human telomerase reverse transcriptase (TERT) gene is of interest as short telomeres have been linked to increased risk of cancers, and the cis-platin resistance related protein CRR9p (CLPTM1L) gene codes for a protein expressed in a range of normal and malignant tissues.

deCODE discovered the first SNP, rs401681, from a genome-wide scan of basal cell carcinoma. They then tested it for association with 16 other cancer types in over 30,000 cancer cases and 45,000 controls from European populations and found associations with lung, urinary bladder, prostate and cervical cancer.

At the same time, the SNP seems to confer protection against melanoma, they said.

“Of note, four of the five cancers associated with the risk variants are cancer types that have strong environmental contribution to risk,” the researchers wrote. These environmental risks include smoking for lung and bladder cancer, UV light for skin cancer and HPV infection for cervical cancers.

A potential link between these cancers is that they tend to arise in the epithelial layer that is in closest contact with the environment, study senior author Kari Stefansson said.

“One of the SNPs we have discovered is in a gene involved in determining the length of the telomeres,” Stefansson said in a statement. “Shorter telomeres have recently been linked to risk of certain cancers, and telomeres are known to become shorter with the accumulation of environmental insults over time.

“These findings may point us towards a means of addressing these risks by altering our lifestyle or by helping to identify targets for new drugs.”

The study is published online in advance in Nature Genetics.