SNPwatch: Genetic Variants Near Tumor Suppressor Genes May Increase Risk For Brain And Skin Cancer

SNPwatch gives you the latest news about research linking various traits and conditions to individual genetic variations. These studies are exciting because they offer a glimpse into how genetics may affect our bodies and health; but in most cases, more work is needed before this research can provide information of value to individuals. For that reason it is important to remember that like all information we provide, the studies we describe in SNPwatch are for research and educational purposes only. SNPwatch is not intended to be a substitute for professional medical advice; you should always seek the advice of your physician or other appropriate healthcare professional with any questions you may have regarding diagnosis, cure, treatment or prevention of any disease or other medical condition.

Abstract DNA

It’s well established that defects in the cellular machinery that controls cell division can lead to cancer.  Now, new research shows that the risk for both brain and skin cancer can also be impacted by common DNA variations near a set of growth-regulating genes.

Five reports, published online this week in the journal Nature Genetics, show that variants near the CDKN2A and CDKN2B genes increase the risk of certain types of tumors.  Previous research has implicated these “tumor suppressor” genes in both skin and brain cancer. Mutations in CDKN2A are found in about 2% of all people with melanoma, and outright deletion of CDKN2A and CDKN2B is seen in approximately half of all brain tumors.

Two of the reports (Wrensch et al. and Shete et al.) focused on gliomas, which account for approximately 80% of all primary brain cancers and generally have a dismal prognosis.

The remaining three papers were skin cancer studies.  Two of these (Bishop et al. and Falchi et al.) focused on melanoma, while the third (Stacey et al.) looked at basal cell carcinoma.  Melanoma accounts for less than 5% of all skin cancers, but is responsible for most skin cancer deaths. Basal cell carcinoma is also serious, though not usually deadly, and is the most common type of cancer overall in people with European ancestry.

(In addition to SNPs near the CDKN2A and CDKN2B genes, several other SNPs were identified for each type of cancer.  23andMe customers can use the links in the table at the end of this post to see their data for all of these SNPs using the Browse Raw Data feature.  SNPs near the CDKN2A/CDKN2B genes are in bold.)

The disease-associated variants near the CDKN2A and CDKN2B genes were distinct for the three types of cancer studied.  This could mean that they each have separate risk-increasing effects, or that they are all pointing researchers in the direction of a single variant in the region that is involved in glioma, melanoma and basal cell carcinoma.

It’s no surprise that these genes, which play important roles in some of the most basic cellular processes, appear to be involved in several types of cancer. In fact, variation in and around CDKN2A and CDKN2B might be important for other diseases as well.  Previous research has also implicated SNPs near these genes in coronary artery disease and type 2 diabetes.

As more research is done, we can probably expect to see more variants in this region of DNA associated with more diseases.  It will be fascinating to see how they all connect to each other, and more importantly, what new insight they give scientists into how tiny DNA changes can have big health consequences.

SNP Risk Version Increase in Odds Notes
Glioma
rs1412829 G 1.22
rs2736100 C 1.27
rs4295627 G 1.36
rs6010620 G 1.28
rs498872 A 1.18
Melanoma
rs7023329 A 1.18 Along with rs2284063, this SNP was also associated with an increased number of cutaneous nevi (large moles). Nevi number is a well-established risk factor for melanoma. When Falchi et al. took nevi number into account, the risk for melanoma conferred by these SNPs disappeared, suggesting that they are measuring the same disease-associated factors as nevi.
rs2284063 A 1.20
rs258322 A 1.67
rs1393350 A 1.29
Basal Cell Carcinoma
rs2151280 G 1.19
rs157935 T 1.23 The overall increase in odds is given here, but Stacey et al. found that risk for BCC is only increased when the T version of this SNP is inherited from the father. This was surprising because previous research has shown that only the copy of the gene containing this SNP inherited from the mother is turned on in cells.
rs11170164 T 1.35