23andMe Researchers Develop A Better Way to Estimate Skin Cancer Risk

A team of scientists at 23andMe created a new model to better estimate skin cancer risk, one of the most commonly diagnosed forms of cancer.

Details of the new model are included in a study published in the journal Nature Communications today.

Using genetic and other data from more than 210,000 customers who consented to participate in research, the 23andMe team created a model to calculate a risk score for the three forms of skin cancer. The model relied on more than 100 known genetic variants for skin cancers and dozens of non-genetic risk factors, including family cancer history, skin pigmentation, and sun exposure.

According to the lead author of the study, Pierre Fontanillas, Ph.D., and a senior statistical geneticist at 23andMe, the new model could help detect skin cancer earlier. 

“There remains considerable room to improve the risk model by including additional data, especially from people of non-European ancestry,” said Pierre. “But we’ve shown the ability to use a risk model to potentially identify people with elevated risk for skin cancer who do not currently have identifiable symptoms.”

23andMe Senior Statistical Geneticist Pierre Fontanillas, Ph.D.

One in Five

Such early detection could have broad benefits. In the United States alone, one in five people is likely to develop skin cancer in their lifetime. Despite being preventable, more than 15,000 Americans die each year from one of the three major types of skin cancer — basal cell carcinoma, squamous cell carcinoma, and melanoma.

Using the new model they developed, the 23andMe scientists found the research participants in this study with the highest risk scores were up to 13 times more at risk of developing skin cancer. The work doesn’t just offer the potential for identifying people with elevated risk for cancer. It also could help predict such things as the age of onset and the severity of cancer.

For skin cancer, early detection and treatment can go a long way in improving outcomes. Currently, early detection relies on regular full-body skin examinations. While inexpensive and non-invasive, there’s little evidence that it’s an effective method for detecting skin cancer in the general population. Developing a more accurate predictor for individual risk for cancer has been difficult.

New Tools

Finding tools for better risk prediction and earlier detection offers hope for better outcomes.

“These scores rely on the long tail behavior of the genetic and non-genetic factors, and potentially enable the identification of asymptomatic individuals with elevated skin cancer risk,” the scientists said in the paper.

Because this initial work included data primarily from customers with European ancestry, the researchers plan to expand the study to include data from individuals with non-European ancestry. Also, they hope to improve how they estimate sun exposure and further refine the genetic risk score. According to the researchers, the goal is to develop risk estimates accurate enough to be used clinically and at an individual level.

Polygenic Risk Scores

Over the last several years, scientists have developed so-called polygenic risk scores that rely on large sets of genetic and non-genetic data to better calculate disease risk. 23andMe has used this kind of risk modeling for its Type 2 Diabetes Report (Powered by 23andMe research). The T2D report calculates a polygenic score based on more than 1000 genetic variants. The report also relied on data from more than 1.1 million 23andMe customers who consented to participate in research. 

As more genetic data become available, polygenic risk models are increasingly being used to help calculate risk. Often these models use many hundreds, or even thousands, of genetic variants to calculate risk. These new models can also include other factors — such as lifestyle and environmental influences — to offer a clearer picture of disease risk. Also, including data from more diverse populations can be used to predict risk in underrepresented populations better.

At this time 23andMe does not offer a report on skin cancer.