Sunday, September 9, 2012

PancPRO – Software for Pancreatic Cancer Risk Assessment

The rapid fatality rate of pancreatic cancer is due in large part to an advanced stage of diagnosis for the majority of cases. Identification of individuals at high-risk of developing pancreatic cancer is a first step towards the early detection of this disease. Individuals who may harbor a major pancreatic cancer susceptibility gene are one such high-risk group.

An estimated 10 percent of aggressive and highly fatal cases of the disease are caused by inherited genes. "Even if there is a 100 percent chance that an individual carries a pancreas cancer gene, their risk for developing the disease is only 20 to 25 percent over their lifetime," says Alison Klein, Ph.D., assistant professor and director of the National Familial Pancreas Tumor Registry at Johns Hopkins. "So, while it's a rare disease, the need for screening in these persons is important."

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The Johns Hopkins Kimmel Cancer Center researchers have developed a new computer software tool that can predict a person's chances of carrying a gene for hereditary pancreatic cancer and can help physicians and genetic counselors decide who would benefit from early screening.

Although researchers have not yet identified specific genes that cause the disease, they can estimate high risk based on clusters of family members with a history of pancreas cancer. "We know how genes behave, and coupled with information about a family - who has the disease, their age, family size, and causes of death - our model can provide a good estimate of an individual's risk," says Alison Klein, director of the National Familial Pancreas Tumor Registry.

Early risk assessment has long been sought for pancreas cancer that runs in families, Klein says because of the difficulty doctors have diagnosing it before it has already spread. Survival rates are extremely low.

The software tool, called PancPRO, is a risk calculator that determines a probability percentage score of whether a person carries a pancreatic cancer gene. The software is based on similar tools for breast and colon cancers. It also computes an individual's lifetime risk of developing the disease.

To test the model's effectiveness for predicting cancer, Klein and her colleagues fed the software family history information given by more than 6,000 individuals in 961 families when they initially joined the Hopkins pancreas cancer registry several years ago. Klein's team divided registrants into groups representing the number of pancreas cancer patients in each family - from one to three or more members. They compared predictions from the PancPRO model with what actually occurred in these families from one to 11 years later. On average, the model calculated higher risk scores for individuals who developed pancreatic cancer than for those who remained disease free.

Current practices for identifying pancreatic cancer risk without the new model are slightly better than a coin toss at 61 percent, but PancPRO correctly assesses risk 75 percent of the time, taking into account all potential threshold values for defining risk. Overall, 26 individuals developed cancer, and PancPRO predicted slightly more at 31.

Klein says that the new model also needs to be assessed in other populations besides the Hopkins registry, and she hopes to determine how insurers would pay for screening procedures. Her group also will be studying whether PancPRO is more effective in selecting candidates for screening than current criteria based only on the number of family members with the disease.

The authors caution that results from PancPRO should only be interpreted by a genetic counselor and a physician. While the software is available for free downloading and public use, it is not designed for non-professionals. However, if you can work with your primary physician to perform this software risk evaluation, if your family history points out on the potential elevated risk of the pancreatic cancer development through your lifetime.

If you still want to try to get this self-assessment by yourselves, you can download CancerGene package from U.T. Southwestern Medical Center at Dallas website:

This package includes the following components: BRCAPRO, MMRpro, PancPRO, and MelaPRO, and it is designed for the functions, listed below:
  • BRCA1 or BRCA2 gene mutation probabilities.
  • MLH1, MSH2, and MSH6 gene mutation probabilities.
  • Hypothetical pancreas cancer gene mutation probability.
  • Age-specific Breast, Ovarian, Colorectal, Endometrial, and Pancreas cancer probabilities.

Note that this package is based on a freeware program R. Get familiar with R through An Introduction to R or any other free R tutorials available on the web.

Sources and Additional Information:

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