Saturday, May 25, 2019

Polygenic Risk Scores

I've collected some recent links related to polygenic risk scores below.

Many experts anticipate large scale clinical use of these scores within the next few years. Research progress has been very rapid -- it will be interesting to see how long it takes for these breakthroughs to be applied in health care. Graph below shows number of papers per year.

See also Harvard Business Review: AI and the Genetic Revolution (podcast).

Guardian article on UK Health Minister's proposal for widespread genetic testing:
"The latest predictive tests for a range of common diseases take a different approach: they aggregate the tiny contributions to risk made by hundreds or even thousands of genes to give a personalised score. Because the risk is spread out over many genes, people can end up at the very high-risk end of the spectrum by chance, without having a family history of a particular illness."

"Prof John Bell, a professor of medicine at Oxford university who led a recent government-commissioned review of the life sciences industry, said the approach could have a “quite profound” effect on the ability to manage disease. ... David Spiegelhalter, professor for the public understanding of risk at the University of Cambridge, agrees that genetic tests could allow the NHS to rapidly identify those who may need closer monitoring."
Editorial in New England Journal of Medicine anticipates broad clinical use of polygenic scores:
Has the Genome Granted Our Wish Yet?

"It is likely that tailoring decisions about prescribing preventive medicines or screening practices will be the main future use of genetic risk scores. If a PRS adds to existing clinical predictors of risk such as the Framingham Risk Score or the Q index for heart disease, it could be incorporated into preventive care as readily as any other biomarker."

"There seems little doubt that interpretation of these scores will become an accepted part of clinical practice in the future..."
Article in The Conversation by two Australian professors of Public Health (discussion refers to both monogenic and polygenic risks, AFAICT):
Population DNA testing for disease risk is coming. Here are five things to know

"As DNA testing becomes cheaper, it becomes more feasible to screen large numbers of healthy people for their risk of disease."

"We modelled the health and economic benefits of offering population DNA screening in Australia, focusing on young adults aged 18-25 years (about 2.6 million Australians). ... At A$200 per test (which could be realistic in the near future), savings in treatment costs could outweigh screening costs, saving the health-care system money and saving lives."
MyHeritage DNA (T2D, Heart Disease and Breast Cancer) joins 23andMe (T2D) in offering polygenic risk scores using common SNPs in their health reports. FDA regulatory stance allows DTC (Direct To Consumer) reports of this type as long as they are provided as information to be discussed with a physician, and not to diagnose a condition or prescribe care.

Someone tweeted me this photo from a recent conference presentation: increase of AUC (predictive power) with sample size. ~100k cases enough to capture most of common SNP heritability for diseases such as Testicular or Breast Cancer?

Figure below from our paper Genomic Prediction of Complex Disease Risk (bioRxiv).

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