On April 16, The New York Times published an article, “Genes Show Limited Value in Predicting Diseases,” based on commentaries and a review article on genetic risk prediction in the April 23 issue of The New England Journal of Medicine. The New York Times quoted one of the authors, David B. Goldstein, as saying, “With only a few exceptions, what the genomics companies [that offer personal genomic information] are doing right now is recreational genomics.” (I inserted the clarification to emphasize that Goldstein was not talking about genomics companies in general—only those that are offering personal genomic information to physicians and patients.) Curious, I downloaded the original papers.
Goldstein’s article, “Common Genetic Variation and Human Traits,” asserts that genomewide association studies are not an efficient way to identify gene variants capable of predicting risk in any meaningful way, and that the more gene variants associated with a given disease, the more time- and resource-intensive it would be to identify a manageable and usable set of risk predictor genes. The article also offers the interesting perspective that the “apparently modest effect of common variation on most human diseases and related traits probably reflects the efficiency of natural selection in prohibiting increases in disease-associated variables in the population.” And Goldstein points to the promise of looking at polymorphisms associated with responses to drugs or infectious agents. (Being a marketer, I am always looking for the silver lining.)
In “Genomewide Association Studies—Illuminating Biologic Pathways,” Joel N. Hirschhorn offers a different perspective—that the main goal of genomewide association studies is not to figure out how to predict individual risk of diseases and traits, but to elucidate underlying biologic pathways. As an example, he notes that of the 23 loci found to be associated with lipid levels in genomewide studies, 11 point to genes that have previously been shown to encode key proteins involved in lipid metabolism. Hirschhorn goes on to enumerate a number of genes encoding sites of action of drugs approved by the FDA that have been similarly identified. Citing the distance between the deciphering of the chemical composition of cholesterol and the development of statins, which were separated by “nearly a century and three Nobel Prizes,” he cautions that “each discovery of a biologically relevant locus is a potential first step in a translational journey” and that “some journeys will be shorter than others.”
Peter Kraft and David J. Hunter raise the question, “Genetic Risk Prediction—Are We There Yet?” and concur that there are few monogenic diseases. For example, Crohn’s disease is associated with more than 30 loci and thus potentially more than 30 genes. The graph on page 1702 of the article shows that the higher the number of undiscovered genetic factors for the disease, the lower the likelihood of assessing the risk level for the disease in any meaningful way. Kraft and Hunter outline factors determining the clinical value of a genetic test, and point out the importance of looking not only at test performance (sensitivity, specificity, positive and negative predictive values) but also at costs and benefits of interventions, as well as outcome data, in determining the clinical value of a genetic test. Most important, the authors suggest that while testing for genetic risk may not be here today, it may only be two or three years away, and advocate the urgent need to develop guidelines for physicians, which are now lacking.
John Hardy and Andrew Singleton’s review article, “Genomewide Association Studies and Human Disease,” is an excellent backgrounder for anyone with any interest in this field. It details the stages of a genomewide association study, summarizes its benefits, misconceptions and limitations and offers a helpful glossary. Importantly, it includes an elegant explanation of genetic variability in gene expression, which adds yet another dimension to the understanding of genetic risk of diseases—“moving from dichotomous to graded genetic risk” as the authors subtitled one of the paragraphs. What I found very interesting, also, is the notion that the interaction between genome and environment, which many people like me believed was a given, has not been demonstrated for the most part. And, like the other reviewers, Hardy and Singleton are largely optimistic about the future and the scientific community’s ability to solve the complex puzzle of genes and diseases.