[PDF][PDF] Letting the genome out of the bottle-will we get our wish?

DJ Hunter, MJ Khoury, JM Drazen - New England Journal of …, 2008 - researchgate.net
New England Journal of Medicine, 2008researchgate.net
PERSPECTIVE n engl j med 358; 2 www. nejm. org january 10, 2008 106 at popularizing
genetic testing seem to neglect key aspects of the established multifaceted evaluation of
genetic tests for clinical applications. First, there is the question of a test's analytic validity,“its
ability to accurately and reliably measure the genotype of interest.” 1 Although appropriate
monitoring and oversight of the analytic validity of genetic tests remain largely unaddressed,
2 most researchers report that the analytic validity of these platforms is very high. It is likely …
PERSPECTIVE n engl j med 358; 2 www. nejm. org january 10, 2008 106 at popularizing genetic testing seem to neglect key aspects of the established multifaceted evaluation of genetic tests for clinical applications. First, there is the question of a test’s analytic validity,“its ability to accurately and reliably measure the genotype of interest.” 1 Although appropriate monitoring and oversight of the analytic validity of genetic tests remain largely unaddressed, 2 most researchers report that the analytic validity of these platforms is very high. It is likely that sample-handling errors are a greater threat to the validity of results than are genotypic misclassification errors. Yet even very small error rates per SNP, magnified across the genome, can result in hundreds of misclassified variants for any individual patient. Without transparent quality-control monitoring and proficiency testing, the real-world performance of these platforms is uncertain. Second, one must consider clinical validity, or the ability of the test to detect or predict the associated disorder. 1 Components of clinical validity include the test’s sensitivity, specificity, and positive and negative predictive value. This is the area in which the data are in the greatest flux, and even the ardent proponents of genomic susceptibility testing would agree that for most diseases, we are still at the early stages of identifying the full list of susceptibility-associated variants. Most of the diseases listed by the direct-to-consumer testing companies (eg, diabetes, various cancers, and heart disease) are so-called complex diseases thought to be caused by multiple gene variants, interactions among these variants, and interactions between variants and environmental factors. Thus, a full accounting of disease susceptibility awaits the identification of these multiple variants and their interactions in well-designed studies. What we have now is recognition of a limited number of variants associated with relative risks of diseases on the order of 1.5 or lower. Risk factors with this level of relative risk clearly do a poor job of distinguishing people who will develop these diseases from those who will not. 3, 4 Finally, there is the issue of the test’s clinical utility, or the balance of its associated risks and benefits if it were to be introduced into clinical practice. 1 Measures of utility address the question at the heart of the clinical application of a test: If a patient is found to be at risk for a disease, what can be done about it? This is the arena in which there are virtually no data available on the health impact of genomewide analysis. There are very few observational studies and almost no clinical trials that demonstrate the risks and benefits associated with screening for individual gene variants—let alone testing for many hundreds of thousands of variants. Thus, any claim to clinical utility currently rests on the assumption that interventions that have proven successful in the general population will behave the same way in a genetically at-risk population. Many of these interventions—such as smoking cessation, weight loss, increased physical activity, and control of blood pressure—are likely to be broadly beneficial in relation to many diseases, regardless of a person’s genetic susceptibility to a specific disease.
It may be argued that knowledge of increased susceptibility to a disease, such as type 2 diabetes, for which protective lifestyle interventions exist, will motivate patients to follow relevant recommendations. Yet as intuitively appealing as this contention may be, evidence to support it, particularly in the case of low-penetrance alleles, is scanty. The flip side, of course, is that patients who test negative may be falsely reassured and thus less motivated to comply with …
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