At the same time, don’t we need to know whether  the  patient  probably  has or does not have the  condition  of  interest?   Yes, prevalence and  other  factors  affect PPV and  NPV, but in my  opinion we  need to move away from the  oversimplified notion that test interpretation depends on  a single factor.



From: Evidence based health (EBH) [mailto:[log in to unmask]] On Behalf Of Mayer, Dan
Sent: Friday, January 30, 2015 8:08 PM
To: [log in to unmask]
Subject: Re: Genetic tests and Predictive validity


Hi Teresa,


You are absolutely correct.  This is why we should demand that diagnostic studies ONLY present the results of Sensitivity, Specificity and Likelihood ratios.


This issue has been a serious problem for many years and it is about time that more people spoke up about it.  Also, journal editors and peer reviewers should be up in arms against the practice of reporting PPV and NPV.


Best wishes


From: Evidence based health (EBH) [[log in to unmask]] on behalf of Benson, Teresa [[log in to unmask]]
Sent: Friday, January 30, 2015 11:59 AM
To: [log in to unmask]
Subject: Genetic tests and Predictive validity

I’ve just started reading the literature on genetic tests, and noticing how many of them tend to focus on predictive value—that is, if a certain test accurately predicts whether a patient will or won’t get a particular phenotype (condition), the authors suggest the test should be used.  But if we’re deciding whether to order the test in the first place, shouldn’t we be focused on sensitivity and specificity instead, not PPV and NPV?  Predictive value is so heavily dependent on disease prevalence.  For example, if I want to get tested for a disease with a 2% prevalence in people like me, I could just flip a coin and regardless of the outcome, my “Coin Flip Test” would show an NPV of 98%!  So what does NPV alone really tell me, if I’m not also factoring out prevalence—which would be easier done by simply looking at sensitivity and specificity?  Someone please tell me where my thinking has gone awry!

For a concrete example, look at MammaPrint, a test which reports binary results.  In addition to hazard ratios, study authors often tout statistically significant differences between the probabilities of recurrence-free survival in the MammaPrint-High Risk vs. MammaPrint-Low Risk groups (essentially the test’s predictive values).  In the RASTER study (N = 427), 97% of the patients with a “Low Risk” test result did not experience metastasis in the next 5 years.  Sounds great, right?  But when you look at Sensitivity, you see that of the 33 patients in the study who did experience metastasis, only 23 of them were classified as “High Risk” by MammaPrint, for a 70% sensitivity.  If patients and clinicians are looking for a test to inform their decision about adjuvant chemotherapy for early stage breast cancer, wouldn’t the fact that the test missed 10 out of 33 cases be more important than the 97% NPV, an artifact of the extremely low 5-year prevalence of metastasis in this cohort (only 33 out of 427, or  0.7%)? 

Drukker et al. A prospective evaluation of a breast cancer prognosis signature in the observational RASTER study. Int J Cancer 2013. 133(4):929-36.

Retel et al. Prospective cost-effectiveness analysis of genomic profiling in breast cancer. Eur J Cancer 2013. 49:3773-9.  (Provides actual true/false positive/negative results)


Thanks so much!


Teresa Benson, MA, LP

Clinical Lead, Evidence-Based Medicine

McKesson Health Solutions
18211 Yorkshire Ave

Prior Lake, MN  55372

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Phone: 1-952-226-4033


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