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Positive Predictive View Calculator

NIPT/Cell Free DNA Screening Predictive Value Calculator

In this video, we provide a walk through of a freely available positive predictive value calculator that can be used by clinicians. Patients should ask their clinician about this calculator. The National Society of Genetic Counselors (NSGC) and the Perinatal Quality Foundation provide an online calculator that allows you to estimate the Positive Predictive Value (PPV) and Negative Predictive Value (NPV) of noninvasive prenatal tests (NIPT or NIPS), also known as Cell Free DNA Screening (cfDNA), based on estimates of population prevalence or by entering your own prevalence numbers. The results of this calculator only apply to patients who have a result from NIPT/NIPS/cfDNA.

Hereditary Cancer Panel Positive Predictive Value Calculator

Germline sequencing test results have inherent uncertainty. While Variants of Uncertain Significance are often discussed, a major source of uncertainty that is not often discussed is the accuracy of Likely Pathogenic or Pathogenic variant classifications.

We developed a calculator to model the positive predictive value – the probability that a positive variant result is a true positive – of germline sequencing tests that incorporates both the analytical and classification sensitivity and specificity. We grouped variants as actionable (LP/P) or inactionable (Benign/Likely Benign/VUS) and analyzed how small deviations in variant classification stringency affect PPV. We grouped labs as high, medium, and low stringency levels based on lab reported analytical test sensitivity/specificities from hereditary cancer testing laboratories (99.99%/99.99%, 99.50%/ 99.50%, and 99.00%/99.00%, respectively) and estimated high, medium, and low variant classification sensitivities/specificities from available studies of laboratory positive rates (99.99%/97.50%, 99.95%/97.75%, and 99.90%/98.00%, respectively).

Preliminary results, shown below, have been presented at the American Society of Human Genetics and that National Society of Genetic Counselors Annual Meetings.

This calculator is currently undergoing revisions in partnership with Statistics Without Borders.

The freely available calculator interface allows users to try adjusting various inputs and see the effects on the PPV.

*Note: This calculator is intended for research use only and applies to situations where variants are not well-characterized founder mutations.