Category Archive: Bioinformatics


FDA Validation of Companion Diagnostic (PCR test)

I’ve been helping get a companion diagnostic get approved as a FDA test. This blog series will describe the statistics (R) used for the FDA validation of the companion diagnostic. The companion diagnostic test is a PCR test to check for a fusion / rearrangement on the customer’s DNA. Normally, people have gene A and …

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Fantasy and Genetics – Do They Go Together Like Science and Fiction?

This could be a disaster. I’m launching a new website that does genetic analyses for fun. It combines make-believe and science. There are a lot of direct-to-consumer genetics products out there, yet genetics is not very predictive at the individual level. The science behind these difficulties is abtruse, so why not have some fun while helping people understand …

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FactPub – a framework for disseminating facts of closed papers

Phen-Gen for finding candidate genes in rare disorders

SIFT (Prediction of Missense Genomes)


Reverse engineering contingency (2×2) table from Odds Ratio (OR)

Given the odds ratio (OR), we will calculate the individual cells in the contingency table (a,b,c,d). In yellow, I’ve highlighted what is known. a,b,c, and d are unknown and what we want to calculate. Odds Ratio = (a/c) / (b/d) Cases Controls Total Exposed a b total_exposed (a+b) Unexposed c d total_unexposed(c+d) Total total_cases(a+c) total_controls(b+d) …

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FDA Validation of a PCR Test: Precision (Repeatability & Reproducibility)

Precision measures the consistancy of results. Precision is not accuracy. While accuracy is getting the answer right, precision is about getting the same answer over and over again. You don’t want to get an answer one day, and the next day, because it’s raining or the lab technician didn’t have their cup of coffee, it’s …

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FDA Validation of a PCR Test: Reportable Range

The Reportable Range plan validates the test under many different conditions. 3 RNA input levels (low, medium, high) and the target at 12 different concentrations, ranging from 0.0488% to 100%. By testing 36 different conditions (12*3), we’ll get: Summary statistics for each fusion concentration and RNA input level Amplification efficiencies at the different % fusion …

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FDA Validation of a PCR Test: Run Control Specification (Part 5)

The purpose of run control specification is to find what is the acceptable range of values to accept a sample. For example, if a Texas Red value is detected in cycle 38 (Ct 38), this is too late in the PCR cycles and the signal could be due to contamination. Thus the sample is thrown …

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FDA Validation of a PCR Test: Limit of Detection (LoD) (Part 7)

Limit of detection is the sensitivity of the assay — how low a concentration can the test detect? To test this, the lab did a dilution series over a range of concentrations. When the concentration is low enough, the fusion won’t be detected. Using the data from the dilution series, we used 4 models to …

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