Category Archive: Bioinformatics

Dec
11

FDA Validation of a PCR Test: Run Control Specification Part 5/n

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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Dec
04

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

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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Nov
27

FDA Validation of a PCR test: Analytical Specificity Part 3 / *

Analytical specificity shows how robust the test is to contamination. Positive controls with the fusion were spiked with EDTA or ethanol at various concentrations. We determined at which concentration the PCR no longer worked. The figures and results in this blogpost were generated by R code corresponding to “AnalyticalSpecificity_R_scripts.txt” on github Pictures always help, so these …

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Nov
27

FDA Validation of a PCR test: Pre-processing data Part 2 / n

All of the data analyzed used the same format to make it easy to re-use code . The data for each PCR experiment was in an Excel file or a comma-delimited (.csv) file with the following format. To be able to complete the FDA sections above, data from the different runs need to be combined …

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Nov
27

FDA Validation of Companion Diagnostic (PCR test) – Part 1 / n

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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Jun
12

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)

Jul
10

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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