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) …

May
10

## Alzheimer’s book: 100 Simple Things You Can Do to Prevent Alzheimer’s and Age-Related Memory Loss

The book “100 Simple Things You Can Do to Prevent Alzheimer’s and Age-Related Memory Loss” was written in 2010. You can find all of the advice on the Internet, and in more succinct terms. The author Jean Carper lists “100 actions” you can take to prevent Alzheimer’s. Each action is written as a chapter. My …

May
09

## Alzheimer’s Books: Tangles and The Little Girl in the Radiator

I read two books on Alzheimer’s from the caretaker’s perspective: The Little Girl in the Radiator Tangles Tangles and The Little Girl in the Radiator are written from the perspective of the caregiver. Tangles is written by Sarah Leavitt about her mother. The main caretaker is her father. In The Little Girl in the Radiator, …

Apr
16

## ApoE4 and increased risk of Alzheimer’s

My significant other (SO) has a good chance of getting Alzheimer’s, based on his family history and genetics (he’s ApoE4 homozygous). We discovered this when he got his DNA tested. So my goal (that sounds really ambitious – maybe I should say “aim”? Trying again…) My aim is to find preventive measures for Alzheimer’s, specifically …

Jan
03

## 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 …

Dec
21

## 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 …

Dec
11

## 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 …

Dec
04

## 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 …

Nov
27

## FDA Validation of a PCR test: Accuracy (Part 4)

In the Accuracy study, we will: Set the acceptable working range Set the cutoffs for calling a sample positive or negative Assess how well our assay agrees with an alternative assay Clinical samples can  be FFPE or fresh frozen. FFPE is usually poorer quality than fresh frozen, so the two sample types are treated separately. …

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 …