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  • 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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  • 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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  • 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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  • 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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  • 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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  • Creating Your Own Personal Silent Retreat

    I was seeking silence and solitude so I spent a few days at Bali Silent Retreat. It was an ascetic vegetarian lifestyle (which was a bit much for me). While I had my moments of revelation, I realized I didn’t have to fly to Indonesia for silence. This blog post will describe how to create …

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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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  • Obsessions in Alzheimer’s

    This video shows a woman with Alzheimer’s who is obsessed with finding and helping a non-existent cat. The obsession happens over a two-month period and you can tell she’s very distressed. She is always looking for a cat — wandering the streets and even breaking windows to go out and find this cat. Her daughter …

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  • Can’t lose weight with Belviq?

    With the holidays nearly over, I have to admit I’m feeling sick overeating with the holiday parties and goodies given as gifts. We’ll be examining the gender differences in the weight loss drug Belviq (generic name lorcaserin). Based on online ratings, Belviq works better in males than in females (men gave 1.18 more points for …

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  • Treating depression: Wellbutrin is more effective for females than males.

    Millions suffer from depression, so it’s important to know which treatments work. Women are underrepresented in clinical trials. Thus, it is possible that they react differently to drugs. To study this, we downloaded online drug reviews to see if women responded to drugs differently than men. Surprisingly, women rated Wellbutrin XL higher than males. Wellbutrin …

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