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Date registered: May 14, 2011

Latest posts

  1. FDA Validation of Companion Diagnostic (PCR test) — November 27, 2018
  2. Creating Your Own Personal Silent Retreat — September 1, 2018
  3. Fantasy and Genetics – Do They Go Together Like Science and Fiction? — June 12, 2018
  4. Obsessions in Alzheimer’s — April 2, 2018
  5. Can’t lose weight with Belviq? — December 27, 2017

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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, …

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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 …

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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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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. …

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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)

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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Choosing the Right College

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Is it worth paying more for a “top 10” school? You get accepted to a private school / Ivy League that will cost a fortune. You’re also accepted by a public university which doesn’t have as good a reputation but costs much less. Does it matter which one you choose? One factor in your decision …

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