Quantifying prion disease penetrance using large population control cohorts

This repository holds the source code, data, and pre-print for the following manuscript:

Minikel et al. Quantifying prion disease penetrance using large population control cohorts. Sci. Transl. Med. 8, 322ra9 (2016). DOI: 10.1126/scitranslmed.aad5169

What's here

In this repository you can:

• Read the pre-print version of the paper in Markdown format: manuscript.md.
• Download tab-delimited text (.tsv) versions of all supplementary tables: supplement.
• Browse IGV screenshots for all rare PRNP variants deemed to be genuine: igv.
• Re-produce the main figures in the manuscript by analyzing data from the supplementary tables in R, per the following instructions.

Instructions for running code

The four figures for the main text can be re-generated solely from the data stored in the supplementary tables. First, make sure you are running R 3.1.2 or later and have the sqldf and binom packages installed for R:

install.packages("sqldf")
install.packages("binom")

Then, on the command line, clone this repo, delete the figures and re-run the generate_figures.r script:

git clone git@github.com:ericminikel/prnp_penetrance.git
cd prnp_penetrance
rm figures/figure1b.pdf
rm figures/figure2.pdf
rm figures/figure3.pdf
rm figures/figure4.pdf
Rscript src/generate_figures.r

See also

• Robert Green's perspective piece about this work, including how it changed one patient's prognosis.
• My CureFFI.org blog post telling the personal story behind this study.
• Coverage in STAT, AAAS, Nature Reviews Genetics, Neurology Today, and El Mundo.