Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

We have performed whole genome and DNA and RNA sequencing of 101 tumor biopsies from patients with metastatic castration-resistant prostate cancer (Quigley, Dang, Zhao et al. Cell 2018). Scripts employed during the analysis are available on github:
https://github.com/DavidQuigley/WCDT.

Whole genome DNA sequence data

mRNA data

Laser-capture microdissected tumor tissue was subjected to RNA-seq. RNA reads were then aligned against HG38-decoy using STAR as described in the manuscript, producing per-gene count files (see below). RNA data were available for 99 of the 101 samples with DNA-seq data, so please expect to see 99 columns in matrix files for this study. A total of 26,485 transcripts were assessed for counts. Count files were then processed to calculate TPM values using the code at https://github.com/DavidQuigley/WCDT/scripts/calculate_RNA_tpm.R, using code adapted from https://gist.github.com/slowkow/c6ab0348747f86e2748b. This script marked as absent any individual gene if no sample had at least 100 counts for that gene and if the mean number of counts across all 101 samples was less than 100. After filtering, 16,844 genes with TPM calls were included in the analysis. You can re-process the count data to your own satisfaction using the raw data linked below.

HTDoseResponseCurve

Source code for the R package HTDoseResponseCurve is available on GitHub at https://github.com/DavidQuigley/HTDoseResponseCurve.
A pre-build ource package (HTDoseResponseCurve_0.99.0.tar.gz) is available.