denghui330's repositories
bioinformatics
The code in bioinformatics, include perl, python, php, awk
chromVARguide
Repo for walking through a chromVAR sample analysis
hrpi
Rmarkdown / compiled html files for human reprogramming dataset analysis
RetroCRCmanu
This repository contains code used in the manuscript entitled “Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival” (https://www.biorxiv.org/content/10.1101/443580v1 ) Genomic instability pathways in colorectal cancer (CRC) have been extensively studied, but the role of retrotransposition in colorectal carcinogenesis remains poorly understood. Although retrotransposons are usually repressed, they become active in several human cancers, in particular those of the gastrointestinal tract. Here we characterize retrotransposon insertions in 202 colorectal tumor whole genomes and investigate their associations with molecular and clinical characteristics. We found highly variable retrotransposon activity among tumors and identified recurrent insertions in 15 known cancer genes. In approximately 1% of the cases we identified insertions in APC, likely to be tumor-initiating events. Insertions were positively associated with the CpG island methylator phenotype and the genomic fraction of allelic imbalance. Clinically, high number of insertions was independently associated with poor disease-specific survival.