yixf-self / synthex

SynthEx

SynthEx is a comprehensive suite of tools for CNA detection and tumor heterogeneity profiling. It is tailored to cater for the multiple characteristics of different next generation sequencing technologies.

SynthEx is the first method aware of the sample-specific bias in targeted regions due to fold enrichment differences in tumor and normal samples. Fundamentally different from current methods, it applies different analytical strategies for single subject and large-scale cancer genomics studies. For large-scale cancer genomics studies, it corrects the technical bias due to capture efficiency by using a "synthetic normal" strategy. The "synthetic normal" samples were generated by stratifying existing normal samples (including samples outside the current study) based on capture protocols. Therefore, instead of requiring a matched pair normal sample from each tumor subject, a "synthetic normal" is used that mimics the targeted sequencing profile with the same capture efficiency level as the tumor sample. This strategy can potentially reduce both the experiment and analysis burden within a sequencing facility.

Pre-processing and preparation

SynthEx takes counts data in non-overlapping genomic bins from tumor and normal samples as input. It has the option to input variant calling results from tumor sample. Thus SynthEx relies on other tools to generate appropriate input files. We recommend BEDtools to get the bin-level count data and freebayes for variant calling. In addition, SynthEx calls the intersectBed function from BEDtools directly, so BEDtools should be installed. The helper function to process VCF files is written in python. So make sure python is installed on the system if applying the script.

Installation

SynthEx relies on the following R packages: mclust, flsa, foreach, DNAcopy, ggplot2, gridExtra, inline, and Rcpp. Among these, DNAcopy is hosted on BioConductor and all the others are hosted on CRAN.

install.packages ("mclust")
install.packages ("flsa")
install.packages ("foreach")
install.packages ("ggplot2")
install.packages ("gridExtra")
install.packages ("inline")
install.packages ("Rcpp")
source("https://bioconductor.org/biocLite.R")
biocLite()
biocLite("DNAcopy")

SynthEx can be installed from github directly as follows:

install.packages ("devtools")
library(devtools)
install_github("ChenMengjie/SynthEx")

Tutorial

A tutorial with examples illustrating the usage of SynthEx is distributed together with the package, also available at: https://github.com/ChenMengjie/SynthEx/blob/master/inst/doc/SynthExUserGuide.pdf. After installation, the tutorial can also be invoked by SynthExUserGuide().

Author

Mengjie Chen (U Chicago)

Bug report, comments or questions please send to [email protected].