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Burton Chia Koh Jia Yu

Welcome to oncoIMPACT. Thank you for taking some time to read through this wiki entry to know more about running oncoIMPACT.

What is it?

OncoIMPACT is a first-in-class algorithmic framework that nominates patient-specific driver genes by integratively modeling genomic mutations (point, structural and copy-number) and the resulting perturbations in transcriptional programs via defined molecular networks.

OncoIMPACT is configured to run in two modes: (1) a database mode that allows it to determine the parameter settings from the datasets provided (2) a discovery mode where information in the provided database is used to predict driver genes for each sample, in an additional data set.

Installation

Download and uncompress the latest version
tar -zxvf oncoIMPACT.tgz
chmod +x oncoIMPACT_v0.9.4/*.pl

Usage

Before running the pipeline, please have the following files ready.

Input files and formats

CNV_data: a tab-separated file with samples as columns and genes as rows. Each entry of this matrix must hold either a value of -1/0/1. A value of -1 would indicate a DELETION event while a value of 1 will indicate an AMPLIFICATION event, and a value of 0 if the is not affected by copy number gene.

SNP_data (point mutations and short indels): a tab-separated file with samples as columns and genes as rows. Each entry of this matrix must hold either the binary values of 0/1. A value of 1 would indicate the presence of a snp in the gene of that particular sample while a value of 0 would indicate otherwise.

EXP_data: a tab-separated file with samples as columns and genes as rows. Each entry of this matrix would represent the log2 fold-change of the gene expression of the tumor compared to a normal control.

Config file
You will need to create a config file for your project. The config file needs to contain the following parameters (you may refer to the sample config file provided with the test datasets under TEST_DATASET/sampleConfig.cfg).

outDir: Full path to destination folder

scriptDir: Full path to folder where oncoIMPACT is installed

numThreads: Number of threads to use

cnv: Full path to cnv data matrix

exp: Full path to expression data matrix

dataType: Flag for expression data type. Vvalid options: ARRAY (default), RNA_SEQ

snp: Full path to snp data matrix

dataBase: Full path to the pre-computed database (implies discovery mode only)

databaseExport: Full path where the database will be exported (implies database + discovery mode)

testMode: Boolean flag to toggle test mode (valid options: 0 / 1)

*at any one time, only one of either the options, <database> or <databaseexport>, may be chosen to run oncoIMPACT.</databaseexport></database>

When you are ready to run the OncoIMPACT pipeline, simply enter the following command
oncoIMPACT.pl path_to_config_file

Test datasets

We have provided test datasets to try OncoIMPACT on its 2 different modes.

Database and discovery mode:
sampleConfig_db_disc.cfg: config file
Glioblastoma.tgz: Glioblastoma (GBM) TCGA dataset (this dataset should be uncompressed)

Discovery mode:
sampleConfig_disc.cfg: config file
single_patient.tgz: data of a single GBM patient (this dataset should be uncompressed)
Glioblastoma_database.tgz: pre-computed database of the TCGA GBM dataset

Change Log

v0.9.4:

NEW: Enable error checks

v0.9.3:

NEW: Enable the processing of RNA-seq data

NEW: Enable the construction of databases

NEW: Enable the discovery mode using a pre-computed database
**
v0.9.2:**

NEW: Option in configuration file to run OncoIMPACT in test mode which performs the simulation with fewer iterations and fixed seed. In this mode, OncoIMPACT should complete in less than 2 hours using a single thread.

NEW: Sanity checks to ensure validity of parameters provided by user

FIX: Improved disk space utilization

FIX: Improved compatibility with Mac OS.

v0.9.1:

oncoIMPACT will now avoid reproducing the input files if COMPLETE_SAMPLES folder exists

fix for bugs introduced in last version

Licensing

The MIT License (MIT) Copyright (c) 2014 Genome Institute of Singapore

Contacts

If you want community-driven support, please visit the forum at https://sourceforge.net/p/oncoimpact/discussion/.

If you have a bug to report, you may raise a ticket at https://sourceforge.net/p/oncoimpact/tickets/.

If you have other questions or feedback, you may direct them to Jayce (kohjy@gis.a-star.edu.sg) and Denis (bertrandd@gis.a-star.edu.sg).

Project Members: