OncoIMPACT Files

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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.

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Installation

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

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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.

When you are ready to run the OncoIMPACT pipeline, simply enter the following command oncoIMPACT.pl <path to config file>

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Test datasets

We have provided test datasets for running the OncoIMPACT pipeline in 2 different ways.

• sampleConfig_disc.cfg: sample config for discovery mode

. single_patient.tgz: data for a single GBM patient (this file should be uncompressed)

. Glioblastoma_database.tgz: pre-computed database of the TCGA GBM dataset

• sampleConfig_db_disc.cfg: sample config for database and discovery mode

. Glioblastoma.tgz: Glioblastoma (GBM) TCGA dataset (this file should be uncompressed)

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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

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Licensing

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

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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).