SEISMIC identifies genomic regions where mutations are positively selected in cancer genomes, by analysing the distribution of mutations across a tumour cohort. In the absence of positive selection, mutations in a given gene will intuitively be found mostly in the tumours with the highest mutation burden overall. As positive selection acts on all tumours regardless of their mutation burden, cancer driver genes tend to exhibit a "skew" towards mutations occurring in low burden tumours compared to passenger genes.
When assessing a gene, SEISMIC uses tumour mutation burden, as well as a trinucleotide-based mutational model, to determine the probability of observing mutations in that gene in each tumour. By ignoring the total number of mutations in the gene and evaluating only which tumours contain mutations, SEISMIC evaluates a selection signal that is independent of recurrence. This comes with other strengths and weaknesses compared to frequency-based methods, and thus provides a complement to other tools.
SEISMIC can be run on a computer or server running Linux, preferably with a decent amount of RAM (at least 32 GB). R is required (version 4.1.0 tested), as well as the following R packages (tested versions in parentheses):
tidyverse(1.3.1)yaml(2.3.5)foreach(1.5.2)doSNOW(1.0.20)stringi(1.7.6)inline(0.3.19)Rcpp(1.0.8.3)fitdistrplus(1.1.8)data.table(1.14.2)plyranges(1.14.0)BSgenome.Hsapiens.UCSC.hg19(1.4.3) and/orBSgenome.Hsapiens.UCSC.hg38(1.4.4)cowplot(1.1.1)R.utils(2.12.2) - This is only required for compressed mutation files.
To use the SEISMIC script, simply clone this repository, and run it according to the usage instructions below.
There is an installation script for the required R packages (demo/install_R_dependencies.R) that can be sourced from the R console to install the most recent versions. Note that simply running the script from the command line (e.g., Rscript install_R_dependencies.R) may not work, as the user may not have permission to install R packages globally, and will not be able to accept local installation outside of the R console. The installation takes approximately 30 minutes if no packages were installed previously.
There is a demo script (demo/run_demo.sh) that uses SEISMIC to analyse TCGA UCEC SNVs in gene CDSs. Before running this script, make sure to install the required R packages (see above). SEISMIC will use the settings in demo/demo_config.yaml. If the machine running the demo has ample RAM, multi-threading can be enabled by changing the "cores" value in the config file to speed up analysis. For reference, 1-2 GB of RAM may be used per thread.
The demo script runs SEISMIC, which first annotates mutation effects in gene CDSs (10 min using 16 GB RAM on our system with 16 threads available), and then runs the test (30 min using ~45 GB RAM running on 30 threads on our system). The expected output is available in demo/expected_output. Note that p-values are partially the result of random simulations, and as such will vary somewhat compared to the expected output.
SEISMIC is run from the command line, with a yaml config file as input argument.
./SEISMIC.R config.yamlThe SEISMIC script requires a yaml config file to run. A template config file with default values is supplied in config/config_template.yaml, annotated with explanations of the variables.
Mutations (hg19 or hg38 coordinates) can either be in MAF format, or tab-separated with column names at the top of the file, with the following columns:
seqnames: chromosome name (e.g., chr1)start: 1-based position of mutationend: 1-based position of mutationstrand: strand of the refnuc/varnuccancer: cancer type. Multiple cancer types in one file will filter to the specified cancer type.refnuc: reference nucleotidevarnuc: variant nucleotidesampleID: patient ID
Compressed files (.gz and .bz2) are supported provided that R.utils is installed.
Mutation calls of high quality are important, as false somatic mutation calls (e.g. misclassified germline mutations) are expected to be indistinguishable from drivers to SEISMIC. This is because they will exhibit a lack of correlation with tumour mutation burden, just like drivers.
A file with region definitions for the regions to be analysed is required. The files used for gene CDSs, promoters, and introns in the paper are available in the data directory.
When running SEISMIC with mutation expectation scaling to replication timing or expression, the relevant files are available in the data directory. Please note that this is only relevant when analysing recurrence as well as cohort distribution, and not required for normal use as in the paper.