MEDICC - Minimum Event Distance for Intra-tumour Copy number Comparisons
MEDICC harnesses the power of a finite-state automaton representation of genomic profiles to model genomic rearrangement events with horizontal dependencies.
Efficient transducer-based implementations allow for the exact computation of evolutionary distances and ancestral reconstructions.
The accompanying R package MEDICCquant implements follow-up analyses including tests for molecular clock, tests for phylogenetic structure, and quantification of clonal expansion and heterogeneity.
Download and Installation
You can download MEDICC from https://bitbucket.org/rfs/medicc
Requirements:
- Cygwin on Windows
- OpenFST 1.3.2 compiled and in your PATH
- Phylip compiled and in your PATH
- FST Framework (git clone git@bitbucket.org:rfs/fstframework.git) and in your PYTHONPATH
Installation:
- Navigate to the "medicc_binaries" subfolder, compile using "make" under Cygwin or Unix
- Main executable "cnv_infer_tree_multichrom.py" takes two arguments (+options):
- Description file indicating the position of the major and minor CNV sequences
- Output directory
- For an example see the "examples" subfolder
References:
-
Quantification of intra-tumor heterogeneity predicts time to relapse in high-grade serous ovarian cancer
R.F. Schwarz, C.K.Y. Ng, S.L. Cooke, S. Newman, J. Temple, A.M. Piskorz, D. Gale, K. Sayal, M. Murtaza, P.J Baldwin, N. Rosenfeld, H.M. Earl, E. Sala, M. Jimenez-Linan, C.A. Parkinson, F. Markowetz^, J.D. Brenton^
in prep. -
Phylogenetic quantification of intra-tumour heterogeneity
R.F. Schwarz, A. Trinh, B. Sipos, J.D. Brenton, N. Goldman, F. Markowetz
PLoS Comp Bio 2014, 10(4): e1003535
PMID:24743184 | doi:10.1371/journal.pcbi.1003535 | arXiv:1306.1685
