MuSiC: Identifying mutational significance in cancer genomes
Top Cited Papers
Open Access
- 3 July 2012
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 22 (8), 1589-1598
- https://doi.org/10.1101/gr.134635.111
Abstract
Massively parallel sequencing technology and the associated rapidly decreasing sequencing costs have enabled systemic analyses of somatic mutations in large cohorts of cancer cases. Here we introduce a comprehensive mutational analysis pipeline that uses standardized sequence-based inputs along with multiple types of clinical data to establish correlations among mutation sites, affected genes and pathways, and to ultimately separate the commonly abundant passenger mutations from the truly significant events. In other words, we aim to determine the Mutational Significance in Cancer (MuSiC) for these large data sets. The integration of analytical operations in the MuSiC framework is widely applicable to a broad set of tumor types and offers the benefits of automation as well as standardization. Herein, we describe the computational structure and statistical underpinnings of the MuSiC pipeline and demonstrate its performance using 316 ovarian cancer samples from the TCGA ovarian cancer project. MuSiC correctly confirms many expected results, and identifies several potentially novel avenues for discovery.Keywords
This publication has 37 references indexed in Scilit:
- Integrated genomic analyses of ovarian carcinomaNature, 2011
- PathScan: a tool for discerning mutational significance in groups of putative cancer genesBioinformatics, 2011
- Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGMBioinformatics, 2010
- Forkhead box M1 transcription factor: A novel target for cancer therapyCancer Treatment Reviews, 2010
- Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovaryThe Journal of Pathology, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- A novel signaling pathway impact analysisBioinformatics, 2008
- Somatic mutations affect key pathways in lung adenocarcinomaNature, 2008
- The Catalogue of Somatic Mutations in Cancer (COSMIC)Current Protocols in Human Genetics, 2008