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Patient-oriented gene set analysis for cancer mutation data

Simina M Boca1, Kenneth W Kinzler2, Victor E Velculescu2, Bert Vogelstein2 and Giovanni Parmigiani3*

Author affiliations

1 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205, USA

2 Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, 1650 Orleans Street, Baltimore, MD 21231, USA

3 Department of Biostatistics, Harvard School of Public Health and Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA

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Citation and License

Genome Biology 2010, 11:R112  doi:10.1186/gb-2010-11-11-r112

Published: 23 November 2010

Abstract

Recent research has revealed complex heterogeneous genomic landscapes in human cancers. However, mutations tend to occur within a core group of pathways and biological processes that can be grouped into gene sets. To better understand the significance of these pathways, we have developed an approach that initially scores each gene set at the patient rather than the gene level. In mutation analysis, these patient-oriented methods are more transparent, interpretable, and statistically powerful than traditional gene-oriented methods.