Predicting cancer drivers: are we there yet?

doi:10.1186/gm389

. 2012 Nov 26;4(11):88.

doi: 10.1186/gm389. eCollection 2012.

Predicting cancer drivers: are we there yet?

Vidhya G Krishnan¹, Pauline C Ng¹

Affiliations

PMID: 23181697
PMCID: PMC3580422
DOI: 10.1186/gm389

Predicting cancer drivers: are we there yet?

Vidhya G Krishnan et al. Genome Med. 2012.

. 2012 Nov 26;4(11):88.

doi: 10.1186/gm389. eCollection 2012.

Authors

Vidhya G Krishnan¹, Pauline C Ng¹

Affiliation

¹ Computational and Mathematical Biology, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672.

PMID: 23181697
PMCID: PMC3580422
DOI: 10.1186/gm389

Abstract

Genomic variants with a key role in causing cancer or affecting the response to cancer therapeutics need to be identified so that they can be targeted for therapy. The transFIC tool aims to identify somatic point mutations that drive cancer in sequencing projects. This package is available as a web service, a stand-alone program and a website. It improves the functional prediction scores generated by popular established prediction tools and will be useful to cancer researchers.

See research article: http://genomemedicine.com/content/4/11/89.

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1. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A. et al.A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010;463:191–196. doi: 10.1038/nature08658. - DOI - PMC - PubMed
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1. Kaminker JS, Zhang Y, Watanabe C, Zhang Z. CanPredict: a computational tool for predicting cancer-associated missense mutations. Nucleic Acids Res. 2007;35:W595–W598. doi: 10.1093/nar/gkm405. - DOI - PMC - PubMed

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[1] Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J. et al.Mutations of the BRAF gene in human cancer. Nature. 2002;417:949–954. doi: 10.1038/nature00766. - DOI - PubMed

[2] Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J. et al.Mutations of the BRAF gene in human cancer. Nature. 2002;417:949–954. doi: 10.1038/nature00766. - DOI - PubMed

[3] Di Nicolantonio F, Martini M, Molinari F, Sartore-Bianchi A, Arena S, Saletti P, De Dosso S, Mazzucchelli L, Frattini M, Siena S, Bardelli A. Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer. J Clin Oncol. 2008;26:5705–5712. doi: 10.1200/JCO.2008.18.0786. - DOI - PubMed

[4] Di Nicolantonio F, Martini M, Molinari F, Sartore-Bianchi A, Arena S, Saletti P, De Dosso S, Mazzucchelli L, Frattini M, Siena S, Bardelli A. Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer. J Clin Oncol. 2008;26:5705–5712. doi: 10.1200/JCO.2008.18.0786. - DOI - PubMed

[5] Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A. et al.A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010;463:191–196. doi: 10.1038/nature08658. - DOI - PMC - PubMed

[6] Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A. et al.A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010;463:191–196. doi: 10.1038/nature08658. - DOI - PMC - PubMed

[7] Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res. 2009;69:6660–6667. doi: 10.1158/0008-5472.CAN-09-1133. - DOI - PMC - PubMed

[8] Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res. 2009;69:6660–6667. doi: 10.1158/0008-5472.CAN-09-1133. - DOI - PMC - PubMed

[9] Kaminker JS, Zhang Y, Watanabe C, Zhang Z. CanPredict: a computational tool for predicting cancer-associated missense mutations. Nucleic Acids Res. 2007;35:W595–W598. doi: 10.1093/nar/gkm405. - DOI - PMC - PubMed

[10] Kaminker JS, Zhang Y, Watanabe C, Zhang Z. CanPredict: a computational tool for predicting cancer-associated missense mutations. Nucleic Acids Res. 2007;35:W595–W598. doi: 10.1093/nar/gkm405. - DOI - PMC - PubMed

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Predicting cancer drivers: are we there yet?

Affiliation

Predicting cancer drivers: are we there yet?

Authors

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Abstract

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