November 2014

Launch of the G-2-O website. Genotype to Outcome is a web-server linking a selected mutation(s) to actual clinical outcome (survival) by utilizing next generation sequencing and gene chip data.

What is the rationale of G-2-O?
Genotype to Outcome is based on the assumption that somatic mutations will not influence outcome alone. Instead, a mutation results in an altered protein product which influences a diverse set of genes. We capture and assess the prognostic potential of this signature.

How does it work?
NGS data generated by the TCGA consortia and publicly available gene chip data obtained from the GEO and EGA repositories are utilized. NGS data was pre-processed using MuTect, SNPeff, GRCh37 and R. RNA-seq data was normalized using DEseq. Gene chip data was MAS5 normalized. Generation of the transcriptomic fingerprint for mutation status is computed by ROC utilizing the RNA-seq and mutation data. Then, the average expression of significant genes identified is designated as a metagene for the given genotype. By utilizing the gene chip data, correlation to survival for this metagene is assessed by computing Cox regression and plotting Kaplan-Meier survival plots.

Which genes can I use?
Currently, G-2-0 recognizes 22,938 gene symbols.

How to cite
Manuscript submitted for publication.

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