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, 8 (12), e1002824

Chapter 14: Cancer Genome Analysis

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Chapter 14: Cancer Genome Analysis

Miguel Vazquez et al. PLoS Comput Biol.

Abstract

Although there is great promise in the benefits to be obtained by analyzing cancer genomes, numerous challenges hinder different stages of the process, from the problem of sample preparation and the validation of the experimental techniques, to the interpretation of the results. This chapter specifically focuses on the technical issues associated with the bioinformatics analysis of cancer genome data. The main issues addressed are the use of database and software resources, the use of analysis workflows and the presentation of clinically relevant action items. We attempt to aid new developers in the field by describing the different stages of analysis and discussing current approaches, as well as by providing practical advice on how to access and use resources, and how to implement recommendations. Real cases from cancer genome projects are used as examples.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Idealized cancer analysis pipeline.
The column on the left shows a list of sequential steps. The columns on the right show the bioinformatics and molecular biology disciplines involved at each step, the types of techniques employed and some of the current challenges faced.
Figure 2
Figure 2. Main tasks in an analysis pipeline.
Starting with the patient information derived from NGS experiments, the variants are mapped between genes and proteins, evaluated for pathogenicity, considered systemically through functional analysis, and the resulting conclusions translated into actionable results.

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Cited by 3 PubMed Central articles

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Grant support

This article was supported in part by the grant from the Spanish Ministry of Science and Innovation BIO2007-66855 and the EU FP7 project ASSET, grant agreement 259348. The funders had no role in the preparation of the manuscript.
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