Analysis of next-generation genomic data in cancer: Accomplishments and challenges

Li Ding, Michael C. Wendl, Daniel C. Koboldt, Elaine R. Mardis

Research output: Contribution to journalArticle

95 Scopus citations

Abstract

The application of next-generation sequencing technology has produced a transformation in cancer genomics, generating large data sets that can be analyzed in different ways to answer a multitude of questions about the genomic alterations associated with the disease. Analytical approaches can discover focused mutations such as substitutions and small insertion/deletions, large structural alterations and copy number events. As our capacity to produce such data for multiple cancers of the same type is improving, so are the demands to analyze multiple tumor genomes simultaneously growing. For example, pathwaybased analyses that provide the full mutational impact on cellular protein networks and correlation analyses aimed at revealing causal relationships between genomic alterations and clinical presentations are both enabled. As the repertoire of data grows to include mRNA-seq, non-coding RNA-seq and methylation for multiple genomes, our challenge will be to intelligently integrate data types and genomes to produce a coherent picture of the genetic basis of cancer.

Original languageEnglish
Pages (from-to)R188-R196
JournalHuman molecular genetics
Volume19
Issue numberR2
DOIs
StatePublished - Oct 15 2010

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