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PMID: 20843826 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Review

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

Human molecular genetics ·Vol. 19 ·No. R2 ·2010-10-15 ·Pages R188-96

Ding L, Wendl MC, Koboldt DC, Mardis ER

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, pathway-based 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.

MeSH Terms
Genomics/methods Humans Neoplasms/genetics Sequence Analysis, DNA/methods,statistics & numerical data
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Ding Li
Department of Genetics, The Genome Center at Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO 63108, USA.
Wendl Michael C
Koboldt Daniel C
Mardis Elaine R
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Article Info
Journal
Human molecular genetics
Abbr.
Hum Mol Genet
ISSN
1460-2083
DOI
10.1093/hmg/ddq391
Published
2010-10-15
Epub
2010-00-15
Pages
R188-96
Language
English
Region
England
NLM ID
9208958
PMCID
PMC2953747
Subset
IM
Grants
NHGRI NIH HHS · U54 HG003079 · United States
External Links
PubMed source DOI: 10.1093/hmg/ddq391 PMC Full Text View journal details
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