Sample type bias in the analysis of cancer genomes.


Journal Article

There is widespread agreement that cancer gene discovery requires high-quality tumor samples. However, whether primary tumors or cultured samples are superior for cancer genomics has been a longstanding subject of debate. This debate has recently become more important because federally funded cancer genomics has been centralized under The Cancer Genome Atlas, which has chosen to focus exclusively on primary tumors. Here, we provide a data-driven "perspective" on the effect of sample type selection on cancer genomics research. We show that, in the case of glioblastoma multiforme, primary tumors and xenografts are best for the identification of amplifications, whereas xenografts and cell lines are superior for the identification of homozygous deletions. We also note that many of the most important oncogenes and tumor suppressor genes have been discovered through the use of cell lines and xenografts, and highlight the lack of published evidence supporting the dogma that ex vivo culture generates artifactual genetic lesions. Based on this analysis, we suggest that cancer genomics projects such as The Cancer Genome Atlas should include a variety of sample types such as xenografts and cell lines in their integrated genomic analysis of cancer.

Full Text

Duke Authors

Cited Authors

  • Solomon, DA; Kim, J-S; Ressom, HW; Sibenaller, Z; Ryken, T; Jean, W; Bigner, D; Yan, H; Waldman, T

Published Date

  • July 15, 2009

Published In

Volume / Issue

  • 69 / 14

Start / End Page

  • 5630 - 5633

PubMed ID

  • 19567670

Pubmed Central ID

  • 19567670

Electronic International Standard Serial Number (EISSN)

  • 1538-7445

Digital Object Identifier (DOI)

  • 10.1158/0008-5472.CAN-09-1055


  • eng

Conference Location

  • United States