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Assessing matched normal and tumor pairs in next-generation sequencing studies.

Publication ,  Journal Article
Goh, L; Chen, GB; Cutcutache, I; Low, B; Teh, BT; Rozen, S; Tan, P
Published in: PLoS One
March 18, 2011

Next generation sequencing technology has revolutionized the study of cancers. Through matched normal-tumor pairs, it is now possible to identify genome-wide germline and somatic mutations. The generation and analysis of the data requires rigorous quality checks and filtering, and the current analytical pipeline is constantly undergoing improvements. We noted however that in analyzing matched pairs, there is an implicit assumption that the sequenced data are matched, without any quality check such as those implemented in association studies. There are serious implications in this assumption as identification of germline and rare somatic variants depend on the normal sample being the matched pair. Using a genetics concept on measuring relatedness between individuals, we demonstrate that the matchedness of tumor pairs can be quantified and should be included as part of a quality protocol in analysis of sequenced data. Despite the mutation changes in cancer samples, matched tumor-normal pairs are still relatively similar in sequence compared to non-matched pairs. We demonstrate that the approach can be used to assess the mutation landscape between individuals.

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Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

March 18, 2011

Volume

6

Issue

3

Start / End Page

e17810

Location

United States

Related Subject Headings

  • Neoplasms
  • Humans
  • Germ-Line Mutation
  • General Science & Technology
  • Cluster Analysis
 

Citation

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Goh, L., Chen, G. B., Cutcutache, I., Low, B., Teh, B. T., Rozen, S., & Tan, P. (2011). Assessing matched normal and tumor pairs in next-generation sequencing studies. PLoS One, 6(3), e17810. https://doi.org/10.1371/journal.pone.0017810
Goh, Liang, Geng Bo Chen, Ioana Cutcutache, Benjamin Low, Bin Tean Teh, Steve Rozen, and Patrick Tan. “Assessing matched normal and tumor pairs in next-generation sequencing studies.PLoS One 6, no. 3 (March 18, 2011): e17810. https://doi.org/10.1371/journal.pone.0017810.
Goh L, Chen GB, Cutcutache I, Low B, Teh BT, Rozen S, et al. Assessing matched normal and tumor pairs in next-generation sequencing studies. PLoS One. 2011 Mar 18;6(3):e17810.
Goh, Liang, et al. “Assessing matched normal and tumor pairs in next-generation sequencing studies.PLoS One, vol. 6, no. 3, Mar. 2011, p. e17810. Pubmed, doi:10.1371/journal.pone.0017810.
Goh L, Chen GB, Cutcutache I, Low B, Teh BT, Rozen S, Tan P. Assessing matched normal and tumor pairs in next-generation sequencing studies. PLoS One. 2011 Mar 18;6(3):e17810.

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

March 18, 2011

Volume

6

Issue

3

Start / End Page

e17810

Location

United States

Related Subject Headings

  • Neoplasms
  • Humans
  • Germ-Line Mutation
  • General Science & Technology
  • Cluster Analysis