Genomic landscape of DNA repair genes in cancer

Young Kwang Chae*, Jonathan F. Anker, Benedito A Carneiro Filho, Sunandana Chandra, Jason B Kaplan, Aparna Kalyan, Cesar Augusto Santa-Maria, Leonidas C Platanias, Francis Joseph Giles

*Corresponding author for this work

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

DNA repair genes are frequently mutated in cancer, yet limited data exist regarding the overall genomic landscape and functional implications of these alterations in their entirety. We created comprehensive lists of DNA repair genes and indirect caretakers. Mutation, copy number variation (CNV), and expression frequencies of these genes were analyzed in COSMIC. Mutation co-occurrence, clinical outcomes, and mutation burden were analyzed in TCGA. We report the 20 genes most frequently with mutations (n > 19,689 tumor samples for each gene), CNVs (n > 1,556), or up-or down-regulated (n = 7,998). Mutual exclusivity was observed as no genes displayed both high CNV gain and loss or high up-and down-regulation, and CNV gain and loss positively correlated with up-and down-regulation, respectively. Co-occurrence of mutations differed between cancers, and mutations in many DNA repair genes were associated with higher total mutation burden. Mutation and CNV frequencies offer insights into which genes may play tumor suppressive or oncogenic roles, such as NEIL2 and RRM2B, respectively. Mutual exclusivities within CNV and expression frequencies, and correlations between CNV and expression, support the functionality of these genomic alterations. This study provides comprehensive lists of candidate genes as potential biomarkers for genomic instability, novel therapeutic targets, or predictors of immunotherapy efficacy.

Original languageEnglish (US)
Pages (from-to)23312-23321
Number of pages10
JournalOncotarget
Volume7
Issue number17
DOIs
StatePublished - Apr 26 2016

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Neoplasm Genes
DNA Repair
Mutation
Genes
Neoplasms
Up-Regulation
Down-Regulation
Genomic Instability
Gene Frequency
Immunotherapy
Biomarkers
Gene Expression

Keywords

  • Cancer
  • Copy number variations
  • DNA repair
  • Gene expression
  • Mutations

ASJC Scopus subject areas

  • Oncology

Cite this

Chae, Y. K., Anker, J. F., Carneiro Filho, B. A., Chandra, S., Kaplan, J. B., Kalyan, A., ... Giles, F. J. (2016). Genomic landscape of DNA repair genes in cancer. Oncotarget, 7(17), 23312-23321. https://doi.org/10.18632/oncotarget.8196
Chae, Young Kwang ; Anker, Jonathan F. ; Carneiro Filho, Benedito A ; Chandra, Sunandana ; Kaplan, Jason B ; Kalyan, Aparna ; Santa-Maria, Cesar Augusto ; Platanias, Leonidas C ; Giles, Francis Joseph. / Genomic landscape of DNA repair genes in cancer. In: Oncotarget. 2016 ; Vol. 7, No. 17. pp. 23312-23321.
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Chae, YK, Anker, JF, Carneiro Filho, BA, Chandra, S, Kaplan, JB, Kalyan, A, Santa-Maria, CA, Platanias, LC & Giles, FJ 2016, 'Genomic landscape of DNA repair genes in cancer', Oncotarget, vol. 7, no. 17, pp. 23312-23321. https://doi.org/10.18632/oncotarget.8196

Genomic landscape of DNA repair genes in cancer. / Chae, Young Kwang; Anker, Jonathan F.; Carneiro Filho, Benedito A; Chandra, Sunandana; Kaplan, Jason B; Kalyan, Aparna; Santa-Maria, Cesar Augusto; Platanias, Leonidas C; Giles, Francis Joseph.

In: Oncotarget, Vol. 7, No. 17, 26.04.2016, p. 23312-23321.

Research output: Contribution to journalArticle

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AU - Giles, Francis Joseph

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