Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

The Cancer Genome Atlas Research Network

Research output: Contribution to journalArticlepeer-review

226 Scopus citations


DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy. Knijnenburg et al. present The Cancer Genome Atlas (TCGA) Pan-Cancer analysis of DNA damage repair (DDR) deficiency in cancer. They use integrative genomic and molecular analyses to identify frequent DDR alterations across 33 cancer types, correlate gene- and pathway-level alterations with genome-wide measures of genome instability and impaired function, and demonstrate the prognostic utility of DDR deficiency scores.

Original languageEnglish (US)
Pages (from-to)239-254.e6
JournalCell Reports
Issue number1
StatePublished - Apr 3 2018


  • DNA damage footprints
  • DNA damage repair
  • The Cancer Genome Atlas PanCanAtlas project
  • epigenetic silencing
  • integrative statistical analysis
  • mutational signatures
  • protein structure analysis
  • somatic copy-number alterations
  • somatic mutations

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology


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