Analytical Validation of SOD2 Genotyping

Marija Debeljak, Stacy Riel, Ming Tseh Lin, James R. Eshleman, Channing J. Paller

Research output: Contribution to journalArticlepeer-review


Manganese superoxide dismutase-2 (SOD2) plays a crucial role in cells’ protection against mitochondrial oxidative damage. A genetic polymorphism in the mitochondrial targeting sequence of the SOD2 gene has been implicated in various diseases, including prostate cancer. Paller et al. have shown an increase in prostate-specific antigen (PSA) doubling time in patients with the Ala/Ala (wildtype) genotype when treated with pomegranate/grape extract antioxidants. We developed and validated a pyrosequencing assay that detects the common germline SOD2 SNP (rs_4880) with the aim of identifying men with castrate-resistant prostate cancer eligible for an antioxidant therapy clinical trial. We first selected 37 samples from the 1000 genomes study with known genotypes determined using Illumina-based sequencing and confirmed them by Sanger sequencing. In a blinded design, we then performed the new pyrosequencing assay on these samples and assigned genotypes. Genotypes for all 37 samples (13 homozygous Ala, 12 heterozygous Ala/Val, and 12 homozygous Val) were all concordant by pyrosequencing. The pyrosequencing assay has been live since May 2018 and has proven to be robust and accurate.

Original languageEnglish (US)
Article number4
JournalMethods and Protocols
Issue number1
StatePublished - Feb 2023


  • SOD2 gene
  • prostate cancer
  • prostate-specific antigen (PSA)
  • pyrosequencing

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Structural Biology
  • Biotechnology


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