Analytical Validation of <i>SOD2</i> Genotyping

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

doi:10.3390/mps6010004

Methods and Protocols (Dec 2022)

Analytical Validation of <i>SOD2</i> Genotyping

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

Affiliations

Marija Debeljak: Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
Stacy Riel: Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
Ming-Tseh Lin: Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
James R. Eshleman: Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
Channing J. Paller: Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA

DOI: https://doi.org/10.3390/mps6010004
Journal volume & issue: Vol. 6, no. 1
p. 4

Abstract

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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.

Published in Methods and Protocols

ISSN: 2409-9279 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Biology (General)
Website: https://www.mdpi.com/journal/mps

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