Genotyping on ALDH2: comparison of four different technologies

PLoS One. 2015 Mar 24;10(3):e0122745. doi: 10.1371/journal.pone.0122745. eCollection 2015.

Abstract

Objectives: This study aimed to compare the accuracy and performance of four genotyping methods for detecting single nucleotide polymorphisms (SNPs) in aldehyde dehydrogenase-2 (ALDH2), which is the principal enzyme involved in alcohol metabolism.

Design and methods: We genotyped rs671 of ALDH2 in 96 coronary heart disease (CHD) patients with four methods including high resolution melting analysis (HRM), TaqMan allelic discrimination assay (TaqMan), allele-specific PCR (AS-PCR) and pyrosequencing. Meanwhile, we compared the accuracy and performance of these methods.

Results: All selected patients were successfully genotyped with referred methods. The results of these four assays showed 100% concordant results and had 100% accuracy as verified by Sanger sequencing.

Conclusions: All of the referred methods can be used for genotyping ALDH2 rs671 with the same accuracy compared to Sanger sequencing. In small size of clinical samples, HRM and AS-PCR outperform over others due to their lower cost and less hands-on operation, which are suitable for clinical application.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Aldehyde Dehydrogenase / genetics*
  • Aldehyde Dehydrogenase, Mitochondrial
  • Alleles
  • China
  • Coronary Disease / genetics*
  • Female
  • Genotyping Techniques / economics
  • Genotyping Techniques / methods*
  • Humans
  • Male
  • Polymerase Chain Reaction / methods
  • Polymorphism, Single Nucleotide / genetics*
  • Predictive Value of Tests
  • Sequence Analysis, DNA / methods
  • Transition Temperature

Substances

  • ALDH2 protein, human
  • Aldehyde Dehydrogenase
  • Aldehyde Dehydrogenase, Mitochondrial

Grants and funding

This work was supported by grants from National “973” project (No. 2012CB518004) and Chinese Medical Association to explore the Cardiovascular Research Foundation (No. DFCMDA201225). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.