Detection of SNP by the isothermal smart amplification method

Methods Mol Biol. 2009:578:437-51. doi: 10.1007/978-1-60327-411-1_28.

Abstract

The complexity of molecular diagnostic assays is a significant barrier to employment in point-of-care diagnostics, despite the growing need for such technologies. We have developed a sensitive, accurate, rapid, and simple DNA amplification scheme that shows potential for translational medicine from pharmacogenomics-based drug discovery through to point-of-care diagnostics. Called the "Smart Amplification process 2" (SmartAmp 2), the method is isothermal, and employs a unique primer design and background suppression technology that can amplify target sequences from crude cell lysates. The specificity of the SmartAmp 2 assay enables detection of single-nucleotide differences such as somatic mutations in tumors and single nucleotide polymorphism (SNP) variants. Because mismatch amplification can be completely suppressed in SmartAmp 2, a reliable diagnostic result can be achieved based exclusively on amplification alone. Furthermore, mutation detection and SNP genotypes can be obtained in as little as 30-40 min from sample preparation of raw blood or tissue specimens.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aldehyde Dehydrogenase / genetics
  • Aldehyde Dehydrogenase, Mitochondrial
  • Alleles
  • Base Sequence
  • Biological Assay
  • DNA / genetics
  • DNA Primers / metabolism
  • DNA-Directed DNA Polymerase / metabolism
  • Electrophoresis, Agar Gel
  • Humans
  • Molecular Sequence Data
  • MutS DNA Mismatch-Binding Protein / metabolism
  • Nucleic Acid Amplification Techniques / methods*
  • Polymorphism, Single Nucleotide / genetics*
  • Temperature*

Substances

  • DNA Primers
  • DNA
  • ALDH2 protein, human
  • Aldehyde Dehydrogenase
  • Aldehyde Dehydrogenase, Mitochondrial
  • DNA-Directed DNA Polymerase
  • MutS DNA Mismatch-Binding Protein