Comparison of three methods for single nucleotide polymorphism typing for DNA bank studies: sequence-specific oligonucleotide probe hybridisation, TaqMan liquid phase hybridisation, and microplate array diagonal gel electrophoresis (MADGE)

Hum Mutat. 1999;14(4):340-7. doi: 10.1002/(SICI)1098-1004(199910)14:4<340::AID-HUMU10>3.0.CO;2-Z.

Abstract

In the near future the number of SNPs identified and mapped will increase and the need for high throughput SNP typing will be paramount for comprehensive examination by association of the role of genomic regions in disease traits. A range of higher throughput methods for typing SNPs is now in routine use in many laboratories worldwide. In this report, we analyse the relative advantages and disadvantages of three such methods, TaqMan, PCR-SSOP, and ARMS-MADGE, currently in use in our laboratories. Throughputs achievable are similar, but there are major differences in cost and time for set-up, equipment, consumables, and staff time, which may determine the choice for individual laboratories.

Publication types

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

MeSH terms

  • Costs and Cost Analysis
  • DNA / genetics*
  • Electrophoresis
  • Gene Library*
  • Genes, MHC Class II*
  • Genetic Techniques* / economics
  • Genotype
  • HLA-DR Antigens / genetics*
  • HLA-DRB1 Chains
  • Humans
  • Nucleic Acid Hybridization
  • Oligonucleotide Probes
  • Polymerase Chain Reaction
  • Polymorphism, Genetic*
  • United Kingdom

Substances

  • HLA-DR Antigens
  • HLA-DRB1 Chains
  • Oligonucleotide Probes
  • DNA