DASH-2: flexible, low-cost, and high-throughput SNP genotyping by dynamic allele-specific hybridization on membrane arrays

Genome Res. 2003 May;13(5):916-24. doi: 10.1101/gr.801103.

Abstract

Genotyping technologies need to be continually improved in terms of their flexibility, cost-efficiency, and throughput, to push forward genome variation analysis. To this end, we have leveraged the inherent simplicity of dynamic allele-specific hybridization (DASH) and coupled it to recent innovations of centrifugal arrays and iFRET. We have thereby created a new genotyping platform we term DASH-2, which we demonstrate and evaluate in this report. The system is highly flexible in many ways (any plate format, PCR multiplexing, serial and parallel array processing, spectral-multiplexing of hybridization probes), thus supporting a wide range of application scales and objectives. Precision is demonstrated to be in the range 99.8-100%, and assay costs are 0.05 USD or less per genotype assignment. DASH-2 thus provides a powerful new alternative for genotyping practice, which can be used without the need for expensive robotics support.

Publication types

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

MeSH terms

  • Alleles*
  • Genotype
  • Humans
  • Membranes, Artificial*
  • Nucleic Acid Hybridization / genetics*
  • Nucleic Acid Hybridization / methods*
  • Oligonucleotide Array Sequence Analysis / economics*
  • Oligonucleotide Array Sequence Analysis / instrumentation
  • Oligonucleotide Array Sequence Analysis / methods*
  • Polymerase Chain Reaction / methods
  • Polymorphism, Single Nucleotide / genetics*
  • Sequence Analysis, DNA / economics
  • Sequence Analysis, DNA / instrumentation
  • Sequence Analysis, DNA / methods
  • Temperature

Substances

  • Membranes, Artificial