Parallel Gene Analysis With Allele-Specific Padlock Probes and Tag Microarrays

Nucleic Acids Res. 2003 Sep 1;31(17):e103. doi: 10.1093/nar/gng104.


Parallel, highly specific analysis methods are required to take advantage of the extensive information about DNA sequence variation and of expressed sequences. We present a scalable laboratory technique suitable to analyze numerous target sequences in multiplexed assays. Sets of padlock probes were applied to analyze single nucleotide variation directly in total genomic DNA or cDNA for parallel genotyping or gene expression analysis. All reacted probes were then co-amplified and identified by hybridization to a standard tag oligonucleotide array. The technique was illustrated by analyzing normal and pathogenic variation within the Wilson disease-related ATP7B gene, both at the level of DNA and RNA, using allele-specific padlock probes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / genetics
  • Alleles
  • Cation Transport Proteins / genetics
  • Copper-Transporting ATPases
  • DNA / chemistry
  • DNA / genetics
  • DNA Mutational Analysis
  • DNA, Complementary / chemistry
  • DNA, Complementary / genetics
  • Genotype
  • Humans
  • Mutation
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Probes / genetics*
  • Polymorphism, Single Nucleotide / genetics*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / methods


  • Cation Transport Proteins
  • DNA, Complementary
  • Oligonucleotide Probes
  • DNA
  • Adenosine Triphosphatases
  • ATP7B protein, human
  • Copper-Transporting ATPases