High-throughput SNP genotyping with the Masscode system

Mol Diagn. 2000 Dec;5(4):329-40. doi: 10.1007/BF03262094.


QIAGEN Genomics, Inc, has developed the Masscode tagging system for DNA labeling and detection. In this application, the Masscode system is described as applied to high-throughput single-nucleotide polymorphism (SNP) genotyping. The labeling system is based on a small-molecular-weight tag that is covalently attached through a photocleavable linker to a DNA oligonucleotide. The tagged oligonucleotide is used as a primer in an allele-specific PCR SNP discrimination assay. The allele-specific amplicons are differentiated through their Masscode tag assignments. After a photolysis step to cleave the tags from the amplicon, the samples are introduced into a single quadrupole mass spectrometry detection system for analysis. Genotyping determinations are based on the relative proportions of the paired allele tags. The system has a lower limit of detection in the femtomolar range (10(-15) M). At present, 30 different Masscode tags may be used simultaneously in a multiplex fashion to routinely provide more than 40,000 SNP genotyping measurements daily. Further developments will allow for the simultaneous detection of several hundred tags.

Publication types

  • Review

MeSH terms

  • Alleles
  • Gene Expression Profiling / methods
  • Genotype
  • Humans
  • Mass Spectrometry / methods
  • Polymorphism, Single Nucleotide / genetics*
  • Proteome


  • Proteome