Hierarchical high-throughput SNP genotyping of the human Y chromosome using MALDI-TOF mass spectrometry

Nucleic Acids Res. 2002 Mar 15;30(6):e27. doi: 10.1093/nar/30.6.e27.


We have established the use of a primer extension/mass spectrometry method (the PinPoint assay) for high-throughput SNP genotyping of the human Y chromosome. 118 markers were used to define 116 haplogroups and typing was organised in a hierarchical fashion. Twenty multiplex PCR/primer extension reactions were set up and each sample could be assigned to a haplogroup with only two to five of these multiplex analyses. A single aliquot of one enzyme was found to be sufficient for both PCR and primer extension. We observed 100% accuracy in blind validation tests. The technique thus provides a reliable, cost-effective and automated method for Y genotyping, and the advantages of using a hierarchical strategy can be applied to any DNA segment lacking recombination.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Primers
  • Genetic Markers
  • Genotype
  • Humans
  • Male
  • Polymerase Chain Reaction / methods
  • Polymorphism, Single Nucleotide*
  • Reproducibility of Results
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods*
  • Y Chromosome*


  • DNA Primers
  • Genetic Markers