title: Hierarchical high-throughput SNP genotyping of the human Y chromosome using MALDI-TOF mass spectrometry.
abstract: 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.
authors.affiliation: CRC Chromosome Molecular Biology Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: Silvia
authors.initials: S
authors.lastname: Paracchini
authors.forename: Barbara
authors.initials: B
authors.lastname: Arredi
authors.forename: Rod
authors.initials: R
authors.lastname: Chalk
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
mesh_terms: D017931:DNA Primers; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D014998:Y Chromosome
chemical_list: D017931:DNA Primers; D005819:Genetic Markers