Open AccessHierarchical high-throughput SNP genotyping of the human Y chromosome using MALDI-TOF mass spectrometry
Author(s) -
Silvia Paracchini
Publication year - 2002
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/30.6.e27
Subject(s) - genotyping , biology , primer extension , multiplex , molecular inversion probe , snp genotyping , primer (cosmetics) , genetics , multiplex polymerase chain reaction , haplogroup , in silico pcr , computational biology , typing , snp , polymerase chain reaction , microbiology and biotechnology , single nucleotide polymorphism , dna , genotype , haplotype , gene , base sequence , chemistry , organic chemistry
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
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