title: Single nucleotide polymorphism analysis in the human phosphatase PTPrj gene using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry.
abstract: Data derived from analysis of single nucleotide polymorphisms (SNPs) are being applied in many diverse fields, from medical studies of disease mechanisms and individual drug response, to population genetics for tracking migration and mixing of ancestral groups and also in forensic science for the identification of human remains and identification of individuals from bodily samples. All these applications have in common the need to generate data for multiple loci from large numbers of samples. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) is a promising platform for the generation of such data and we present a simple, flexible and robust technique for SNP determination. We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human phosphatase gene PTPrj, which has been implicated in the aetiology of colon, lung, breast and thyroid cancers. A nucleotide depletion primer extension assay using no commercial kits or dideoxyNTPs was used to genotype a panel of DNAs derived from thyroid cancer patients and normal volunteers. The results obtained were in perfect agreement with those generated via restriction fragment length polymorphism analysis. No significant association was noted between possession of either allelic variant and a disease state, but the technique was validated as simple, flexible and appropriate for application in this context. Furthermore, it was highly cost-effective and required minimal optimisation, rendering it ideal for this type of pilot study.
authors.affiliation: Human Cancer Studies Group, Swansea Medical School, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, Wales, UK. n.g.powell@swansea.ac.uk
authors.forename: Ned
authors.initials: N
authors.lastname: Powell
authors.forename: Ed
authors.initials: E
authors.lastname: Dudley
authors.forename: Mariko
authors.initials: M
authors.lastname: Morishita
authors.forename: Tetyana
authors.initials: T
authors.lastname: Bogdanova
authors.forename: Mykola
authors.initials: M
authors.lastname: Tronko
authors.forename: Gerry
authors.initials: G
authors.lastname: Thomas
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000032:analysis / Q000235:genetics*; D002648:Child; D015331:Cohort Studies; D004252:DNA Mutational Analysis / Q000379:methods; D004273:DNA, Neoplasm / Q000032:analysis / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D020022:Genetic Predisposition to Disease / Q000235:genetics; D005820:Genetic Testing / Q000379:methods; D006801:Humans; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017027:Protein Tyrosine Phosphatases / Q000032:analysis / Q000235:genetics*; D054631:Receptor-Like Protein Tyrosine Phosphatases, Class 3; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D013964:Thyroid Neoplasms / Q000175:diagnosis / Q000201:enzymology* / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm; C486288:PTPRJ protein, human; D017027:Protein Tyrosine Phosphatases; D054631:Receptor-Like Protein Tyrosine Phosphatases, Class 3