MALDI-TOF MS genotyping of polymorphisms related to 1-carbon metabolism using common and mass-modified terminators.
BACKGROUND
Large cohort studies may provide sufficient power to disentangle the role of polymorphisms related to 1-carbon metabolism and chronic diseases, but they require fast, accurate, high-throughput genotyping techniques. MALDI-TOF mass spectrometry has been adapted to rapid fine mapping using various approaches for allele discrimination. We developed a genotyping method based on MALDI-TOF MS and compared assay performance for formats based on standard and mass-modified terminators.


METHODS
The assay includes 20 polymorphisms of 14 genes involved in 1-carbon metabolism (BHMT 742G>A, CBS 844ins68 and 699C>T, CTH 1364G>T, DHFR del19, NOS3 -786T>C and 894G>T, FOLR1 1314G>A, MTHFD1 -105T>C and 1958G>A, MTHFR 677C>T and 1298A>C, MTR 2756A>G, MTRR 66A>G and 524C>T, SLC19A1 80G>A, SHMT1 1420C>T, TCN2 67A>G and 776C>G, and TYMS 1494del6).


RESULTS
Missing calls were observed for 4.7% of the DNA samples, attributed to failed liquid sample handling. Highly accurate genotyping was obtained by mass-modified as well as standard ddNTPs, with an average error rate of < or =0.1% by analysis of sample duplicates. A semiquantitative approach enabled unambiguous identification of the CBS 844ins68. Cluster plots of the relative allele intensities showed allele-specific bias according to type of minisequencing terminator and revealed a potential structural variation in the BHMT gene.


CONCLUSIONS
MALDI-TOF MS-based genotyping using either standard or mass-modified terminators allows the accurate determination of single nucleotides as well as structural genetic variants. This was demonstrated with 20 polymorphisms involved in 1-carbon metabolism.
Meyer
Klaus
K
Bevital A/S, Armauer Hansens Hus, University of Bergen, Bergen, Norway. klaus.meyer@farm.uib.no
Fredriksen
Ase
A
Ueland
Per Magne
PM
D000483:Alleles; D050940:Betaine-Homocysteine S-Methyltransferase / Q000235:genetics; D002244:Carbon / Q000378:metabolism*; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
D002244:Carbon; D004247:DNA; C494548:BHMT protein, human; D050940:Betaine-Homocysteine S-Methyltransferase