Direct genetic analysis by matrix-assisted laser desorption ionization mass spectrometry

An approach to analyzing single-nucleotide polymorphisms (SNPs) found in th e human genome has been developed that couples a recently developed invasiv e cleavage assay for nucleic acids with detection by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The invasive cleavage assay is a signal amplification method that enables the a nalysis of SNPs by MALDI-TOF MS directly from human genomic DNA without the need for initial target amplification by PCR. The results presented here s how the successful genotyping by this approach of twelve SNPs located rando mly throughout the human genome. Conventional Sanger sequencing of these SN P positions confirmed the accuracy of the MALDI-TOF MS analysis results. Th e ability to unambiguously detect both homozygous and heterozygous genotype s is clearly demonstrated. The elimination of the need for target amplifica tion by PCR, combined with the inherently rapid and accurate nature of dete ction by MALDI-TOF MS, gives this approach unique and significant advantage s in the high-throughput genotyping of large numbers of SNPs, useful for lo cating, identifying, and characterizing the function of specific genes.