Single nucleotide polymorphism analyses by MALDI-TOF MS

Abstract Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been used to detect single nucleotide polymorphisms (SNPs). Methods of generating allelic-specific DNA fragments to facilitate MALDI analysis have been employed. Interactive data acquisition has been developed to ensure high data quality for multiplexed assays, making possible ultra-high throughput, real-time genotyping. DNA pooling strategies combined with MALDI-MS have been used for SNP validation and to estimate allelic frequencies. The impact of these strategies on genome-wide association studies and phamacogenomics are discussed.