The advantage of precision in high throughput genetic, expression and epigenetic studies
We use MALDI-TOF mass spectrometry to provide high throughput precise quantitative analysis of DNA, RNA, and DNA methylation. After PCR sample preparation, the status of individual DNA polymorphisms or the levels of individual RNA transcripts can be measured by single base primer extension reactions specific for the site of interest. These reactions can be studied at 12- to 30-fold multiplexing. Hence the cost of the overall process is very reasonable. The level of individual genes, polymorphisms or transcripts can be measured with typical precisions of a few percent concentration. Thus, very small genetic or expression changes can be detected quite reliably. The sensitivity is far better than real time PCR measurements, so even single molecules can be detected after amplification.
A different procedure is used for DNA sequencing or methylation discovery. Here a PCR amplicon is fragmented in a base specific way and all the fragments are analyzed simultaneously in a single mass spectrum. The procedure seems to have more sensitivity than conventional DNA sequencing. For methylation analysis, the DNA is subjected to conventional bisulfite procedures prior to amplification and fragmentation. This offers a combination of high throughput and high precision quantification that is unavailable with any other existing technique.
Examples of the application of these techniques to stratify patient samples in lung cancer and AML.