Analysis of Short Tandem Repeat Polymorphisms in Human DNA by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

The analysis of an important class of human genetic polymorphisms, short tandem repeats (STRs), using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is described. Several model STR systems have been investigated to evaluate MALDI-TOFMS as a realistic alternative to established electrophoresis procedures, and to develop rapid and generally applicable approaches to polymerase chain reaction (PCR) product purification for MALDI-TOFMS analysis. A purification/preconcentration method for PCR product preparation based on affinity capture of biotin-labeled PCR products is demonstrated to be directly compatible with MALDI-TOFMS analysis. The entire sample preparation for MALDI-TOFMS analysis immediately following PCR amplification from human DNA extracts can be accomplished routinely in under 12 min in a single Eppendorf tube. The simplicity of this approach essentially eliminates the sample preparation bottleneck encountered with MALDI-TOFMS analysis of PCR products using existing methods. Using this method, encouraging genotyping results are demonstrated for the THO1 and TPOxx STR systems using subpicomole quantities that represent a fraction of the original dsDNA from a single PCR reaction. The technique is also demonstrated to facilitate rapid sizing of PCR fragments larger than 200 bases using MALDI-TOFMS. As described here, the analysis of DNA can be accomplished in a manner that takes advantage of the rapid and accurate analysis capabilities offered by MALDI-TOFMS.