Multiplex PCR electrospray-ionization mass spectrometry (ESI-MS): Application to forensic mitochondrial DNA examinations

Mitochondrial DNA (mtDNA) examinations play an important role in criminal investigations, identification of victims of mass disasters, and association of unidentified remains with family members. Typically, HV1 and HV2 are amplified via polymerase chain reaction (PCR) followed by fluorescent sequencing. While this method produces the highest level of resolution, it is labor intensive and unable to distinguish components of a mixture. Previously, an electrospray-ionization mass spectrometry (ESI-MS) method was described to determine the base composition profile of enzymatically digested PCR amplified fragments derived from the HV1 and HV2 regions. Advantages of ESI-MS compared to sequencing include speed of analysis, automation, and increased sensitivity, while retaining a high degree of resolution. Here, we report the next generation of this method in which a base composition profile is determined from 24 overlapping PCR reactions. Because ESI-MS provides the relative abundance of each component present, this method allows for the quantitative typing of mixtures. This ESI-MS method does not rely on a priori knowledge of variable sites, allowing the capture of private mutations and individual-specific variation. Due to the multiplex design, automation, speed of analysis, and ability to interrogate mixtures, this method provides a powerful and rapid tool for forensic mtDNA examinations.