Detection and analysis of mitochondrial DNA deletions by whole genome PCR

Abstract

Southern blot analysis has been the best method available for the screening and detection of mitochondrial DNA (mtDNA) rearrangements. Recent developments in polymerase chain reaction (PCR) technology allowed the amplification of the whole mitochondrial genome (16.6 kb), making PCR a potentially useful technique for the detection of mtDNA deletions. We tested the usefulness of whole mitochondrial genome PCR by studying skeletal muscle DNA from seven patients with single and multiple deletions and controls from ages 3 to 91 years old. Specific patterns for single and multiple deletions were obtained with whole genome PCR, which were confirmed by the Southern analysis with probes hybridizing to mtDNA sequences. Amplifications from young controls (3 to 23 years old) yielded only one band (16.5 kb) while amplification from older controls revealed one or more additional smaller bands. The amplification from the 91-year-old control showed a pattern similar to amplifications from patients with multiple mtDNA deletions. Although single and multiple mtDNA deletions could be readily detected from patient samples, the high sensitivity of this method can lead to false positive results due to the presence of age-related deletions in old control samples. Despite its limitations, whole mitochondrial genome PCR can be useful for the detection of single deletions in muscle samples obtained from young individuals since the levels of age-related deletions are too low to be amplified.