Pathogenic mitochondrial DNA (mtDNA) mutations are usually present in heteroplasmic forms that vary in concentration among different tissues. Manifestation of clinical phenotypes depends on the degree of mtDNA mutation heteroplasmy (mutation load) in affected tissues. It is therefore important to quantify the degree of mutation heteroplasmy in various tissues. In this chapter, we outline the design of allele refractory mutation system (ARMS)-based quantitative PCR (qPCR) analysis of common mtDNA point mutations, a cost-effective and sensitive single-step method to simultaneously detect and quantify heteroplasmic mtDNA point mutations.
