The accidental amplification of nuclear mitochondrial pseudogenes (NUMTs) can pose a serious problem for mitochondrial disease studies. We demonstrate that the mutation spectrum left by spurious amplification of a NUMT can be detected because it usually differs from the authentic natural spectrum considerably. We examine the problem introduced by a ND5 gene NUMT that was recorded in a proband with hearing loss as well as other disease studies erroneously reporting NUMT variation as genuine mutations in their patients. We also show that NUMTs can emerge in population genetic studies, as exemplified here by cases in our laboratory and from published sources. Appropriate database searches and a phylogenetic approach can prevent hasty claims for novelty of mitochondrial DNA (mtDNA) variants inadvertently derived from NUMTs and help to direct one to the real source.
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