title: Phantom mutation hotspots in human mitochondrial DNA.
abstract: Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30 000 published hypervariable segment I sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.
authors.affiliation: Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
authors.forename: Anita
authors.initials: A
authors.lastname: Brandstätter
authors.forename: Timo
authors.initials: T
authors.lastname: Sänger
authors.forename: Sabine
authors.initials: S
authors.lastname: Lutz-Bonengel
authors.forename: Walther
authors.initials: W
authors.lastname: Parson
authors.forename: Eliane
authors.initials: E
authors.lastname: Béraud-Colomb
authors.forename: Bo
authors.initials: B
authors.lastname: Wen
authors.forename: Qing-Peng
authors.initials: QP
authors.lastname: Kong
authors.forename: Claudio M
authors.initials: CM
authors.lastname: Bravi
authors.forename: Hans-Jürgen
authors.initials: HJ
authors.lastname: Bandelt
mesh_terms: D016477:Artifacts; D001322:Autoanalysis; D001483:Base Sequence; D022801:Complementarity Determining Regions / Q000032:analysis / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics*; D004586:Electrophoresis; D006801:Humans; D009154:Mutation / Q000235:genetics*; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D022801:Complementarity Determining Regions; D004272:DNA, Mitochondrial