title: The case for the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies.
abstract: Since the determination in 1981 of the sequence of the human mitochondrial DNA (mtDNA) genome, the Cambridge Reference Sequence (CRS), has been used as the reference sequence to annotate mtDNA in molecular anthropology, forensic science and medical genetics. The CRS was eventually upgraded to the revised version (rCRS) in 1999. This reference sequence is a convenient device for recording mtDNA variation, although it has often been misunderstood as a wild-type (WT) or consensus sequence by medical geneticists. Recently, there has been a proposal to replace the rCRS with the so-called Reconstructed Sapiens Reference Sequence (RSRS). Even if it had been estimated accurately, the RSRS would be a cumbersome substitute for the rCRS, as the new proposal fuses--and thus confuses--the two distinct concepts of ancestral lineage and reference point for human mtDNA. Instead, we prefer to maintain the rCRS and to report mtDNA profiles by employing the hitherto predominant circumfix style. Tree diagrams could display mutations by using either the profile notation (in conventional short forms where appropriate) or in a root-upwards way with two suffixes indicating ancestral and derived nucleotides. This would guard against misunderstandings about reporting mtDNA variation. It is therefore neither necessary nor sensible to change the present reference sequence, the rCRS, in any way. The proposed switch to RSRS would inevitably lead to notational chaos, mistakes and misinterpretations.
authors.affiliation: Department of Mathematics, University of Hamburg, Hamburg, Germany.
authors.forename: Hans-Jürgen
authors.initials: HJ
authors.lastname: Bandelt
authors.affiliation: Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria.
authors.forename: Anita
authors.initials: A
authors.lastname: Kloss-Brandstätter
authors.affiliation: School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK.
authors.forename: Martin B
authors.initials: MB
authors.lastname: Richards
authors.affiliation: Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China.
authors.forename: Yong-Gang
authors.initials: YG
authors.lastname: Yao
authors.affiliation: Exmouth, Devon, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Logan
mesh_terms: D004272:DNA, Mitochondrial / Q000235:genetics*; D030561:Databases, Nucleic Acid / Q000592:standards*; D005260:Female; D006801:Humans; D008297:Male; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000592:standards*
chemical_list: D004272:DNA, Mitochondrial