Ambiguities with respect to mtDNA nomenclature can result in two different analysts calling the same sample differently. Likewise population databases could have multiple entries for the same mtDNA haplotype preventing an accurate estimate for the frequency of a particular type. Thus, standardization in designation of mtDNA sequences is important to have data that can easily be shared between laboratories.
Length variants present a challenge when alignments are made between a sample of interest and the Cambridge Reference Sequence. Treatments of insertions and deletions (gaps) can vary between laboratories causing some laboratories to code the same sequence differently. Mark Wilson and colleagues at the FBI Laboratory have made a number of recommendations to enable consistent treatment of length variants (Wilson et al. 2002a, 2002b). Three primary recommendations were made: (1) characterize profiles using the least number of differences from the reference sequence; (2) if there is more than one way to maintain the same number of differences with respect to the reference sequence, differences should be prioritized in the following manner: (a) insertions/ deletions (indels), (b) transitions, and (c) transversions; (3) insertions and deletions should be placed 3' with respect to the light strand. Insertions and deletions should be combined in situations where the same number of differences to the reference sequence is maintained. These recommendations are hierarchical meaning that recommendation (1) should take precedence over recommendation (2) and (3). A total of 41 specific examples are provided to demonstrate the need for consistent treatment of length variants in mtDNA sequence analysis and reporting (Wilson et al. 2002a, 2002b).
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