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Yoruban to rCRS Conversion

Human mitochondrial nucleotides are commonly identified using positions derived from the sequence first published by Anderson et al. and later amended by Andrews et al. This sequence, which has become known as the revised Cambridge sequence (RCRS) (accession number NC_012920), has become the standard for notating mtDNA variants. Because the Affymetrix data used notation based on an African Yoruban sequence (accession number AF347015), position values were converted. A pairwise alignment of the RCRS and Yoruban sequence was made using the Seaview (Galtier et al.) program. The presence of three single-nucleotide insertions in the Yoruban sequence and a placeholder position introduced during revision of the original Cambridge sequence cause the nucleotide positions in the two sequences to differ significantly. Corresponding Yoruban positions were mapped to their RCRS equivalent (see table below).

Anderson, S., Bankier, A. T., Barrell, B. G., de Bruijn, M. H., Coulson, A. R., Drouin, J., Eperon, I. C., Nierlich, D. P., Roe, B. A., Sanger, F., Schreier, P. H., Smith, A. J., Staden, R. and Young, I. G. (1981). "Sequence and organization of the human mitochondrial genome." Nature 290(5806):457-465.

Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Turnbull, D. M. and Howell, N. (1999). "Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA [letter]." Nature Genetics 23(2):147.

Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci., 12, 543-548.

The Illumnia chip uses nucleotide numbers which are relative to a Yoruban sequence. To convert those numbers to ones relative to the revised Cambridge sequence follow the rules in the table below.

Converting from Yoruban positions to rCRS positions

Position Range Conversion Operation
1-309 nothing
310 Yoruban insertion, position does not exist in rCRS
311 - 316 decrement by 1
317 Yoruban insertion, position does not exist in rCRS
318 - 3108 decrement by 2
3109 - 16190 decrement by 1
16191 Yoruban insertion, position does not exist in rCRS
16192 - 16571 decrement by 2
* No Yoruban position maps to 3107 in the rCRS since this is merely a placeholder introduced during revision.

Examples:
  • Yoruban position 100 maps to position 100 in the rCRS
  • Yoruban position 3100 maps to position 3098 in the rCRS
  • Yoruban position 3111 maps to position 3110 in the rCRS
  • Yoruban position 16191 does not map to any position in the rCRS
  • Yoruban position 16225 maps to position 16223 in the rCRS

Topic revision: r1 - 20 Oct 2016, MarieLott
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