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The case for the continuing use of the revised cambridge reference sequence (rCRS)...

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  • The case for the continuing use of the revised cambridge reference sequence (rCRS)...

    Bandelt, H.-J., Kloss-Brandstätter, A., Richards, M. B., Yao, Y.-G., and Logan, I. (2013). The case for the continuing use of the revised cambridge reference sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies. Journal of Human Genetics.

    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.

    Link:
    http://www.nature.com/jhg/journal/va...g2013120a.html

  • #2
    Originally posted by Rebekah Canada View Post
    Bandelt, H.-J., Kloss-Brandstätter, A., Richards, M. B., Yao, Y.-G., and Logan, I. (2013). The case for the continuing use of the revised cambridge reference sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies. Journal of Human Genetics.

    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.

    Link:
    http://www.nature.com/jhg/journal/va...g2013120a.html

    Will there be a response to this paper? Will FTDNA change it's policy in using RSRS as a reference haplotype?

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    • #3
      From the paper:
      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.
      No, it's not wild type, rCRS is H2a2a1 which seems like it should lead to more chaos and misunderstandings than switching to something more intuitive. I'm always surprised how few mutations some mtdna H's get under rCRS and how many the rest of us get. Seems to me, genetic researchers, anthropologists, and others are smart enough to incorporate a better system that better reflects that H2a2a1 is not some kind of mitochondrial Eve.

      Comment


      • #4
        Originally posted by Littlest bit View Post
        From the paper:


        No, it's not wild type, rCRS is H2a2a1 which seems like it should lead to more chaos and misunderstandings than switching to something more intuitive. I'm always surprised how few mutations some mtdna H's get under rCRS and how many the rest of us get. Seems to me, genetic researchers, anthropologists, and others are smart enough to incorporate a better system that better reflects that H2a2a1 is not some kind of mitochondrial Eve.
        I agree with you, under the old system I was given H2a2a due to my 15314A even though the base markers for H2 branch I do not have. Only under the new system was I removed from H2 branch.

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