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A problem with the "Eddowes Shawl" DNA match

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  • A problem with the "Eddowes Shawl" DNA match

    In "Naming Jack the Ripper", Russell Edwards quotes Dr Jari Louhelainen's comments about the match between a segment of mitochondrial DNA obtained from the area of a possible blood stain on the "shawl" and the corresponding segment from a female-line descendant of Catherine Eddowes:
    "One of these amplified mtDNA segments had a sequence variation which have a match between one of the shawl samples and Karen Millers DNA only; i.e. the DNA sequence retrieved from the shawl did not match with control reference sequences. This DNA alteration is known as global private mutation (314.1C) and it is not very common in worldwide population, as it has frequency estimate of 0.000003506, i.e. approximately 1/ 290,000. This figure has been calculated using the database at Institute of Legal Medicine, GMI, based on the latest available information."

    Just over a week ago, Tracy I'anson posted an excerpt from a paper describing software designed to identify missing persons, which discusses the conventions for describing variations in the mitochondrial DNA sequence:
    "An insert, such as the common extra C after base position 315 is listed as 315.1 C. For matching purposes, the program tolerates errors in nomenclature for equivalent variants such as the extra C in the poly-cytosine region being reported as 314.1 C."
    http://forum.casebook.org/showpost.p...postcount=2968

    The paper she quoted can be found here:
    http://www.genecodesforensics.com/ne...%20revised.pdf

    The authors refer to 314.1C as an "error in nomenclature". This is because 314.1C indicates that the measured sequence differs from the standard reference sequence for mitochondrial DNA by the insertion of one additional C (cytosine) after position 314 in the sequence. But the reference sequence actually has a string of five Cs in a row around here, in positions 311 to 315. The additional C could be inserted at any point in this string, and the resulting sequence - which is all that can be measured - would be exactly the same. The convention in forensic genetics is to describe the insertion as having occurred after the last possible position - that is, in this case, after position 315. So the conventional description for this mutation is 315.1C, not 314.1C.

    The problem is that 315.1C is not a rare mutation, as the authors quoted by Tracy indicate. In fact the presence of an extra C in this position is much more common than its absence, because this is a case in which the reference sequence itself contains an uncommon mutation. The database referred to in the book can be found at http://empop.org/ and it indicates that 315.1C is present in 99.2% of the sequences which have information for this position.

    It appears that something has gone badly wrong with the analysis here, and obviously the quoted figure of 1 in 290,000 can't be accepted without further explanation.

  • #2
    Thanks for the summary, Chris.
    Excellent find, Tracy.
    This needs explanation before anything else, for sure.
    ,,`,, Debs ,,`,,

    I am not DJA. He's called Dave.

    Comment


    • #3
      Thanks for that Chris.

      I admit I'm still absorbing it, but it looks like another nail in the coffin for Mr Edwards' hypothesis if I am understanding it right.
      G U T

      There are two ways to be fooled, one is to believe what isn't true, the other is to refuse to believe that which is true.

      Comment


      • #4
        Originally posted by Debra A View Post
        Thanks for the summary, Chris.
        Excellent find, Tracy.
        This needs explanation before anything else, for sure.
        Thanks, Debs. Perhaps it would help if I posted the four-line summary of that.

        (1) This is the reference sequence for mitochondrial DNA starting at position 310:
        TCCCCCG

        (2) This is what 314.1C means (claimed frequency 1 in 290,000):
        TCCCCCCG

        (3) This is what 315.1C means (frequency in database 99.2%):
        TCCCCCCG

        The problem is that (2) and (3) are identical.

        Comment


        • #5
          Originally posted by Chris View Post
          Thanks, Debs. Perhaps it would help if I posted the four-line summary of that.

          (1) This is the reference sequence for mitochondrial DNA starting at position 310:
          TCCCCCG

          (2) This is what 314.1C means (claimed frequency 1 in 290,000):
          TCCCCCCG

          (3) This is what 315.1C means (frequency in database 99.2%):
          TCCCCCCG

          The problem is that (2) and (3) are identical.
          Thanks Chris that's what I thought it all meant, so more to question the conclusion over.
          G U T

          There are two ways to be fooled, one is to believe what isn't true, the other is to refuse to believe that which is true.

          Comment


          • #6
            And Jari is unaware of this?

            Comment


            • #7
              Originally posted by MrBarnett View Post
              And Jari is unaware of this?
              I doubt it, but hasn't already expressed reservations that Mr Edwards took it further than he was prepared to go.
              G U T

              There are two ways to be fooled, one is to believe what isn't true, the other is to refuse to believe that which is true.

              Comment


              • #8
                Originally posted by Chris View Post
                Thanks, Debs. Perhaps it would help if I posted the four-line summary of that.

                (1) This is the reference sequence for mitochondrial DNA starting at position 310:
                TCCCCCG

                (2) This is what 314.1C means (claimed frequency 1 in 290,000):
                TCCCCCCG

                (3) This is what 315.1C means (frequency in database 99.2%):
                TCCCCCCG

                The problem is that (2) and (3) are identical.
                Hi Chris,

                I think it may just be that the software that Tracy found can not accurately distinguish between the two, this doesn't mean that they are the exact same thing, 314.1c is in 'Poly-cytosine region' where as 315.1c is 'after the base position' - they sound like different mutations to me

                I would suggest
                310 TCCCCCG
                314.1c TCCCCCCG
                315.1c TCCCCCG-C

                just my opinion

                Comment


                • #9
                  Originally posted by MrBarnett View Post
                  And Jari is unaware of this?
                  I understand he has been made aware of it.

                  Comment


                  • #10
                    G'day Gut ,

                    It was while ago now that I listened to Jari's radio interview. But from memory while he seemed reluctant to endorse RE's 100%, case closed conclusions, he did seem to be saying that there was a 'match' with Eddowes descendent. If what he neglected to tell us is the vast majority of the population would also be a match, that surely borders on dishonesty.

                    MrB

                    Comment


                    • #11
                      Originally posted by MrBarnett View Post
                      G'day Gut ,

                      It was while ago now that I listened to Jari's radio interview. But from memory while he seemed reluctant to endorse RE's 100%, case closed conclusions, he did seem to be saying that there was a 'match' with Eddowes descendent. If what he neglected to tell us is the vast majority of the population would also be a match, that surely borders on dishonesty.

                      MrB
                      G'day Mr B

                      I'm trying to cut the poor bloke some slack, I suspect that he really didn't expect the attention he has got. We here on casebook tend at times to forget that a lot of people have no idea that Jack even attracts much interest anymore. And is now engaged in that time honoured practice of CYA.
                      G U T

                      There are two ways to be fooled, one is to believe what isn't true, the other is to refuse to believe that which is true.

                      Comment


                      • #12
                        Originally posted by Mr Lucky View Post
                        Hi Chris,

                        I think it may just be that the software that Tracy found can not accurately distinguish between the two, this doesn't mean that they are the exact same thing, 314.1c is in 'Poly-cytosine region' where as 315.1c is 'after the base position' - they sound like different mutations to me

                        I would suggest
                        310 TCCCCCG
                        314.1c TCCCCCCG
                        315.1c TCCCCCG-C

                        just my opinion
                        If there is a 314.1c and a 315.1c, one would predispose that there was a reason for making the distinction. Whether it lies if the sequencing of the Cs and Gs or in anything else is something I do not possess the knowledge to say, but surely there must be some sort of identifiable difference?

                        The best,
                        Fisherman

                        Comment


                        • #13
                          Originally posted by Mr Lucky View Post
                          I think it may just be that the software that Tracy found can not accurately distinguish between the two, this doesn't mean that they are the exact same thing , 314.1c is in 'Poly-cytosine region' where as 315.1c is 'after the base position' - they sound like different mutations to me ...
                          No - what that paper is saying is that there are two different ways of describing the same sequence, and that the software correctly allows for that.

                          Originally posted by Mr Lucky View Post
                          I would suggest
                          310 TCCCCCG
                          314.1c TCCCCCCG
                          315.1c TCCCCCG-C
                          I think you may have miscounted. The reference sequence is:
                          T at 310
                          C at 311
                          C at 312
                          C at 313
                          C at 314
                          C at 315
                          G at 316

                          What I should have done above was to underline the inserted C, to make it clearer. That gives:
                          314.1C TCCCCCCG
                          315.1C TCCCCCCG

                          Comment


                          • #14
                            Originally posted by MrBarnett View Post
                            If what he neglected to tell us is the vast majority of the population would also be a match, that surely borders on dishonesty.
                            I think this has to be some kind of mistake, not dishonesty. Whether it's a mistake in the description of the sequence or the estimation of the sequence's rarity isn't clear.

                            Comment


                            • #15
                              Originally posted by GUT View Post
                              G'day Mr B

                              I'm trying to cut the poor bloke some slack, I suspect that he really didn't expect the attention he has got. We here on casebook tend at times to forget that a lot of people have no idea that Jack even attracts much interest anymore. And is now engaged in that time honoured practice of CYA.
                              I suppose it depends what position he thought he was defending. If by match he meant not a mismatch, then all becomes clear. From his cosy ivory tower it probably didn't occurred to him that the ravening wolves of Ripperology would demand absolute certainty. He probably assumed that even as laymen they knew that wasn't possible. By saying it was a match he was saying there was nothing to indicate that it couldn't be Eddowes' blood.

                              Poor guy indeed.

                              MrB

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