A problem with the "Eddowes Shawl" DNA match

[Debra A]

No - I'm saying I've been very patient and explained it to you several times, and apparently you still can't understand it. So I am now giving up trying to explain it to you. Life's too short.

And frankly, comments like the one you've just made only go to confirm that that's the right decision.

You have been very patient, Chris. Thanks for questioning the claims about the rarity of the global private mutation (314.1c.) and bringing the problems to our attention.

[Chris]

I wasn't going to say any more on this, but Lucky and Chris, can you tell me what this means?

global private mutation: mutation never observed in Phylotree, probably due to inconsistent alignments, phantom mutations or point heteroplasmies (R, Y, K...)

It seems to be saying that a 'global private mutation' is sufficently rare to have never been seen in Phylotree, and is probably due to an analysis 'stuff up'. Is that a fair interpretation? I really don't know but would like to.

Yes, I think so. I read it as saying that a global private mutation is probably due either to some kind of error in the sequencing or to the effects of a confounding factor, Heteroplasmy is the present of more than one sequence in the same person, which could obviously cause problems in sequencing.

Really, that definition is another red flag in itself, quite separately from the equivalence of 314.1C and 315.1C.

[GUT]

You have been very patient, Chris. Thanks for questioning the claims about the rarity of the global private mutation (314.1c.) and bringing the problems to our attention.

I Second that.

Right or wrong you've gone above and beyond.

[mickreed]

Yes, I think so. I read it as saying that a global private mutation is probably due either to some kind of error in the sequencing or to the effects of a confounding factor, Heteroplasmy is the present of more than one sequence in the same person, which could obviously cause problems in sequencing.

Really, that definition is another red flag in itself, quite separately from the equivalence of 314.1C and 315.1C.

Thanks Chris. Lucky seems to agree, if I read his reply correctly.

I really do not understand what JL could have meant in his communication as quoted by RE in the book.

As I think you said in an earlier post, the CRS gives for locations 310 to 316

TCCCCCG

A single additional cytosine anywhere between 311 and 315 (inclusive) will give

TCCCCCCG

How can anyone pin the extra cytosine to a specific location within that range?

[mickreed]

Yes, I think so. I read it as saying that a global private mutation is probably due either to some kind of error in the sequencing or to the effects of a confounding factor, Heteroplasmy is the present of more than one sequence in the same person, which could obviously cause problems in sequencing.

Really, that definition is another red flag in itself, quite separately from the equivalence of 314.1C and 315.1C.

Yes, I cannot conceive of any other interpretation than yours, Chris, based on the information provided.

Advanced Topics in Forensic DNA Typing: Methodology: Methodology
By John M. Butler p. 429 says as much:

[Chris]

Yes, I cannot conceive of any other interpretation than yours, Chris, based on the information provided.

Advanced Topics in Forensic DNA Typing: Methodology: Methodology
By John M. Butler p. 429 says as much:

Thanks for that. Hopefully that clear explanation in an authoritative source will knock on the head some of the wilder suggestions as to what "314.1C" means.

I note that a review of Dr Butler's book in the Journal of Clinical Forensic Medicine began:
"When they write the history of forensic science for our times, Forensic DNA Typing will be cited as the classic text on the subject."

[mickreed]

I note that a review of Dr Butler's book in the Journal of Clinical Forensic Medicine began:
"When they write the history of forensic science for our times, Forensic DNA Typing will be cited as the classic text on the subject."

Better than ever, Chris.

[Stewart P Evans]

Despite...

Despite my earlier remarks about Chris and Kosminski on another thread I should like to put it on record that I have never, ever, doubted his honesty and perseverance. I apologise to him if the remarks caused any distress.

[Chris]

Despite my earlier remarks about Chris and Kosminski on another thread I should like to put it on record that I have never, ever, doubted his honesty and perseverance. I apologise to him if the remarks caused any distress.

No problem, Stewart.

[Debra A]

I Second that.

Right or wrong you've gone above and beyond.

Don't get me wrong, GUT. I think everything Chris has posted has been correct.
DR JL is suggesting 314.1c is a global private mutation, it says so in the book. Chris has shown 314.1c is exactly the same mutation as 315.1c, an extra cytosine inserted in the c stretch between 310T and 315C.
What would be rare is if there was no extra cytosine inserted in this region and the sample matched the rCRS in having only 5 cytosines.

[tji]

Hi all

"The variation is known as a Global Private Mutation, a rare gene variation that is usually found only in a single family or a small population.

I think again the word's used are again a little misleading. Unless I am misunderstanding the above is the given quote of the rarity of the 314.1C. We have to leave the 314.1C aside for a moment (you may have a break Chris )

So from what I have read, you have -

Global Private mutation (as mentioned by previously,) never observed in Phylotree - probably due to inconsistent alignment's. This normally means error in the difference softwares.

Phantom mutations - 'Phantom mutations are systematic artifacts generated in the course of the sequencing process, especially in the HV1 and HV2 areas of the D loop.'
The single single strand sequencing is the most vulnerable to mistakes in this area, so I would assume if the double strand sequencing was performed it would lessen the risk.

Point heteroplasmies - it seems that heteroplasmy is to do with the fact that the person has more than one type of mtDna. (Tsar Nicholas had this apparently.)

So these are the explanation's (in my opinion) of the Global Private Mutations as quoted by Mr Edward's in his book. Do any sound like the rare gene variation found in a small family?

I will now point out the definition of a LOCAL private mutation -

A distinct gene alteration usually observed in a single family.

As an added bonus we also have the definition of just a 'Private mutation' - A rare genetic mutation that is usually found in a single or small population. A private mutation occurs's and is passed to a few family member's, but not to future generation's.

Again nothing conclusive here, and it doesn't seem to explain itself very clearly, does it mean that ancestor's have it but not descendant's, if so where is the cut off point. If Karen Miller has it and Catherine Eddowes does then that would mean any descendant of Karen's shouldn't, right? How would this work, it doesn't seem very likely to me.

Another explanation would be that it mean's family member's of the same generation would have it but not future generation's. This would mean that both Catherine Eddowes and Karen Miller couldn't have it.

It could also just be another way of stating one the other 2 with added information (I would go with the local mutation)

Am I nitpicking? dunno, I think I am a little but given the circumstances you would have to decide for yourself. I do understand that this could be nothing more than Edward's misunderstanding the description given to him but yet again you would think that this sort of thing would have been checked before hand.
I mean if a lowly person without a doctorate can figure this out then thy certainly should have noticed it

Tracy

*disclaimer - I am in now way indicating that Catherine Eddowes maybe related to Tsar Nicholas!

[mickreed]

Don't get me wrong, GUT. I think everything Chris has posted has been correct.
DR JL is suggesting 314.1c is a global private mutation, it says so in the book. Chris has shown 314.1c is exactly the same mutation as 315.1c, an extra cytosine inserted in the c stretch between 310T and 315C.
What would be rare is if there was no extra cytosine inserted in this region and the sample matched the rCRS in having only 5 cytosines.

Hi Debs (and GUT)

Yes, Chris is absolutely right based on the way the issue is described in the book.

314.1C is a non-standard way of expressing 315.1C. As my post just now proves, they are exactly the same. 315.1c is quite common. I have it myself.

Moreover, a global private mutation doesn't seem to mean anything (see my earlier post together with Chris's and Lucky's responses. Most of them seem to arise from an amplification and/or sequencing error.

In the absence of clarification by JL, we can say, I think, that the claim by RE is quite wrong on this point.

[mickreed]

I mean if a lowly person without a doctorate can figure this out then thy certainly should have noticed it

Tracy

Well Tracy, RE has a vested interest in not noticing it. The book is full of examples where he clutches at any passing straw and makes a big thing out of it.

As for JL, I really don't know WTF is going on. There has to be something that we don't know. Surely nobody in his position could possibly not know about these things?

I do hope he responds to Chris's questions soon. I have no doubt now, that he has a real responsibility to find the time asap.

[John G]

Wow this thread's still going! Anyway, even if the shawl is deemed eventually to belong to Eddowes that still leaves the tricky problem of the Kosminski DNA. From the information I cited on the other related thread, it doesn't seem as if Kosminski had a particularly rare mtDNA group- or to be more scientific haplogroup sub-type- as it seems to apply to about 2% of the European population. Although, interestingly, it seems to be rare in Siberia, so we might be able to reasonably rule out a Cossack!

And, if the shawl really is over 150 years old, I would have thought so many people would have had contact with it over that period that it may even be probable that one of those people would have been someone who shared Kosminski's mtDNA group.

[mickreed]

Wow this thread's still going! Anyway, even if the shawl is deemed eventually to belong to Eddowes that still leaves the tricky problem of the Kosminski DNA. From the information I cited on the other related thread, it doesn't seem as if Kosminski had a particularly rare mtDNA group- or to be more scientific haplogroup sub-type- as it seems to apply to about 2% of the European population. Although, interestingly, it seems to be rare in Siberia, so we might be able to reasonably rule out a Cossack!

And, if the shawl really is over 150 years old, I would have thought so many people would have had contact with it over that period that it may even be probable that one of those people would have been someone who shared Kosminski's mtDNA group.

Yes John, and the common haplogroup T1 (and therefore its sub-clade T1a1) that purports to be from Kosminski (despite being quite uncommon amongst Ashkenazis) includes 315.1C, or, as it is described by JL and RE, 314.1C and, as we know, that is extremely rare