A problem with the "Eddowes Shawl" DNA match

[Chris]

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 C´s and G´s or in anything else is something I do not possess the knowledge to say, but surely there must be some sort of identifiable difference?

If I understand correctly, the only thing that can be measured in the lab is that string of letters - TCCCCCCG. There is no identifiable difference between the two.

[tji]

Hi all

Chris is being entirely too humble here. I was lucky enough to find the information in question, but it is he who spent the time deciphering and understanding it all.

I am posting this because it is not something that is easy to come by and he has spent a lot of time on this and so I think regardless of whether people think he is right or wrong he should be credited for his perseverance .



Tj

[MrBarnett]

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.

Agreed. See my previous post. The idea that a respected academic would try to blag the world's media is absurd. I think he is the innocent party in this.

And in some respects RE is also innocent - inasmuch as you can't blame a great white shark for taking a bite out of your leg. He's a businessman, not an historian. He's playing fast and lose with the facts to tell a story and make some dosh (bet that doesn't go down too well)

MrB

[Chris]

People may want to experiment with the EMPOP database (the same referred to in the book for the frequency estimate):

http://empop.org/modules/haplotype/

For example, putting in a range of 314-316 and specifying 314.1C gives 32770 profiles out of a total of 33691.

[Mr Lucky]

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.

No, the paper is nothing to do with identifying genes at all - according to your post it's a - "paper describing software designed to identify missing persons" and what the paper explains is that the software cannot distinguish between these two particular sequences

The paper is not claiming that these mutations are identical, just that the software cannot tell the difference between 314.1c and 315.1c

I think you may have miscounted. The reference sequence is:

I haven't 'miscounted' anything I had copied your example.

The 'Poly-cytosine region' is the chain of C's - 314.1C is located there
'After the base position' is after the G - 315.1C is located there

[mickreed]

Hi all

I am posting this because it is not something that is easy to come by and he has spent a lot of time on this and so I think regardless of whether people think he is right or wrong he should be credited for his perseverance .

Tj

Right on, Tracy, Chris has done well. If he's right then it's a bizarre turn. When you and me discussed this on jtrforums a week or more back I didn't hve the knowledge to pin it down but there was obviously something going on.

So congrats to you and Chris for following this up, and, perhaps, showing a fatl flaw. We need Jari.

[Debra A]

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

Hi Pete
There are a few online discussions and scholarly articles mentioning the fact that Cambridge Reference sequence, used to compare mtDNA sequences for differences, does in fact have a cytosine deletion in this area and that the usual amount of cytosines in a row is six, as opposed to the 5 in the CRS and rCRS.
Chris's example shows 6 in a row, yours shows only 5.
Just my opinion though, I'm no expert.

[Mr Lucky]

Hi Pete
There are a few online discussions and scholarly articles mentioning the fact that Cambridge Reference sequence, used to compare mtDNA sequences for differences, does in fact have a cytosine deletion in this area and that the usual amount of cytosines in a row should be six, as opposed to the 5 in the CRS and rCRS.
Chris's example shows 6 in a row, yours shows only 5.
Just my opinion though, I'm no expert.

Hi Debs

the above sounds like the extra C -in the Poly-cytosine chain mutation - 314.1c

I not sure what you're pointing out ? have I just put the wrong number of c's in the chain? - apologies if so

The point I'm trying to make is just because the software cannot tell the difference between the two mutations, this doesn't mean that they are the same.

[Fisherman]

If I understand correctly, the only thing that can be measured in the lab is that string of letters - TCCCCCCG. There is no identifiable difference between the two.

Yeah, I realized that when you posted the underlined version

Extraordinary, to say the least.

The best,
Fisherman

[Debra A]

Hi Debs

the above sounds like the extra C -in the Poly-cytosine chain mutation - 314.1c

I not sure what you're pointing out ? have I just put the wrong number of c's in the chain? - apologies if so

The point I'm trying to make is just because the software cannot tell the difference between the two mutations, this doesn't mean that they are the same.

Hi Pete

The way I understand this is the CRS and rCRS (revised version) only contains 5 cytosines in a row at this area 311-315 inclusive but it has become evident with widespread mtDNA testing that it is the CRS that is the rare sequence, with a C deletion. The most common sequence is to have 6 cytosines in this area, but because the CRS only has 5 the extras must be reported in a specific way as a .1C., as an extra cytosine (as well as the one expected to be there) on the last position at 315C. To report it at 314 as 314.1C is saying exactly the same thing-there's an extra cytosine than the CRS in this area.

I'm rubbish at explanations!

[Mr Lucky]

Hi Pete

The way I understand this is the CRS and rCRS (revised version) only contains 5 cytosines in a row at this area 311-315 inclusive but it has become evident with widespread mtDNA testing that it is the CRS that is the rare sequence, with a C deletion. The most common sequence is to have 6 cytosines in this area, but because the CRS only has 5 the extras must be reported in a specific way as a .1C., as an extra cytosine (as well as the one expected to be there) on the last position at 315C. To report it at 314 as 314.1C is saying exactly the same thing-there's an extra cytosine than the CRS in this area.

I'm rubbish at explanations!

Hi Debs,

Ok, thanks, I see what you mean now, but surely whether the chain has five cytosines or six , the correct notation for this would always have been 315.1C ?

So where does 314.1C come from ? and to quote myself - "314.1c is in 'Poly-cytosine region' where as 315.1c is 'after the base position' - they sound like different mutations to me"

[Debra A]

Hi Debs,

Ok, thanks, I see what you mean now, but surely whether the chain has five cytosines or six , the correct notation for this would always have been 315.1C ?

So where does 314.1C come from ? and to quote myself - "314.1c is in 'Poly-cytosine region' where as 315.1c is 'after the base position' - they sound like different mutations to me"

Hi Pete, yes, the correct reporting should be 315.1C. That is what I understood the paper Tracy discovered to be saying though, that 314.1C is a misreporting of 315.1C?
I understood the alignment position to be 310 T and then 5 cytosines to position 315 in the CRS? Is that wrong?

[Debra A]

Hi Debs,

Ok, thanks, I see what you mean now, but surely whether the chain has five cytosines or six , the correct notation for this would always have been 315.1C ?

So where does 314.1C come from ? and to quote myself - "314.1c is in 'Poly-cytosine region' where as 315.1c is 'after the base position' - they sound like different mutations to me"

Pete, Just one last thing to try and clarify the way I am understanding things:
If the chain has 5 cytosines nothing will be reported as it is the differences between a sequence and the reference sequence (e.g. CRS) that are reported. 315.1C is one cytosine extra and so is reported. There can also be two or more extras reported at this position as 314.2C etc.

[Debra A]

Pete, Just one last thing to try and clarify the way I am understanding things:
If the chain has 5 cytosines nothing will be reported as it is the differences between a sequence and the reference sequence (e.g. CRS) that are reported. 315.1C is one cytosine extra and so is reported. There can also be two or more extras reported at this position as 314.2C etc.

Genuine typo there! That should be 315.2C

[tji]

Hi Deb's

Genuine typo there! That should be 315.2C

Lol my eyes are twitching so God know's how you are doing it and making sense

Tracy