A problem with the "Eddowes Shawl" DNA match

[mickreed]

By whom mick? The university, Edwards, the publisher?

And if there is no response ever - does that not look bad too?

cheers, gryff

Hey Gryff

According to a poster on this forum, he received an email from Jari, saying that his university Communications people had advised him to refrain from giving interviews 'for the time being'.

[mickreed]

Thanks Tracy

But perhaps you are being a bit too humble yourself. After all, the key points about 314.1C being an error in nomenclature for 315.1C, and 315.1C being common, are explicitly there in what you posted.

.

I agree. Whatever the outcome of this, you've all done very well. No undue modesty please.

[Theagenes]

Having five Cs there is just referred to as 311C-315C in this discussion of rare polymorphisms in the reference sequence:
"Seven nucleotides are considered to be rare polymorphisms and were determined to be correct as originally sequenced (J01415 gi:337188). Nucleotides 263A, 311C-315C, 750A, 1438A, 4769A, 8860A, and 15326A are considered to be rare polymorphisms and are maintained as part of the true reference sequence."

http://www.mitomap.org/MITOMAP/HumanMitoSeq

I don't think it would make sense to describe 5 Cs as the insertion of a C, at whatever position. The other thing is that having five Cs is rare, but nowhere near as rare as 1 in 290,000. The figure I quoted above would suggest something like 1%, but it may be commoner than that in the UK because the reference sequence was based on someone from Britain.

As Debs suggests, it would make sense to report agreement with the reference sequence, where the reference sequence contains a rare polymorphism. At least the EMPOP database (and probably others) takes care of that automatically - if you put a range of 315.1 and nothing in the right-hand box, it will give only a small number of exact matches, reflecting the rare condition of only five Cs.

Yeah, that makes sense. It really is strange. Where did the 1 in 290,000 number come from? As you noted, EMPOP gives the 32,000 out of 33,000 when you enter 314.1C -- which is the frequency for 315.1C, as apparently EMPOP like these other programs just treats 314.1C as 315.1C. And yet EMPOP was what Jari supposedly used. What did he enter to get that 1 in 290,000 result?

[lynn cates]

command

Hello Theagenes.

"What did he enter to get that 1 in 290,000 result?"

Were there any commands marked "Edwards"? (heh-heh)

Cheers.
LC

[Fantasio]

But there was a recent poster in the other thread whose wife was a geneticist and has been following this. Maybe she can chime in.

The poster is me and yes, I could try. But as yourself noticed:

The problem is that even if we got someone knowledgeable in this area to help, we have no real information to give them.

Exactly. Is the book enough? I don't think so. If Edwards did not clearly understand what was told, we could do worse. Is there any chance dr. JariLou will explain the matter?

[Robert]

"Whatever the outcome of this, you've all done very well."

http://www.youtube.com/watch?v=p6ddSA9lrkc

[mickreed]

"Whatever the outcome of this, you've all done very well."

http://www.youtube.com/watch?v=p6ddSA9lrkc

I'm free!

[tji]

[QUOTE]

"Whatever the outcome of this, you've all done very well."

Thank you Mr Linford

Tracy

[Mr Lucky]

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.

Hi Debs,

I have used a couple of hours googling myself, my word, how things have moved on in the last ten years or so ! some things that I'm curious about are

Do we know for sure which database(s) Dr Louhelainen was using ?

The mutation at 314.1c/315.1c is the one being described as a global private mutation - is this a definite coding mutation ?

I am still totally baffled by the 315.2c reference.

[Mr Lucky]

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.

this is not a summary of the article you posted in Post 1 - you have clearly taken this information from the mitomap (hopelessly out of date, btw) link you have quoted elsewhere - it definitely isn't in the article about soft ware analysis you mistakenly think is relevant.

You really need to learn how to present an argument honestly - despite what you think I was genuinely trying to help you , I don't think I bother again.

[Chris]

this is not a summary of the article you posted in Post 1 ...

The article I quoted in the first post was simply the one which brought this problem to our attention when Tracy quoted it previously. None of what I've been saying depends on that article. So the post you've just quoted was in no way meant to be a summary of it. It was attempt to make things as simple as possible for those who were having difficulty understanding.

Have I succeeded? Do you see now that the sequences denoted by 314.1C and 315.1C are identical, or are you claiming that this is incorrect?

(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

If you are claiming it is incorrect, where is the error?

[Mr Lucky]

The article I quoted in the first post was simply the one which brought this problem to our attention when Tracy quoted it previously. None of what I've been saying depends on that article. So the post you've just quoted was in no way meant to be a summary of it.

What exactly are you struggling with here, do you want to get a grown up to help you with this? - let's go over it again. This is what you wrote in post 4 "Perhaps it would help if I posted the four-line summary of that." what you then went on to post, however, is NOT a summary of the article you cited in post 1, but something you copied from a DNA database, and now you are determined not to acknowledge that this is wrong.

It was attempt to make things as simple as possible for those who were having difficulty understanding.

Insulting the users of the forum isn't helping you at all, the problem has been caused by nothing other than your fundamental inability to present an argument honestly.

Have I succeeded? Do you see now that the sequences denoted by 314.1C and 315.1C are identical, or are you claiming that this is incorrect?

(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

If you are claiming it is incorrect, where is the error?

If you had been honest enough to correctly source this from the start <EMPOP?> , then, no, I wouldn't have questioned it at all.

Clearly there is a problem with the nomenclature of the region of the 314/315 which will effect every sample of mtDNA analysed. However this may well have nothing to do with the "global private mutation" located at 314.1c. allegedly found in the Eddowes family mtDNA, and nothing you have produced so far leads me to believe otherwise

To be frank about it, judging by your behaviour alone, nothing you say on these matters should be trusted at all.

[Chris]

Mr Lucky

I'll try again.

What I am asking you is whether you agree that the sequence denoted by 314.1C is identical with the sequence denoted by 315.1C, as shown in (2) and (3) below:

(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

If you don't agree with that, I am asking you to point out where you claim the error is in what I have posted.

By all means say that you don't understand what 314.1C means, if that is the problem.

[tji]

Insulting the users of the forum isn't helping you at all,

Yet you have no problem with insulting people Mr P?

To be frank about it, judging by your behaviour alone, nothing you say on these matters should be trusted at all.

[/QUOTE]


Seriously below the belt!! Chris has posted everything he can to help ensure poster's have the correct information available, although I can see why people stop sharing when all they do is get **** on!

Tj

[mickreed]

Yet you have no problem with insulting people Mr P?

Tj

Mr P - or Mr Lucky - Tracy?. Or are they the same?