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The Ketchum Report (Continued)


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SY, you are correct about the table, it has on several occasions put me off from trying to figure it out. I was going to use the Cambridge Reference Sequence, NC_012920.1, as the basis for any recreation. But again I don't think the table shows anything other than the mutations for the haplotype. Sample 33 has only two mutations, and sample 95 only one. It don't believe there are no other mutations in the whole sequence of 16,569bp. And I think it is the other mutations not shown that are the interesting bit of the data (and currently unavailable).

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I'm sure it would be a huge job to manually combe through 20 whole mito genomes looking for these mutations but something tells me todays software is pretty good at finding them. Of coarse from what I was told, you have to isolate each one and BLAST it with about 120 bases each side of it to find matches in Genbank and determine it's novelty.

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I thought I had at least tried to answer that in my post #1775. I don't think there is any sequence that identify a specific person, unless there is a record (linking their sequence to an ID) to compare it too.

Well, I think you are wrong here, depending on which locus you are talking about and or if using STR's also known as microsatelites. You may not know ahead of time when or where a comparison sequence might turn up.

Check out this paper and it's authors.

http://link.springer.com/article/10.1007%2Fs00414-005-0545-9?LI=true#page-2

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I thought I had at least tried to answer that in my post #1775. I don't think there is any sequence that identify a specific person, unless there is a record (linking their sequence to an ID) to compare it too.

Well, I think you are wrong here, depending on which locus you are talking about and or if using STR's also known as microsatelites. You may not know ahead of time when or where a comparison sequence might turn up.

Check out this paper and it's authors.

http://link.springer...?LI=true#page-2

I totally agree, except where you said I was wrong! I very carefully said that you needed a record to compare it to. I totally agree, LOOKING FORWARD this is an easier task. Now, I don't know what kind of mischief BF has been getting up to, and whether its DNA is in some criminal database for unknown nefarious activities (if some of the suggestions of kidnapping human females and, well, you know, ending up with the human mtDNA in the resulting offspring). I totally agree that there are unique sequences that CAN identify an individual, but only if on the other side of the equation there is a comparable sample, that is linked to a known identity.

And thanks for the link. I will see if my institution is a subscriber to this journal and will download it if possible (I am a bit short at the moment and can not afford another $30 outlay :-). But based on the abstract, I am not sure exactly what you think the relevant part is. I do note our dear Dr. Ketchum as a co-author, but I would appreciate your opinion as to it's relevancy of our discussion!!

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I thought I had at least tried to answer that in my post #1775. I don't think there is any sequence that identify a specific person, unless there is a record (linking their sequence to an ID) to compare it too.

Well, I think you are wrong here, depending on which locus you are talking about and or if using STR's also known as microsatelites. You may not know ahead of time when or where a comparison sequence might turn up.

Check out this paper and it's authors.

http://link.springer...?LI=true#page-2

I totally agree, except where you said I was wrong! I very carefully said that you needed a record to compare it to. I totally agree, LOOKING FORWARD this is an easier task. Now, I don't know what kind of mischief BF has been getting up to, and whether its DNA is in some criminal database for unknown nefarious activities (if some of the suggestions of kidnapping human females and, well, you know, ending up with the human mtDNA in the resulting offspring). I totally agree that there are unique sequences that CAN identify an individual, but only if on the other side of the equation there is a comparable sample, that is linked to a known identity.

And thanks for the link. I will see if my institution is a subscriber to this journal and will download it if possible (I am a bit short at the moment and can not afford another $30 outlay :-). But based on the abstract, I am not sure exactly what you think the relevant part is. I do note our dear Dr. Ketchum as a co-author, but I would appreciate your opinion as to it's relevancy of our discussion!!

I thought I had at least tried to answer that in my post #1775. I don't think there is any sequence that identify a specific person, unless there is a record (linking their sequence to an ID) to compare it too.

Well, I think you are wrong here, depending on which locus you are talking about and or if using STR's also known as microsatelites. You may not know ahead of time when or where a comparison sequence might turn up.

Check out this paper and it's authors.

http://link.springer...?LI=true#page-2

I totally agree, except where you said I was wrong! I very carefully said that you needed a record to compare it to. I totally agree, LOOKING FORWARD this is an easier task. Now, I don't know what kind of mischief BF has been getting up to, and whether its DNA is in some criminal database for unknown nefarious activities (if some of the suggestions of kidnapping human females and, well, you know, ending up with the human mtDNA in the resulting offspring). I totally agree that there are unique sequences that CAN identify an individual, but only if on the other side of the equation there is a comparable sample, that is linked to a known identity.

And thanks for the link. I will see if my institution is a subscriber to this journal and will download it if possible (I am a bit short at the moment and can not afford another $30 outlay :-). But based on the abstract, I am not sure exactly what you think the relevant part is. I do note our dear Dr. Ketchum as a co-author, but I would appreciate your opinion as to it's relevancy of our discussion!!

When you click on the link there is a tab above the word abstract that says "Look Inside" , this will let you see the article. The paper simply outlines some protocols and processes for forensic identity of animals, which also applies to humans. Yes, identity needs a comparison sample, but logic would say it is out there , and could provide identity of the uploaded Data.

Edited by southernyahoo
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Hi everyone,

I thought I would take a stab at addressing the comments on Scott Carpenter's website regarding the haplotypes in the Trent and DNA Solutions reports on the Smeja tissue sample. Scott notes that the haplotype reported in the summary table on page 1 of the Trent report is type "A", whereas the haplotype reported by DNASolns is type "T". I believe that Scott has suggested that this indicates different samples were sent to the 2 labs.

However, the description of haplotype on page of the Trent report says...

Further analysis indicates that it is a European haplotype; it occurs with highest frequency in East Europe (11%) and Caucasus (10%) (i.e. it initially originated from near the Caucasus mountains regions between the Black and Caspian Seas). It is not known to have originally occurred in East Asia, Southeast Asia, Australia, Oceania (i.e. New Zealand, Papua New Guinea, etc.), North America, South America or Central America.

This is consistent with haplotype "T", while type "A" is common to east Asia and Amerindian population. I believe the type "A" shown in the summary table of the Trent report is a simple typo.

Moreover, I compared the partial human hypervariable region sequence in the Trent report to the hypervariable sequence from DNASoln, and there are homologous regions (see attached PDF). That proves unequivocally that the tissue samples sent to the 2 labs were the same. Ain't it great when science is reproducible!

Genes

Edited by GenesRUs
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Guest Tyler H

Hi everyone,

I thought I would take a stab at addressing the comments on Scott Carpenter's website regarding the haplotypes in the Trent and DNA Solutions reports on the Smeja tissue sample. Scott notes that the haplotype reported in the summary table on page 1 of the Trent report is type "A", whereas the haplotype reported by DNASolns is type "T". I believe that Scott has suggested that this indicates different samples were sent to the 2 labs.

However, the description of haplotype on page of the Trent report says...

Further analysis indicates that it is a European haplotype; it occurs with highest frequency in East Europe (11%) and Caucasus (10%) (i.e. it initially originated from near the Caucasus mountains regions between the Black and Caspian Seas). It is not known to have originally occurred in East Asia, Southeast Asia, Australia, Oceania (i.e. New Zealand, Papua New Guinea, etc.), North America, South America or Central America.

This is consistent with haplotype "T", while type "A" is common to east Asia and Amerindian population. I believe the type "A" shown in the summary table of the Trent report is a simple typo.

Moreover, I compared the partial human hypervariable region sequence in the Trent report to the hypervariable sequence from DNASoln, and there are homologous regions (see attached PDF). That proves unequivocally that the tissue samples sent to the 2 labs were the same. Ain't it great when science is reproducible!

Genes

Hi Genes, that is a great catch! thanks!

I was confident that Trent meant to say type "T" based on the description they used on page 2 of the Trent report: "Analysis of the human mitochondrial control region sequence obtained from Huggins_1 (based on 402 bp consensus based on forward and reverse of the mtDNA HVS1 non-coding region) was 100% identical at sites 15999-16400 of the complete mtDNA genome of Accession #JQ705199 (used in the publication by Behar et al., 2012). Further analysis indicates that it is a European haplotype; it occurs with highest frequency in East Europe (11%) and Caucasus (10%) (i.e. it initially originated from near the Caucasus mountains regions between the Black and Caspian Seas). It is not known to have originally occurred in East Asia, Southeast Asia, Australia, Oceania (i.e. New Zealand, Papua New Guinea, etc.), North America, South America or Central America. " - but it's great to see the prrof that we are dealing with the same sample between at least Trent and OK labs. Can we see if any of these sequences happen to turn up in the .1% of data that we have from Melba? Is this an easy software trick, or time intensive manual task?

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This is consistent with haplotype "T", while type "A" is common to east Asia and Amerindian population. I believe the type "A" shown in the summary table of the Trent report is a simple typo.

You assume it is a Typo, But what if it wasn't. Shouldn't it be called into question instead of making the assumption it was a typo? This would have caused more reasonable doubt in a court of law or even in a Peer Review paper. If the report is official documentation it should have been proof read for mistakes like this NO?

I don't think you can just assume its a typo. If it isn't a typo then what else in the report may be incorrect?

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Homolgous is not in the same realm as a microsatelite match. Did I hear someone accuse Ketchum of changing her haplotype for her sample? now someone is changing the Trent report Hap. Anyone want to change Justins while we're are at it?

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Guest Tyler H
This is consistent with haplotype "T", while type "A" is common to east Asia and Amerindian population. I believe the type "A" shown in the summary table of the Trent report is a simple typo.

You assume it is a Typo, But what if it wasn't. Shouldn't it be called into question instead of making the assumption it was a typo? This would have caused more reasonable doubt in a court of law or even in a Peer Review paper. If the report is official documentation it should have been proof read for mistakes like this NO?

I don't think you can just assume its a typo. If it isn't a typo then what else in the report may be incorrect?

Homolgous is not in the same realm as a microsatelite match. Did I hear someone accuse Ketchum of changing her haplotype for her sample? now someone is changing the Trent report Hap. Anyone want to change Justins while we're are at it?

Both

We have a credentialed, objective third party here, quoting the type as DESCRIBED by Trent, and noting the fact that it does not match what they put in their TABLE. The DESCRIPTION DOES however completely match the TYPE LETTER, used by OK's DNA Solutions. Pretty big cioncidence. Then, on top of it, in the HYPERVARIABLE region, we see that we have exactly matching sequence... use Occam's razor folks: "Typo" by Trent is about all we have left as a reasonable option.

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