About Behar2012b use of the FTDNA clones


Posts: 2283
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
R- Z2110 (KV7Y2)
MtDNA:
K1a1b1e/HQ176413
PostPosted: Sat Jan 25, 2014 10:39 am
mtDNA hg. K1a4 is important also to deepen a discourse I have elsewhere hinted: the use of Behar2012b of the FTDNA clones. If we look at the 13 samples given for the K1a4 haplogroup, we can see that the FTDNA samples, once used, should have been deleted, so it would have appeared that those clones were sequenced again in Israel's labs. But not always it has happened:
1) MC947/JQ702505 is the same of the MC16484/FTDNA/EU139551
2) MC1353/JQ702911 is the same of the MC16851/FTDNA/EU564851
3) MC4098/JQ705656 is (probably) the same of the MC16527/FTDNA/EU219921, because they differ in the mutations:
C150T C264T C6518TT C10961T A13681G A15613G T16093C with "topologically missing" A11914G the second

C264T C6518TT C10961T A13681G A15613G T16093C C16189Y with "topologically missing" A11914G and C16189T the first.
Was this clone actually sequenced again or has been done a great confusion in reporting the results?


Haplogroup K1a4 has 13 samples
Sample Id: MC947 NCBI Id: JQ702505 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] A12358G; A16051G;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] Country: Italy Geography: Ancestry:
Reference: Behar 2012b Contact:
Sample Id: MC1072 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] 315.1C T372C 522.1A 522.2C 522.3A 522.4C G10586A T12957C T16093Y
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] C152T
Country: United States Geography: PA Ancestry: Reference: Contact:
Sample Id: MC1353 NCBI Id: JQ702911 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] G207A; G3010A; C4137T; G5237A; A8531G; G15930A;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] Country: Geography: Ancestry: Reference: Behar 2012b Contact:
Sample Id: MC1738 NCBI Id: JQ703296 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] T3290C; A6437G;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.]Country: Geography: Ancestry: Reference: Behar 2012b Contact:
Sample Id: MC1803 NCBI Id: JQ703361 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] G5237A; A8531G; A8642G; A11167G; G15497A;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] Country: Geography: Ancestry: Reference: Behar 2012b Contact:
Sample Id: MC3604 NCBI Id: JQ705162 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] A7358G; A8350c; A11566G; T16093Y;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] Country: Geography: Ancestry: Reference: Behar 2012b Contact:
Sample Id: MC4098 NCBI Id: JQ705656 Unresolved Options: K1a4; Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] C264T; C6518T; C10961T; A13681G; A15613G; T16093C; C16189Y;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] A11914G(L1'2'3'4'5'6); C16189T(L2'3'4'6);
Country: Switzerland Geography: Ancestry: Reference: Behar 2012b Contact:
Sample Id: MC14636 NCBI Id: AY495261 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.]
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] Country: Geography: Ancestry: Reference: Coble 2004 Contact:
Sample Id: MC14638 NCBI Id: AY495263 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.]
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] Country: Geography Ancestry: Reference: Coble 2004 Contact:
Sample Id: MC16484 NCBI Id: EU130551 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] A12358G; A16051G;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] Country: Geography: Ancestry: Reference: FamilyTreeDNA Contact:
Sample Id: MC16527 NCBI Id: EU219921 Unresolved Options: K1a4; Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] C150T; C264T; C6518T; C10961T; A13681G; A15613G; T16093C;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] A11914G(L1'2'3'4'5'6);
Country: Geography: Ancestry: Reference: FamilyTreeDNA Contact:
Sample Id: MC16851 NCBI Id: EU564851 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] G207A; G3010A; C4137T; G5237A; A8531G; G15930A;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] Country: Geography: Ancestry: Reference: FamilyTreeDNA Contact:
Sample Id: MC17438 NCBI Id: FJ348212 Unresolved Options: Verified Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] T4313C; G9064A;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] C152T(L2'3'4'5'6);
Country: Geography: Ancestry: Reference: Pichler 2008 Contact:

Posts: 61
Joined: Wed Mar 14, 2012 4:29 pm
PostPosted: Sat Jan 25, 2014 12:57 pm
Gioiello wrote:mtDNA hg. K1a4 is important also to deepen a discourse I have elsewhere hinted: the use of Behar2012b of the FTDNA clones. If we look at the 13 samples given for the K1a4 haplogroup, we can see that the FTDNA samples, once used, should have been deleted, so it would have appeared that those clones were sequenced again in Israel's labs. But not always it has happened:
1) MC947/JQ702505 is the same of the MC16484/FTDNA/EU139551......
Hi Gioiello and all,

First of all, there are no "Israel's labs" involved in this problem. I just looked at the first example you list and it and probably most or all of the others are from FTDNA. (A few of the sequences from Behar 2012b were from the co-authors' lab in Estonia, as I remember.) In some cases, small changes were made in the reported sequencing between the time t he mtDNA full sequence was sent directly to GenBank by the recipient and when Dr. Behar sent them in 2012. He was trying to exclude duplicates, but some "near-duplicates" were sent anyway. For example, years ago FTDNA had no way to report heteroplasmies. So an old sequence without heteroplasmies and a new sequence with them might be on GenBank and be from the same person. In most cases, the more recent version should be used. However, there are some identical sequences on GenBank twice for reasons I don't understand. I reported all the duplicate K sequences to Dr. Behar in July, 2012.

Bill Hurst

Posts: 2283
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
R- Z2110 (KV7Y2)
MtDNA:
K1a1b1e/HQ176413
PostPosted: Sat Jan 25, 2014 1:58 pm
Bill Hurst wrote:Hi Gioiello and all,

First of all, there are no "Israel's labs" involved in this problem. I just looked at the first example you list and it and probably most or all of the others are from FTDNA. (A few of the sequences from Behar 2012b were from the co-authors' lab in Estonia, as I remember.) In some cases, small changes were made in the reported sequencing between the time t he mtDNA full sequence was sent directly to GenBank by the recipient and when Dr. Behar sent them in 2012. He was trying to exclude duplicates, but some "near-duplicates" were sent anyway. For example, years ago FTDNA had no way to report heteroplasmies. So an old sequence without heteroplasmies and a new sequence with them might be on GenBank and be from the same person. In most cases, the more recent version should be used. However, there are some identical sequences on GenBank twice for reasons I don't understand. I reported all the duplicate K sequences to Dr. Behar in July, 2012.

Bill Hurst


I thank you for your letter, but my note had been written for a post of mine on Anthrogenica to answer a question about mtDNA K1a4, that Maciamo (Eupedia) says of Middle Eastern origin and linked to the expansion of R1b. I think the other way around of both. I posted this note also here, because you know that Behar gets some strong friend there, always ready to delete my posts.
Anyway this is written on GenBank about these clones of Behar et alii:

AUTHORS Behar,D.M., van Oven,M., Rosset,S., Metspalu,M., Loogvaeli,E.-L.,
Silva,N.M., Kivisild,T., Torroni,A. and Villems,R.
TITLE Direct Submission
JOURNAL Submitted (23-FEB-2012) Molecular Medicine Laboratory, Rambam
Health Care Campus, Efron 9 st, Haifa 31096, Israel

Kind Regards, Gioiello Tognoni

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