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  • Zaleski
    replied
    Originally posted by rojamg
    Rceived this from FTDNA:

    A Polish Pole marrying a Southeast Asia Indian makes more sense than a Persian Pole marrying a Finnish Indian, but isn't quite as fun
    The Ray Banks Haplogroup G Website has me identified with the Ossetian's on his Haplogroup G Cluster Chart. I also have a long line of cute little Polish grandmothers. EGADS! I'M POLISH PERSIAN.

    Leave a comment:


  • cacio
    replied
    rojamg:

    R & R - certainly a match!

    cacio

    Leave a comment:


  • rojamg
    replied
    Well it's final, for now

    Rceived this from FTDNA:

    I've checked with Dr. Behar and he has confirmed that the correct haplogroup
    assignment has been made, and that there is no mutation in the HVR1 region
    that has not already been reported.


    So I'm now a R1a1 instead of a R1a. My wife is a R instead of a U.

    A Polish Pole marrying a Southeast Asia Indian makes more sense than a Persian Pole marrying a Finnish Indian, but isn't quite as fun

    Thanks All for Help.

    Bests, Glenn

    Leave a comment:


  • vraatyah
    replied
    Efgen, it seems you underestimate the useless of the hvs sequencing. Some coding-region mutations can be outweighted by a particular HVS motif. From the more formal viewpoint, all we have in phylogeny, is the characters and their weights. It is the border where biology ends and math starts

    Leave a comment:


  • Jim Denning
    replied
    Originally posted by rojamg
    Just revisited the Genographic site. My wife went from U to F which made sense since not alot of Finns passed thru India on their journey up north. I went from R1a to R1a1.

    How do these changes i groups occur?

    Secondly, ran my wife thru MitoSearch, and not a single match. Is the database that small, or are mtdna Haplogroup F folks just "special".

    Best, Glenn

    actually they did

    Leave a comment:


  • efgen
    replied
    Originally posted by curlygirl_3d
    Thanks for the info. I did upload my info to FamilyTreeDNA and Mitosearch already, but missed mention of a second test. I'll look into that.
    The other, pricy one, I guess I'll just have to wait on.
    At the top right of your myFTDNA page, there's an "order tests" link. I think they need to make that more noticable

    Elise

    Leave a comment:


  • curlygirl_3d
    Guest replied
    Originally posted by efgen
    Ronda,

    Have you transferred your mtDNA results to FTDNA yet? If not, that should be your first step, and it's free. Genographic Project tests only HVR1. Through FTDNA, you can order the HVR2 test (I think it's $75), which will give you more mutations and refine who you match.

    The one other test you could take which would further refine your matches is the mtDNA Full Sequence, which tests the entire mtDNA. However, it's very pricey right now, so relatively few people order this test and therefore it wouldn't immediately be beneficial for matching against other people.

    You should also upload your results to Mitosearch, which is a public database that people who tested with any company can upload their results to.
    Elise
    --

    Hi Elise,

    Thanks for the info. I did upload my info to FamilyTreeDNA and Mitosearch already, but missed mention of a second test. I'll look into that.
    The other, pricy one, I guess I'll just have to wait on.

    Thanks so much!
    Ronda

    Leave a comment:


  • efgen
    replied
    Originally posted by curlygirl_3d
    In reading the above, it makes me wonder if there are other mtDNA tests I could take that would give further info on mutations...? I only have 4 mutations listed with the Genographic Project...and my current Haplogroup is T. Would further testing be worthwhile?
    Ronda (curlygirl_3d)
    Ronda,

    Have you transferred your mtDNA results to FTDNA yet? If not, that should be your first step, and it's free. Log in to your GP webpage, and at the very bottom, there's a link to learn more about Family Tree DNA. Follow the instructions there to create your FTDNA account. Once you have your FTDNA account, you will be able to see everyone in the FTDNA database who you match.

    Genographic Project tests only HVR1. Through FTDNA, you can order the HVR2 test (I think it's $75), which will give you more mutations and refine who you match. However, be aware that even with HVR1+HVR2, your matches still probably won't be within a genealogical timeframe.

    The one other test you could take which would further refine your matches is the mtDNA Full Sequence, which tests the entire mtDNA. However, it's very pricey right now, so relatively few people order this test and therefore it wouldn't immediately be beneficial for matching against other people.

    You may want to read through the mtDNA tutorial page for more info:

    http://www.ftdna.com/mtDNA_tutorial.html

    You should also upload your results to Mitosearch, which is a public database that people who tested with any company can upload their results to. There's will be a link to do that on the mtDNA Matches page of your FTDNA account.

    Elise

    Leave a comment:


  • curlygirl_3d
    Guest replied
    Originally posted by efgen
    Glenn - For many mtDNA haplogroups, the defining mutations are not in the HVR1 or HVR2 regions that most of us have tested. Instead, they are in the coding regions, so FTDNA has to test for additional mutations in the coding region in order to correctly identify the haplogroup.

    vraatyah - FTDNA doesn't automatically provide the list of coding region mutations that they test to determine haplogroup. I don't know if they would provide the info if asked.
    --

    In reading the above, it makes me wonder if there are other mtDNA tests I could take that would give further info on mutations...? I only have 4 mutations listed with the Genographic Project...and my current Haplogroup is T. Would further testing be worthwhile?

    Ronda (curlygirl_3d)

    Leave a comment:


  • efgen
    replied
    Originally posted by cacio
    FTDNA does not usually test for coding region mutations, they may do only in certain dubious cases and for basic European groups like H and U. And, to be fair, they cannot do otherwise. There are literally hundreds of haplogroups when moving out of Europe, essentially they'd have to test the whole mtdna - not something they can do for $100.
    There are not hundreds of haplogroups -- maybe hundreds of subclades. And FTDNA most certainly does determine the haplogroup by testing the coding region -- finally found the reference, in FTDNA's new mtDNA Tutorial:

    http://www.familytreedna.com/mtDNA_tutorial.html#9

    Subclades are another story. The only mtDNA haplogroup that FTDNA currently offers a subclade test for is H. For all other haplogroups, the only way to test for the subclade is to order the mtDNA Full Sequence test.

    Leave a comment:


  • cacio
    replied
    efgen:

    of course, they may have tested for F. I am skeptical, however, because I have seen previous cases of misassignment and seen similar emails before for more than one case. As you suggest, the only way to know is to ask. And to ask precise questions. Usually, the first answer one gets is from a customer rep, a non-scientist, who only answers with standard sentences that don't mean anything (everything is always a clerical error), as in this case. One gets through and talks to a scientist only after a couple of emails with a very precise question such as: is the assignment based only on HVR1 or were other locations in the coding region tested, and if so which ones? Or an even better question, this sequence looks similar to (cite academic article): how is your assignment reconciled with this?

    FTDNA does not usually test for coding region mutations, they may do only in certain dubious cases and for basic European groups like H and U. And, to be fair, they cannot do otherwise. There are literally hundreds of haplogroups when moving out of Europe, essentially they'd have to test the whole mtdna - not something they can do for $100. Which I suppose is the reason why we don't have a mtdna SNP haplogroup test being offered by companies (while there are more than a few companies offering Y SNP tests.)


    cacio

    Leave a comment:


  • efgen
    replied
    I have to disagree with cacio's assessment of the email from FTDNA. The way I read it, they predicted the haplogroup from HVR1 as U, but their haplogroup test showed it to be F. However, through a clerical error, they uploaded the predicted haplogroup instead of the tested haplogroup to the GP database. They then caught their own error while doing a review, hence the change.

    I believe FTDNA always does a haplogroup test for mtDNA since many haplogroups are defined by coding region mutations rather than HVR1/2 mutations.

    Glenn - For many mtDNA haplogroups, the defining mutations are not in the HVR1 or HVR2 regions that most of us have tested. Instead, they are in the coding regions, so FTDNA has to test for additional mutations in the coding region in order to correctly identify the haplogroup.

    vraatyah - FTDNA doesn't automatically provide the list of coding region mutations that they test to determine haplogroup. I don't know if they would provide the info if asked.

    Leave a comment:


  • cacio
    replied
    rojamg:

    as vraatyah explained, the initial answers from ftdna are just standard clerical responses of little content. Only after some insistence and more specific questions does one reach more knowledgeable people in the company. For instance, in your case, what they ought to have said was exactly what they tested. They say they didn't find the marker for U. But I don't think they tested for F, they just guessed it based on 16304, which is also present in F.

    Regarding your question about HVR1, you are right that it is a specific region. Mtdna is composed of around 16600 letters, HVR only comprises the last 600. However, it is often not enough to determine the haplogroup. The mutations defining the haplogroup are usually in the other parts of the mtDNA. Moreover, unlike for the Y chromosome, mutations appear independently in more than one haplogroup, so often one has to check a whole set of them, not just an isolated one. As vraatyah said, I don't think FTDNA at this point has the test for the mutations defining most non-European haplogroups, I think they do have that for haplogroups like H and U, which are common in Europe.

    What FTDNA does usually is to look at HVR1, and then _predict_ the haplogroup based on their database. Their system works relatively well for European haplogroups, since they have a huge database. But it breaks down for the non-European ones. And this also explain why they tend to overpredict European haplogroups (you are not the only case of such misassignment) - customers are usually of European origin, so H and U are usually good guesses.

    cacio

    Leave a comment:


  • vraatyah
    replied
    Originally posted by rojamg
    Response from E-Mail:

    ""There are two systems for determining a haplogroup; one based on the HVR1
    results and the other based on additional haplogroup testing. Sometimes
    these will be in conflict. In your wife's case, her HVR1 region looks like
    she ought to belong to haplogroup U, but her haplogroup test clearly
    indicated that she is not in U. This is a good example of why it's
    important to test for haplogroups rather than depending on the HVR1 region,
    since the latter can sometimes be misleading.

    A clerical error when the results were initially uploaded caused the HVR1
    haplogroup determination to be used rather than the haplogroup test result.
    Our mtDNA team periodically reviews the database of the thousands of tests
    performed to check for any errors. They caught this one, and had us correct
    the haplogroup assignment. Based on a combination of the haplogroup test
    results and the HVR1 region, her correct haplogroup assignment is F.""

    I still waiting from my beginers guide to DNA testing from amazon.com May be then the fog of DNA terminology will lift. I assume the HVR1 region is a specific region of genetic code whose variations are the basis for genetic analysis. What exactly is a a Haplogroup test if not the summation of variation of a specific DNA strand?

    I'll forward the request for additional tesing. I'd hate for my wife to live in U, F, R purgatory.

    Bests, Glenn (R1A1)

    their comment does not seem to be of great importance. At least, until they list the markers included in multiplex.

    Leave a comment:


  • rojamg
    replied
    Reply from FTDNA

    Response from E-Mail:

    ""There are two systems for determining a haplogroup; one based on the HVR1
    results and the other based on additional haplogroup testing. Sometimes
    these will be in conflict. In your wife's case, her HVR1 region looks like
    she ought to belong to haplogroup U, but her haplogroup test clearly
    indicated that she is not in U. This is a good example of why it's
    important to test for haplogroups rather than depending on the HVR1 region,
    since the latter can sometimes be misleading.

    A clerical error when the results were initially uploaded caused the HVR1
    haplogroup determination to be used rather than the haplogroup test result.
    Our mtDNA team periodically reviews the database of the thousands of tests
    performed to check for any errors. They caught this one, and had us correct
    the haplogroup assignment. Based on a combination of the haplogroup test
    results and the HVR1 region, her correct haplogroup assignment is F.""

    I still waiting from my beginers guide to DNA testing from amazon.com May be then the fog of DNA terminology will lift. I assume the HVR1 region is a specific region of genetic code whose variations are the basis for genetic analysis. What exactly is a a Haplogroup test if not the summation of variation of a specific DNA strand?

    I'll forward the request for additional tesing. I'd hate for my wife to live in U, F, R purgatory.

    Bests, Glenn (R1A1)

    Leave a comment:

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