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Big Y and New SNP Panels . . .

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  • ajmr1a1
    replied
    I have had the same experience with chip technology in general.
    23andme and Geno 2.0 both reported erroneous results with regard
    to yDNA and mtDNA haplogroups.

    Leave a comment:


  • wkauffman
    replied
    Originally posted by dna View Post
    I seem to recall that the first SNP panel there was a beta test. That seemed obvious.

    Are you saying that the other panels did not undergo such testing?

    W. (Mr.)
    I do not know..... I am curious what type of validation goes in BEFORE the panel is released for sale.

    Leave a comment:


  • dna
    replied
    Originally posted by wkauffman View Post
    The technology differences between sequencing and "SNP panels" is enough that one needs to acknowledge that placing a SNP or INDEL identified via NGS or Sanger sequencing onto a panel does NOTT mean that it will work on panel. Remember all of the failed SNPs in the Illumina chips that 23andMe used and in the Geno 2 chip? What is FTDNA's success rate for correct results from a panel?

    What I have not heard is how FTDNA validates the reporting of the SNPs placed onto a panel. They are not going to get all of the expected SNPs to work due to technical issues. In previous years FTDNA lab scientists would ask approval to run experimental tests on client samples to help validate new SNP primers. Have those types of requests for access to samples for the new SNPs been going out to the individuals who have them?

    I have a sinking feeling that FTDNA needs a lot of panel orders in order to figure out what is working before they return results to the client. That is technically very scary. We may still be a situation where we need to have individuals test elsewhere to confirm what is being seen on a SNP panel.
    I seem to recall that the first SNP panel there was a beta test. That seemed obvious.

    Are you saying that the other panels did not undergo such testing?

    W. (Mr.)

    Leave a comment:


  • wkauffman
    replied
    The technology differences between sequencing and "SNP panels" is enough that one needs to acknowledge that placing a SNP or INDEL identified via NGS or Sanger sequencing onto a panel does NOTT mean that it will work on panel. Remember all of the failed SNPs in the Illumina chips that 23andMe used and in the Geno 2 chip? What is FTDNA's success rate for correct results from a panel?

    What I have not heard is how FTDNA validates the reporting of the SNPs placed onto a panel. They are not going to get all of the expected SNPs to work due to technical issues. In previous years FTDNA lab scientists would ask approval to run experimental tests on client samples to help validate new SNP primers. Have those types of requests for access to samples for the new SNPs been going out to the individuals who have them?

    I have a sinking feeling that FTDNA needs a lot of panel orders in order to figure out what is working before they return results to the client. That is technically very scary. We may still be a situation where we need to have individuals test elsewhere to confirm what is being seen on a SNP panel.

    Leave a comment:


  • John
    replied
    to be clear . . .

    I am NOT being negative about the SNP panels, or packs I guess is the current denomination. I think in some circumstances they might present an useful option, if they are presented to fully informed customers who have not done SNP testing previously and are seeking a cost effective way to identify their most likely SNP lineage.

    I do not think that is being done at present. I realize that this is a fast changing science and business, and that it can be challenging to add new products while also keeping the present database and customer/project dashboards up to date. Still, making allowances for all that, the manner that these packs have been and are being presented is not ethically acceptable, in my most humble opinion.

    My other major objection continues to be the disconnect between the SNP trees, SNP packs and Big Y results. If the SNP packs offer results for SNPs downstream of identified SNPs on the trees of Big Y takers, and the status of those SNPS are within the Big Y test data, then the SNP trees of the Big Y takers should be updated to show that. This is closely related to my concern about how the packs are being presented to customers, as I feel that by not updating the trees FTDNA is in effect withholding information which may be crucial to the customers making informed decisions.

    Caveat emptor may be the common practice, but I'll always prefer emptor conscii. Esse informata emptor perussi eaque omnia facta esse sensit. Ethica concionatorum educandi perussi.

    Leave a comment:


  • Peter MacDonald
    replied
    Anyone who has their Big Y results should go to a third party for interpretation of their results. The cost for this ranges from $40-$50 and will save you a great deal of frustration.

    As a side note, when I purchase something and the sales representative tries to sell me something I don't need during or after the fact….I remember this and go elsewhere the next time I make a similar purchase.

    Leave a comment:


  • lgmayka
    replied
    Originally posted by boutrosdu93 View Post
    so are the snps really the same or note? as the other member seemed to imply it'not the same testing methodology i'm confused...
    A SNP with the same name is the same SNP. However:

    - Some SNP panels reportedly include a few SNPs that are not usually covered by the Big Y.

    - The technology used by the SNP panels is reportedly different from that used by the Big Y, so experts or the well-to-do might have a reason to order both.

    The real difficulty is that FTDNA is not distinguishing between offering and advertising. An excellent example is the new Z283 SNP Pack. The product's content makes clear that:

    - Anyone predicted to belong to the R1a haplogroup should be able to order it.

    - Only those confirmed or predicted to belong to R1a-Z284 (or, arguably, R1a-M458) should see an advertisement for it.

    Leave a comment:


  • boutrosdu93
    replied
    ahahah no worries have fun i'd rather you play with my typos than ftdna plays with custommers money....

    mmm ok anyway i'll wait for my results to come thanks bro.

    Leave a comment:


  • John
    replied
    Are the SNPs really the same or note?

    Originally posted by boutrosdu93 View Post
    so are the snps really the same or note? as the other member seemed to imply it'not the same testing methodology i'm confused...
    Yes, they are the same. The bit about the differing methodologies is close to a red herring; while the Big Y and the SNP panels use different tech to look at the SNP locations they are still looking at the same locations.

    Look up Paris on a paper map, then look up Paris on a GPS. Same Paris in the end, is it note or not?

    PS: Hope you don't mind my play with your typo, I found it amusing in the context of the question.

    Leave a comment:


  • boutrosdu93
    replied
    so are the snps really the same or note? as the other member seemed to imply it'not the same testing methodology i'm confused...

    Leave a comment:


  • John
    replied
    A few facts and opinions . . .

    I've waited to make sure I have the proper information on at least the L338 panel and the Big Y results. According to the analysis of the panel and my Big Y results: " . . . your Big-Y covered ALL of the SNPs listed on the panel, so you've already tested for them all. You are negative for almost all of them as they mostly refer to A376+ members much further down the L338+ Tree, not your end of the tree . . ." Another project member was told "another ******* kin has paid $98 to test this A376+ Panel ... all he'll get for his money is to test one useful new SNP, S12289 and he will most likely be negative for that. All the rest of the SNPs tested on the panel are irrelevant, he'll be negative for them all. For his money, he won't even be testing your new SNP A1944".

    Paying $98 dollars to test the unknown in order to advance the science is one thing, but paying the same amount to test already known facts is nonsense.

    So once again I'll assert that it almost certainly does not make sense for FTDNA to advertise the SNP panels on the pages of those who have done the Big Y, and what should happen is the Haplotree for those who have done Big Y should be updated to show which SNPs in the panel have a "+" result according to the Big Y. And I'll add this suggestion, when FTDNA is looking to put together these SNP panels they should consult with the project leaders whose 'territory' is involved.

    Leave a comment:


  • RDickinson
    replied
    I don't think it's possible to repeat this too many times:

    Originally posted by lgmayka View Post
    - When FTDNA adds a new SNP to its official haplotree, via a SNP Pack or otherwise, FTDNA should add the corresponding Big Y results for that SNP (if any) to customer accounts.
    ...But the following--well, for me, at least, this is not a repetition at all, but a succinct summary of new information I have not come across before. I can only say "really???" and "that certainly explains a few things":

    Originally posted by lgmayka View Post
    By the way, I thought of one more major reason that a Big Y participant might order a SNP Pack. In order to list a new full-fledged (not italicized) SNP, current ISOGG rules require either Sanger sequencing (individual SNP tests) or a combination of next-generation sequencing and microarray results. Next-generation sequencing (e.g., the Big Y) is not sufficient to list a full-fledged SNP on ISOGG's haplotree. Thus, a Big Y participant who is particularly eager to get his newly discovered SNP on ISOGG's tree might reasonably order a SNP Pack, in order to obtain the evidence necessary for full-fledged listing.

    Leave a comment:


  • BBA64
    replied
    Originally posted by lgmayka View Post
    But I do not think that our primary message to FTDNA should be, "Don't tell us about SNP Packs. Don't show them to us or advertise them to us. Don't let us buy them at all." One might say that I prefer an information-based approach to a nanny-state approach.
    I would agree with you on that. The proper information should accompany the advertisement (devil in the details). Even as you said, you pretty much tell folks in your project, the Big Y is the last test you'll need. And suddenly and ad appears suggesting testing you about which you just thought you had already gotten the definitive word. That's the primary complaint in the OP.

    It would be helpful to update project admins on the details of incoming panel tests, too. What I find interesting is the relatively detailed explanations from admins the last few days detailing more about the Big Y is (and isn't) and why folks should consider outlaying the significant funds to test that way. This is far more helpful than just telling folks to get a Big Y test done.

    Leave a comment:


  • lgmayka
    replied
    Originally posted by BBA64 View Post
    This would have been a far more appropriate answer from the outset.
    You're right.
    Originally posted by BBA64 View Post
    Perhaps you should enlighten project managers to this? This is NOT the message they are giving, at least in the R1b-related projects that I've been a part of (and some of these admins really know their stuff - but apparently not at your elevated level).
    The more experienced project administrators have at least as much knowledge as I do about these matters. But I see a big difference between
    - The message to give project members vs.
    - The message to send to FTDNA.

    I myself tell project members that "the Big Y is essentially the last Y chromosome test you will ever need." If ever a SNP Pack becomes available in a Central-Eastern European haplogroup, I will tell my own project members that "in general, Big Y participants do not need a SNP Pack--you may help your investigation more by buying a SNP Pack for one of your near-matches."

    I certainly agree that:
    - When FTDNA adds a new SNP to its official haplotree, via a SNP Pack or otherwise, FTDNA should add the corresponding Big Y results for that SNP (if any) to customer accounts.
    - FTDNA should give project administrators prior notice when introducing a new SNP Pack so that they are ready to answer questions about its usefulness.
    - FTDNA should mention, in the description of each SNP Pack, that customers are encouraged to consult an administrator to confirm the usefulness of the SNP Pack in their case.

    But I do not think that our primary message to FTDNA should be, "Don't tell us about SNP Packs. Don't show them to us or advertise them to us. Don't let us buy them at all." One might say that I prefer an information-based approach to a nanny-state approach.

    By the way, I thought of one more major reason that a Big Y participant might order a SNP Pack. In order to list a new full-fledged (not italicized) SNP, current ISOGG rules require either Sanger sequencing (individual SNP tests) or a combination of next-generation sequencing and microarray results. Next-generation sequencing (e.g., the Big Y) is not sufficient to list a full-fledged SNP on ISOGG's haplotree. Thus, a Big Y participant who is particularly eager to get his newly discovered SNP on ISOGG's tree might reasonably order a SNP Pack, in order to obtain the evidence necessary for full-fledged listing.
    Last edited by lgmayka; 6 June 2015, 09:45 PM.

    Leave a comment:


  • BBA64
    replied
    Why didn't you explain this the first time?

    Originally posted by lgmayka View Post
    False. You two apparently don't understand the technology or other issues involved at all.
    This is a much different answer than your "not meaning to rag on you" answer about consumerism and marketing. This would have been a far more appropriate answer from the outset.

    Perhaps you should enlighten project managers to this? This is NOT the message they are giving, at least in the R1b-related projects that I've been a part of (and some of these admins really know their stuff - but apparently not at your elevated level).

    Cheers!

    Leave a comment:

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