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Thread: R1b SNP Packs from FTDNA

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    R1b SNP Packs from FTDNA

    I get questions about this on various forums and will open a general thread here as I think we will have some updates soon. I have some insight (not much) in to the queue of new FTDNA packs and pack updates, particularly on the P312 side of things and things that directly touch the R1b project.

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    Quote Originally Posted by Mikewww View Post
    I get questions about this on various forums and will open a general thread here as I think we will have some updates soon. I have some insight (not much) in to the queue of new FTDNA packs and pack updates, particularly on the P312 side of things and things that directly touch the R1b project.
    Any new developments of the inclusion of a lot of private YSNPs with these new YSNP pack tests ? If FTDNA is using chip array technology, the ongoing testing costs would not be much more - but the up front development costs would be a lot more as it takes time to develop chip array tests. It is very difficult to get others to test private YSNPs based on YSTR patterns of the NGS tester and panel test results. If we had private panel packs, this would provide an option to discover smaller and more genealogical branches vs. just finding where you fit on the existing haplotree (which provides value to analysis but will never discover new branches).

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    Quote Originally Posted by RobertCasey View Post
    Any new developments of the inclusion of a lot of private YSNPs with these new YSNP pack tests ?
    The number of SNPs and the corresponding cost is limited to maxing out the current panels at about 150 variants. While technically possible for FTDNA to add another well (+50 variants) or more to the mix that becomes a lab logistics processing issue if various packs are various 'sizes'. How would FTDNA make money on such low volume private panels when each panel takes a lot of effort to validate? The cost of developing private panels will quickly exceed the cost of several Big-Y's. It is just easier to pay for full y sequencing up front to establish a small pool of 10-20 variants that can be processed at YSEQ for family specific investigations.

    In terms of adding specific private variants to a panel I have been able to select S-, CTS, and PH- series variants present in individuals unmatched list and get most of those added to say the R-Z326 panel up to the point where I hit the ~150 variant limit. Note that I also selected specific early Z-series not covered by Big-Y. All of these are useful since they have been seen in other samples. Due to the amount of validation effort changing a panel's composition may occur only about once a year. FTDNA has a limited capacity to add new or update existing panels. One of the problems that will become more of an issue later in 2016 and into 2017 is the need to split existing panels to provide capacity for new clades and auxiliary variants of interest. Getting solid leader variants from those new panels back into upstream packs such as the r1b backbone will be a challenge.

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    Quote Originally Posted by Cofgene View Post
    .... How would FTDNA make money on such low volume private panels when each panel takes a lot of effort to validate? The cost of developing private panels will quickly exceed the cost of several Big-Y's...
    Cofgne, I think your assumptions related to FTDNA pack costs are off a bit. They have a surprisingly low break-even point on the number of SNP Packs orders from a single product. I can't give the number but this means packs could be designed for haplogroups in fairly youthful ranges.

    It does depend on the target population of testers for that haplogroup but we definitely can look in closer than 1500 year old haplogroups. Keep in mind I'm familiar with high test penetration R1b populations.

    I think they semi-arbitrarily set a limit on SNPs in a pack to 160. However, as noted, this is not a hard core threshold. This is a little bit of a card game. We have the hg G pack and L21 top-layer up close to a 190 if my memory serves me correctly.
    Last edited by TigerMW; 03-21-2016 at 10:09 PM.

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    Quote Originally Posted by Mikewww View Post
    I think they semi-arbitrarily set a limit on SNPs in a pack to 160. However, as noted, this is not a hard core threshold. This is a little bit of a card game. We have the hg G pack and L21 top-layer up close to a 190 if my memory serves me correctly.
    Right now, FTDNA advertises:
    Get 112 SNPs related to M201 for only $119!
    Get 170 SNPs related to L21 for only $119!

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    Quote Originally Posted by Cofgene View Post
    The number of SNPs and the corresponding cost is limited to maxing out the current panels at about 150 variants. While technically possible for FTDNA to add another well (+50 variants) or more to the mix that becomes a lab logistics processing issue if various packs are various 'sizes'. How would FTDNA make money on such low volume private panels when each panel takes a lot of effort to validate? The cost of developing private panels will quickly exceed the cost of several Big-Y's. It is just easier to pay for full y sequencing up front to establish a small pool of 10-20 variants that can be processed at YSEQ for family specific investigations.
    I am assuming that the FTDNA SNP packs are small chip array tests vs. tiered testing of Sanger Sequencing like YSEQ. I base this on the fact that they do not use any tiering and test more real YSNPs - suggesting a lower cost chip array of some sort. Also, I have noticed that there appears to be no-calls with FTDNA SNP packs since many Z253 SNP packs are missing two L226 SNPs on a regular basis - another indication of chip array tests. The only issue that I really see is that chip array tests take more time to develop and require more setup costs - therefore, requiring high expected sales to cover initial costs.

    I was hoping that Nat Geo or BritainDNA would replace their old and tired offerings with a massive L21, U106, etc. private SNP tests for around $100 to $150 for thousands of private YSNPs. These tests would sell very well since so many smaller genealogical branches would be revealed at a much lower cost than just more Big Y tests. I think that we need a combination of more NGS tests, economical large quantity private YSNP test (missing now) and panel tests of known branches discovered to date. To date, Big Y tests cost $1,400 per L226 branch discovered (major branches mostly but only 20 branches from 48 NGS tests). Individual YSNP testing has revealed 5 new L226 branches at around 10 % of the cost per branch (but these are much smaller and recent branches). It is doubtful that NatGeo is interested in genealogical YSNPs since they are really more interested in deep ancestry. BritainDNA would be our best hope as YSEQ or FGC do not seem to interested in chip array testing (even though FGC promised large scale / low cost testing testing of private YSNPs early on).
    Last edited by RobertCasey; 03-22-2016 at 07:10 AM.

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    Quote Originally Posted by RobertCasey View Post
    I am assuming that the FTDNA SNP packs are small chip array tests
    This is not true. The FTDNA SNP packs are not microarray-based tests. Instead, they use iPLEX Assay chemistry and MassARRAY System for a detection of reaction products. The first stage of iPLEX Assay is the multiplex PCR. The sequences flanking target SNP are not always applicable for a development of good PCR-based test. The multiplex PCR is even more sensitive.

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    Quote Originally Posted by smal View Post
    This is not true. The FTDNA SNP packs are not microarray-based tests. Instead, they use iPLEX Assay chemistry and MassARRAY System for a detection of reaction products. The first stage of iPLEX Assay is the multiplex PCR. The sequences flanking target SNP are not always applicable for a development of good PCR-based test. The multiplex PCR is even more sensitive.
    So this is yet another type of test that have different characteristics (with some similar characteristics of micro-array based tests). The actual technology used is not as important as the characteristics of the technology:

    1) Substantially less cost per YSNP than Sanger Sequencing (used by both FTDNA and YSEQ for individual YSNPs and YSEQ panel tests). The net impact would be that there could be many more YSNPs included in these tests. But the cost per YSNP would be much higher than chip array tests.
    2) Similar to array tests, there will be no-calls for a low percentage of test results (observed in Z253 SNP packs). The percentage of no calls (omitted results) is not very high (less than 5 %) but that 5 % could be your part of the haplotree.
    3) Less development costs and setup costs than array tests, so adding, modifying and deleting YSNPs can happen more frequently. But more development and higher setup costs than Sanger sequencing. Also, longer times between updates than Sanger Sequencing.
    4) No major advantage for a tiered testing approach - just test all branches since the production costs are low vs. two or three tests combined into one order based on previous results of first and second tiers.


    I agree with Mike W, that the number of YSNPs included in the FTDNA YSNP packs is probably more driven by setup, quality, etc. than ongoing costs once in production mode. This means that FTDNA could continue to add many more branches over time - if the market orders justify it. L21 is one of the largest since market demand is also high.

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    You can review the MassARRAY system here. They've recently added a nice sales-pitch oriented video overview.

    By my understanding, each target site uses a thee-primer set with single base extension per variant target: two primers to amplify the target region, and one primer immediately adjacent to the variant site for the mass spectrometer to lock in on.

    The main constraints are the number of multiplexed targets detectable per pad: the limit is 40.

    All primers in the multiplex have to behave nicely with each other, and all need to have different lengths so that the mass spectrometer can discern them correctly. So there is significant fine-tuning involved to get each multiplex mix just right, but they have software to help with that. The problem is, that it becomes tricky every time additional targets are added to a multiplex. The multiplex may need to be redesigned to re-balance the primer mix, and this could have a domino effect if primers need to be re-jigged across several multiplexes to avoid discarding previously testable variants.

    I think there was a nice technical overview provided at the 2015 Group Administrators Conference in Houston, and slides of the process were made available somewhere, but I've misplaced that link.

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    Quote Originally Posted by RobertCasey View Post
    ...
    4) No major advantage for a tiered testing approach - just test all branches since the production costs are low vs. two or three tests combined into one order based on previous results of first and second tiers.
    ...
    Yes, since there is no advantage to tree traversing I've pushed for adding phylogenetic equivalent SNPs from lightly tested phylogenetic equivalent blocks. We've had good luck with this in busting up some lightly tested blocks. The new branching refinements oftentimes come from unexpected haplotypes. For instance, there is a long list of SNPs in the L226 block. This may be broken up some day, but it probably won't be broken up by an Irish III haplotype person, although you never know, such a person might pick off the most youthful SNP or two in the block. NGS testing is still much better but if you can get 50 relevant people to test a block with SNP packs versus 5 with NGS testing then so be it.

    Of course, shared private SNPs could be added and are being added. I'm quite fine with that but I think singletons are problematic. Other folks that run surname project disagree with me on that. Also, there are those that keep NGS results close to the vest so it is hard to know what is a singleton and what is not from the outside looking in.
    Last edited by TigerMW; 03-23-2016 at 05:49 PM.

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