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  • Regarding Affy to Illumina move.

    I recently saw post on rootsweb DNA e-mail list stating a person heard Affy made decision to exit genealogy related testing and thus forced FTDNA to change. First time I heard something like this and I'm not buying it.

    Word I was given directly from Bennett Greenspand and Max Blankfeld stated the primary reason was related to error rate and miscalls for the Affy and I think something to that effect may have been stated in various places when the move was initially announced.

    Meanwhile, found this article which provides interesting comparison on input material requirements and material costs.

    http://www.illumina.com/Documents/pr...hnote_maqc.pdf
    http://www.fda.gov/ScienceResearch/B...ct/default.htm

    Of course with only two commercial companies with any name recognition offering the microarray testing for genealogy, one on Illumina, and the the other choosing to change from Affy to Illumina, the decision with regard to "Affymatrix withdrawing from the market for genetic
    genealogy testing" may have been made for them.

    If you happen to google, you can also find some interesting articles on the lawsuits related to patent infringement between Illumina and Affymatrix which apparently have been going on since 2005 with a settlement in 2008, but subsequent suits resulting in Illumina's suit being dismissed in Dec 2010, but Affy's countersuit apparently still in motion.

    Personally I speculate that FTDNA's primary driver is their pursuit of market share and database growth (the later of which they brag about for everything EXCEPT the autosomal DNA testing) and given their database deficiency compared to 23andMe and lack of compatability between Affy and Illumina, the only way they can feasibly narrow the gap was to make themselves compatible with their competitor so they can eventually offer an upload service at a nominal fee. Of course a decision to scrap Affy less than a year into production with most likely no return on investment, the cost comparison and future cost savings must have been considered before making their decision. Meanwhile, the free retesting (affy to illumina convesions) was also necessary so they can eliminate the duplicate cost of maintianing two platforms without having a total loss of trust from their client base. However, not sure they gave adequate consideration to SNP overlaps and potential differences in results when they made statement to effect that there would be no material difference between the two. So now, they have a little damage control and their official position will be focused on the quality issue and claim the new Illumina matches added are more likely "real" as compared to those lost from the Affy, so they will be saving you the time of trying to figure out connection for these "false" matches. I'm not sure I buy this spin, but that is the feedback I have been seeing

    Comment


    • Originally posted by gtc View Post
      A little bird tells me that after a project admin conferred with FTDNA about lack of matches, FTDNA discovered that there is a software bug with the new Family Finder tests which results in kits being compared to only half of the database. Apparently a fix is being implemented today.

      I have no more information other than that, so let's see what eventuates ...

      If, and big IF, this is true would be interesting to know how the half it wasn't comparing against were limited to include matches with primary segments in the same locations. Unless the "bug" failed to look at and compare certain portions of certain segments, I see no way this could be true and not have the primary segments for the "missing" Affy matches spread fairly proportionately across all chromosomes.

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      • The data drop is here!

        At about 0800 this morning I suddenly received 8 new matches in Family Finder. Perhaps the new matches that Matt spoke of are going to be showing up today.
        Last edited by JPHutchins; 29 April 2011, 11:10 AM.

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        • What????

          I just checked back and the 8 new matches have now vanished. In the frame of 30 minutes I went from 57 to 65 and back to 57. I hope that just the 8 that were added disappeared, not others.

          This makes no sense at all!??!

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          • How many Affy matches are people now missing?

            Missing Affy matches compared to original number of Affy matching kits:

            Myself: 33 out of 73
            my mother: 33 out of an 66

            Only one person in both my missing and my mother's missing is the same match to us both..

            I also have a few kits that showed up for either myself or my mother but not both whereas before they were to us both.

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            • FTDNA is looking into it.

              I was just asked to send in some data.

              As far as I can see, hence my last question, it looks like it's not just an isolated incident - but everyone is missing approx. 50% or more matches.

              MD.

              Comment


              • Originally posted by mkdexter View Post
                How many Affy matches are people now missing?

                Missing Affy matches compared to original number of Affy matching kits:

                Myself: 33 out of 73
                my mother: 33 out of an 66

                Only one person in both my missing and my mother's missing is the same match to us both..

                I also have a few kits that showed up for either myself or my mother but not both whereas before they were to us both.
                I had 17 on Affy and now only 4 on Illumina, and as far as I can tell only 2 of those carried over from Affy

                Comment


                • I think this is the message Matt referred to earlier that can be found at top of the matches page in Affy section:

                  Family Finder Matches
                  We are pleased to announce that the conversion of all Family Finder results to the Illumina Omni Express platform is now complete. Please note, this means your Affymetrix results will be removed from the system on Tuesday, May 3rd, and will no longer appear on your "myFTDNA" page

                  Comment


                  • Missing Affy

                    Originally posted by mkdexter View Post
                    How many Affy matches are people now missing?

                    Missing Affy matches compared to original number of Affy matching kits:

                    Myself: 33 out of 73
                    my mother: 33 out of an 66

                    Only one person in both my missing and my mother's missing is the same match to us both..

                    I also have a few kits that showed up for either myself or my mother but not both whereas before they were to us both.
                    Hi Matt,
                    I put this on a day or so ago. Since you asked . Thank you for looking into this..

                    total Affy Matches 77
                    Affy matches I did not get with Illumina 52
                    Affy convertd to Illumina 25

                    Wish my uncle got put into Affy like he should of been instead it took months because of the planning of the conversion. Which we did not know about when I put him in for family finder.

                    My father did not get any of the matches I lost due to the conversion and I am surprised with this.

                    My mothers brother got 4 of the matches I lost due to the conversion. One of his matches I did not get is Junior but we both got his father.

                    Better Luck in my next life I guess I will have to wait to see.
                    Cheryl

                    Comment


                    • Affy matches: 75
                      Affy conversions that are Illumina matches: 41
                      Affy matches not showing up in Illumina: 34

                      Thanks!

                      Comment


                      • Originally posted by mkdexter View Post
                        How many Affy matches are people now missing?

                        Missing Affy matches compared to original number of Affy matching kits:

                        Myself: 33 out of 73
                        my mother: 33 out of an 66
                        myself:
                        Affymetrix total 28
                        Illumina total 7
                        new 4
                        Affymetrix converted to Illumina 3

                        my husband:
                        Affymetrix total 32
                        Illumina total 17
                        new 8
                        Affymetrix converted to Illumina 9

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                        • Exactly half of my father's Affy matches carried over to Illumina:

                          Total Affy 58
                          Total Illumina 60
                          matches common to both Affy and Illumina 29

                          Susan

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                          • If the loss of Affy matches is due to differences in SNPs being tested and not some other system/software related snafu, a possible solution to help mitigate the lost matches would be some way of allowing customers to connect and compare with non-matches, similar to what you can do with 23andMe. At least then you can see which segments are still there versus which went away and reduce some of the speculation. Any chance something like this will ever be available for FF?

                            Comment


                            • I never really checked before, but I'm missing 32 of my 46 Affymetrix matches!

                              I do have 10 new ones with Illumina.

                              So, my big question is, should I stop trying to find any relationship between myself and the old matches and just concentrate on the new ones?

                              Carol Anne

                              Comment


                              • how many missing

                                I'm missing a good number of the Affy matches. I'm most sad that I have lost my confirmed third cousin. I know he is my third cousin--we've compared trees. My PF has also changed. I now have a blander genetic profile.I'm glad I had the Affy to show the broader range.

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