Affy to Illumina conversions complete?

[Geneadict]

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?

[similligan]

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

[KarenZ]

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

[dwight]

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

Thanks!

[CAM]

Missing Affy

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

[Geneadict]

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

[dawer]

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

[mkdexter]

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.

[mkdexter]

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.

[JPHutchins]

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!??!

[JPHutchins]

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.

[Geneadict]

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.

[Geneadict]

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/products/technotes/technote_maqc.pdf

http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/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

[similligan]

Your example of tracing the paper trail to distant cousins is exactly what I was asking about before. If they don't want to adjust the criteria for matches, the least they could do is provide a way to manually enter known relationships that aren't showing up. It shouldn't be that hard: enter the two kit numbers and known relationship. FTDNA could then compare both FF results internally, to verify there's some shared DNA, just not enough to meet the normal match threshold.

You should put this on "Which features would you be nice to have at FTDNA" so they see it at the company. I've been wishing for this, too. I paid for what I thought would be a distant cousin's test and didn't get a match. Now I don't know if my research was correct, but DNA was below the threshhold, or if I was completely wrong.

Susan

[nolnacsj]

My suggestion would be to give direct feedback, starting now since we have been given some pretty clear responses... email the contact numbers given as a start, call reps, etc...

But, there could be some power in the use of social media to let concerns be known. Afterall, there are 10,000+ "likes" in the mix and a certain degree of public awareness/pressure to respond in an appropriately sensitive and thoughtful manner. This could impact potential future customers as well as existing ones who may not know about the bumps that have been experienced as a part of the transition. Maybe now is the time to use FB for something other than a "like" count and state the issue publicly.

The beauty of that last option is that we have been encouraged to use it by FTDNA themselves... as their chosen means of communication with us.
__________________________

The upgrade and free testing to existing Affy customers to convert to the new platform should have been a HUGE positive PR move. It had the potential power to create enthusiastic supporters and good will going forward indefinitely... So, what happened? Why are people STILL grumbling about a free upgrade?

What analysis was done on what the customers wanted/needed/expected from the move? How was it communicated? Even now, how do the customers FEEL about the changes being made?

When you put a lot of work and personal effort into a project like family research, you want to know it's going somewhere. This loss of data without any official recognition or explanation FEELS somewhat like a betrayal of trust.



.

I agree, and for me, I am annoyed because a year ago I paid for the FF Affy test information which also comes with the supporting technical tools (FTDNA personal page DNA results/data, compare DNA, etc), and it has become a resource for me, and the focus of my genealogical research. Sure I can download the data, but I will loose the ability to apply the FTDNA tools to my Affy data, and supposedly Affy matches are real matches, so I believe that FTDNA should leave the information there for us to continue using, UNLESS, they know that the Affy results were inaccurate or severely flawed. If they are truly "real matches", then they need to stay where we can continue to use the FTDNA tools to work with them. If not, I think a lot of people are going to assume that all the Affy data was wrong since FTDNA is removing it, and our matches in Affy may no longer think our match was real and pull away from communicating. And, a year of communications with these Affy relatives who we thought we were related to, goes down the drain.

Don't get me wrong, I really appreciate the free upgrade, but unless the old data is now null and void, it needs to remain somewhere where we can still use it as long as the Affy results are also viable, because the two results appear to compliment each other. Remember, back when the conversion was first underway, we were told by some that we may loose "a few" Affy matches, but we were never told that we would loose such a high percentage and cause us to question our original Affy matches. So, are they real, or are they Memorex???!! If real, then they remain important since it looks like most of them will not be available to us in Illumina.

As of now, still only 7 of my Affy matches have shown up in Illumina, and 26 are still Affy only. That big final dump of matches I have been dreaming about has not happened to me yet!

Judy