Affy to Illumina conversions complete?

[Geneadict]

So it sounds like some Affy to Illumina conversions are yet to take place including for those who may have required an additional sample. Based on Matt Dexter's "a few thousand" comment and best guess of abt 10-12k in total FF database (since FTDNA is not publishing the number like all their other databases), sounds like about 80-90% complete. For those still waiting for 15-25% of their Affy matches, you may get a few more depending on which have already converted and which have not. For those with more material number not making it to Illumina (50%+), very reasonable to assume you will loose many of your Affy matches on Illumina.

Given different SNPs being tested on Illumina vs Affy, you may find some matches lost, especially those with largest segment in location not tested on Illumina, but also some where total of 500+SNP segment shares fall under that threshhold, and others with change in predicted relationship due to having larger or smaller total share. Most can also see several new matches as result of new SNPs being tested and not simply due to new kits being tested. Some may see net gain in total, but still have loss of some Affys.

Numbers for two kits I had Affy results for:
father-in-law - 85 Affy - 75 Illumina (43 from Affy, 32 new)
me - 87 Affy - 29 Ilumina (17 from Affy, 12 new including 2 that I purchased)

While my father in-law's numbers are closer to Affy, will probably be some loss there, unclear what degree with some additonal conversions yet to take place.

For mine, I see no way for the 70 Affy results (out of 87) that haven't made it to Illumina to show up and most of these I find having largest segment in location where none of the Illumina matches are showing ANY segment shares (including the 10-15+ between 1 cM and 5 cM for each FF match) for either myself, or my father-in-law, or my parents that have only been tested on Illumina.

[dtvmcdonald]

conversion time

I'm still waiting for my conversion, and I got the request
in within hours of the announcement. They had to send a new
sample kit.

My aunt, who I requested at the exact same time, has long
since been done.

Doug McDonald

[CAM]

fAMILY fINDER

This may help from the FF faqs . I found this on the site a while back. I was concerned because I know at least one of my matches has passed away.

"What if the person tested for Family Finder will not submit a new DNA sample? What if they are dead? faq id: 317

A new sample should not be needed. In the majority of cases, there will be more than enough DNA remaining from the previous Family Finder sample to rerun the test. In the unlikely event that we cannot rerun the test, we will work with individual families on a case by case basis."

Cheryl

*Matt thank you for keeping us updated *

[JohnG]

Upgrades

As I understand it, a large part of the reason to convert to Illumina is that upgrades of Illumina would still be compatible with earlier chips. They have announced tests up to all SNPs that occur in at least 1 percent of the population. So older tests would mean something but would not have all the content of tests that come later. (I imagine after that we will have $500 full genome sequence tests!)

The Illumina family of chips is also engineered to support the new population studies, the different steps in HapMap, the 1000 Genomes project, etc. So the population matching has the capability of improving over time.

One of my close matches has passed away and I am working on building his family tree for matches, since he cannot. But I guess the basic data will be there as long as anyone's is. I think many of us will be building trees by social network types of efforts.

All of this is leading edge, or perhaps what we used to call 'bleeding edge', technology. It is new stuff and can't be expected to run like something that has been static for a long time. So some tests have to be rerun or checked. Seems normal to me, but I have lived this from the vendor side for 40 years. Lots of work, but it will settle down in a while and get better as they have time to attend to things.

It reminds me of census data in lots of ways. One is that each census is different. You can wish they asked for names of all family members in 1790, but they did not until 1850. That is how I see the Illumina upgrade path, but it is lots better since they did the conversion so 1790 will be in 1850 format, and there will be common data elements in all the years. ( With the real census they changed what they asked fairly freely.) And I remember as Ancestry put census data online we were all waiting for the decades they had not finished, and finding errors in the transcription. Now it is a great resource and we wait for 1940 to come out.

[mkdexter]

Im pretty sure there is another gentleman on this forum who is still waitng for his conversion, and was in the requested batch.
I can see no reason for "taking their time" to do the rest of the conversions, as others are waiting for the results, to see what matches they will have/have not.

They aren't. They're doing conversions as fast as the lab can do them.

I'm curious as to what happens if someone was tested for Affy and they have trouble converting and want a new sample. What happens if that person has passed away or is not available. (I'm thinking specifically of those of us who have tested our older relatives for different family lines.) Are you left with a Affy kit not compatable with the new Illumina and therefore useless. Do you get a refund?

The Illumina system has much better performance and less errors than Affy so the chance of issues is reduced compared to Affy. When they first tested Illumina in January they were really happy with its performance and the fact that it required less sample and that equates to requiring less from storage. One of my matches passed away before the Affy version of FF became available last year and that kit was still able to be converted to Illumina.

What happens if they decide to upgrade again and need more samlpes and more of us have passed away. Does the database become redundant with every upgrade.

I'm sure they plan on staying with Illumina. If FF-I V1 was to upgrade to V2 then 710K SNPs will still be more than enough for a backward compatible system. I doubt they'd retest again.

[rivergirl]

Another account which I am aware of has not been converted yet, and he did not request to have it done when the email went out. His due date under pending results is sometime next month.

My guess is that everyone that requested it has already been done, and they are taking their time with the people who were not as motivated to get their new results.

Im pretty sure there is another gentleman on this forum who is still waitng for his conversion, and was in the requested batch.
I can see no reason for "taking their time" to do the rest of the conversions, as others are waiting for the results, to see what matches they will have/have not.

I'm curious as to what happens if someone was tested for Affy and they have trouble converting and want a new sample. What happens if that person has passed away or is not available. (I'm thinking specifically of those of us who have tested our older relatives for different family lines.) Are you left with a Affy kit not compatable with the new Illumina and therefore useless. Do you get a refund?

What happens if they decide to upgrade again and need more samlpes and more of us have passed away. Does the database become redundant with every upgrade.

[JamesKelley]

Another account which I am aware of has not been converted yet, and he did not request to have it done when the email went out. His due date under pending results is sometime next month.

My guess is that everyone that requested it has already been done, and they are taking their time with the people who were not as motivated to get their new results.

[gtc]

I wanted to add that I really appreciate FTDNA for doing these conversions for free. It seems like a huge undertaking.

I appreciate it too, although I don't think they had an alternative. Had they charged for it I guess there would have been howls of protest and perhaps only a small percentage would agree to pay, so they'd be stuck with a new product waiting for new customers together with an old non-compatible results database.

I wonder if Illumina kicked the can to help with the conversion?

[similligan]

I had three kits in batch 400. Two came back very quickly (2/28 and 3/7). A week or so ago I got a package from FTDNA with a new sample kit for the third. I suppose the kits that went smoothly for batch 400 are complete and the rest will trickle in.

I wanted to add that I really appreciate FTDNA for doing these conversions for free. It seems like a huge undertaking.

Susan

[mkdexter]

My nephew is in batch 400 & still is not here. His page still says pending 3/30

Apparently my info was wrong about 400 being done. I had known that they were into batch 402 on Monday and I was expecting they had gone in order. Not the case I see .

[ragnar]

My nephew is in batch 400 & still is not here. His page still says pending 3/30

[nolnacsj]

batch 400 is complete but there are other batches too (like 401, 402, 403, 404) .. so the total set is not complete. A few thousand to go.

I was batch 400, and I had jumped on the conversion request immediately, and began receiving my Illumina results on 2/28, well within the FTDNA estimated time period. However, I am still missing 27 out of my original 33 Affy matches. I had two new Illumina and one Affy come in this past Monday, but no more since then this week. I am hoping that tomorrow night (Friday), maybe there will be a huge dump of matches....and maybe my Affy's will appear

I wonder if the Affy's who never requested the updrade have been processed yet. If they have not, then I guess most of my Affy matches never formally requested an upgrade......and they will be bringing up the rear.

[Javelin]

Thanks for the kind word, LSSmith, and sorry, I didn't mean to rain on your parade. I know there are still a few of us in this boat, so I am guessing calling won't make much difference, but I may try that if nothing shows up by Monday.

[LSSmith]

Maybe for you: atrocious turnaround for me.

I absolutely understand your frustration and anger. Not being told what the problem is makes it worse. I ordered a FF test the day they went on sale to the public way back when. My brothers DNA was already at FTDNA so I just ordered the test and waited for the results and I waited and waited and got a new kit and waited and waited and then they wanted to send me another new kit and I said no. I asked for and got a refund instead. I waited a few months, did some gardening and decided to test myself and later on some other people too. It is just awful to wait and FTDNA doesn't do themselves any favors by sticking their heads in the sand and not communicating the problem either. I hope you get your results soon have you called FTDNA yet?

[Javelin]

Unless you are reading that final date as April 06, 2011 (Day/month/year) your pending lab result tab indicates that your results could be back as late as early June, 2011.

I double-checked. The admin page is ordered date/month/year, so it is supposed to have been ready.