Affy to Illumina conversions complete?

[JPHutchins]

Right now, based purely on the amount of data I've gotten from either service, 23andMe wins. Plus, they appear to be fixing some of the issues finally. I'm not real impressed with FTDNA buying out some other YDNA outfit. From my point of view, it's a waste of time/money for half their customers. Anyone want to add items to any of the lists that I use to determine who I will recommend?

Kasandra, does 23andme do Y-DNA testing? I have never heard that they did and I just went to their website and could find out nothing about their test(s).

They were offering a special of $99.00 to "new low price for all", but they did not explain what that meant. They did mention that to get this price you must sign a 1 year contract for the "Personal Genome Service" at $9.00 per month.

I, personnally, would rather be able to choose the test that I take. But if they are offering mtDNA, YDNA and RF as a package for just $99.00 then that would definitely be worth it. However, I seriously doubt that.

[mkdexter]

Anyone want to add items to any of the lists that I use to determine who I will recommend?

Search and Filter:
FF matching lists allow us to view, filter and sort in a multitude of ways; by name, by surname, by longest block, etc., etc. making searches through the list efficient.

RF searches (for a surname as an example) will provide the customer's userid and are limited to the first 100. Can't sort or filter from with the list of our matches.


Chromosome Segment Comparison:
FF chromosome browser allows us to filter our relations and then compare up to 5. This is a big plus for FTDNA as it is very important to find in common segments if you have the ability to distinguish the paternal from maternal (still a plus even if the lineage is unknown because its better than not being able to compare side by side).

RF chromosome browser (equivalent) allows us to only compare ourselves and our immediate relatives to another person . Comparisons are one at a time between ourselves and/or relatives and the other person. Only large segements are shown (although I don't have an issue with this being longest blocks only, some might).

Service:
FTDNA has a full-time in office staff specifically there to answer phone calls, 23andMe does not.


Tests:
FTDNA allows matching and has databases for YDNA and MTDNA
23andME does not.
The only issue here seems to be that FF customers would like to see their FF match's YDNA or mtDNA haplogroups. That's possible. Request this in the FEEDBACK button at the top of the FTDNA page.

Comment:
The 23andMe database is only much larger because they took their entire tested medical community and made them available for RF at its onset in Nov 2009. Those in their database at the start of RF were never there because they wanted to use 23andMe for genealogical purposes - and many still aren't. If we took just those from Nov 2009 on and then compared to FTDNA FF Feb 2010 on, we would have a much closer quantity. I still think the RF db would be a little larger but not as much as it is stated to be now though.


I do get your point though. I think the real solution is not here yet. We need to best of both worlds in one place.

MD.

[nathanm]

Kasandra, does 23andme do Y-DNA testing? I have never heard that they did and I just went to their website and could find out nothing about their test(s).

They were offering a special of $99.00 to "new low price for all", but they did not explain what that meant. They did mention that to get this price you must sign a 1 year contract for the "Personal Genome Service" at $9.00 per month.

I, personnally, would rather be able to choose the test that I take. But if they are offering mtDNA, YDNA and RF as a package for just $99.00 then that would definitely be worth it. However, I seriously doubt that.

They do test the Y chromosome, but only to the extent so they can assign a haplogroup. They don't test any STRs at all, so you won't get the standard haplotype listing for any number of markers. It's similar for mtDNA. They test enough SNPs to assign a haplogroup, but not enough to actually compare your mtDNA to the CRS or anyone else.

They use the same chip FTDNA does for the FF, which is essentially the only service 23andMe offers. They just added a few custom SNPs to get the information I mentioned above. If you're getting DNA tests for genealogical purposes, FTDNA is the place to go, IMHO.

[dwight]

John - 23andMe gives you your y- and mt-DNA haplogroup based on SNP analysis. I don't know the methodological details of the differences, but the 23andMe analyses seem to be more precise than what you get with an estimate based on 12 marker or HVR1 STRs. (E.g., my initial hg predictions were N (y) and L1 (mt); 23andMe called it as N1c1 (which agrees with my deep clade results at FTDNA) and L1b1a)

Kasandra, does 23andme do Y-DNA testing? I have never heard that they did and I just went to their website and could find out nothing about their test(s).

They were offering a special of $99.00 to "new low price for all", but they did not explain what that meant. They did mention that to get this price you must sign a 1 year contract for the "Personal Genome Service" at $9.00 per month.

I, personnally, would rather be able to choose the test that I take. But if they are offering mtDNA, YDNA and RF as a package for just $99.00 then that would definitely be worth it. However, I seriously doubt that.

[CAM]

Matches

I am amazed that you have no exact matches at 1 markers. I am also R1ba2 and I have 1322 exact 12 marker matches. But at 37 markers I have only 2 at GD=4.

I have 24 conversions for my 65 Affy matches. I have 33 Illumina only matches. I have not received any matches this week, either.

Hi John,
The reason being 2 people have told me this that my fathers "DYS values are unique." This is his first 12 markers. He has 24 matches with 12 markers but the distance 1.
the rest 0.
If you would like you can contact me of the list. just send a private message.
PANEL 1 (1-12)
Locus 1 2 3 4 5 6 7 8 9 10 11 12
DYS# 393 390 19* 391 385a 385b 426 388 439 389-1
Alleles 12 22 14 11 11 14 12 12 12 13 13 28

Thank you

Cheryl

[nathanm]

I think you missed my point. If the response rate here is going to continue to drop then why should I recommend this company over 23andMe? Because I like the people that run it more? That doesn't seem like a good enough reason when folks are looking for their birth families.

I'm getting about a 18% response rate at 23andMe which, because of the database size, gives me about 80 matches that are sharing and talking to me. Here, I have 54 matches total and 6-8 of them are talking to me (To be fair, I haven't contacted all the new ones until this week so I'll report back in a week or so on the honest response rates I'm getting). My guestimate is that it will end up being half of them responding... that will be about a third of the number at 23andMe.

I'm not blaming FTDNA, not even for the slow turnover to Illumina although I think a bit more communication would have kept them out of the doghouse more. I'm just saying, let's compare apples to apples and then encourage FTDNA to do something to improve things. As I told Mr. Greenspan, I want them to succeed. That doesn't mean I'm going to sing their praises when I don't believe I have a logical leg to stand on. So let's compare:

FTDNA
Good customer service
Right goals (Genealogy)
Email addresses from the get go (sometimes no good)
Sometimes some surnames

Problems:
Dropping response rates
No individual pages where folks can link trees already on the web in case their interests wane or they change their email addresses and don't remember to change them here, or sadly, die.
No haplogroup info
No way to search for matches found on HIR or GEDmatch or Ancestry-this is a subheading of the no personal pages issue but deserves attention on it's own.

Who says the response rate at FTDNA is going down? I've been consistently running about an 80% reply rate.

Haplogroups are listed for Y-DNA and mtDNA matches, where it's most appropriate. For FF matches, it's a tossup whether haplogroups would even help find how you're related. Since autosomal DNA is good for finding relatives who match ancestors within the past 5 generations, haplogroups are only good for 2 out of the 32 family lines. I think it would be a good feature for them to add, but it's not essential.

Elsewhere on the forum, somebody (mkdexter, IIRC) previewed a personal profile type page FTDNA was working on. So it's probably coming eventually. However, that got put on the back burner while they're transitioning to the Illumina platform. I don't think many people realize how big of an undertaking that switch really is. It's not like replacing your Dell with an HP, or even a Mac. That's why they had to retest all the previous FF customers, and did it at no additional cost.

What does your last problem have to do with FTDNA? It's the same over at 23andMe. At least you're able to download your raw data and use 3rd party tools like those. Ancestry's the only commercial outfit I've found that allows people to import DNA info from other sources. Which is good, because apparently their in-house testing isn't doing so well, and their DNA site is down all the time. Plus, FTDNA operates free databases (Ysearch & mitosearch) so people who tested elsewhere can input their data and find matches.

23andMe
Large database
Haplogroup info for every match
Personal pages
Ancestral locations for most my matches

Problems:
CS kinda sucks. I've had a very mixed bag of experiences there.
Genealogists second class citizen
Search function is soso
Mail system is horrendous
Sharing invite system a black hole

"Ancestral locations for most my matches" [emphasis added] might be a pro for you, but many others have different experiences. Almost none of my dad's matches on 23andMe have locations, surnames, or respond to any contact.

Genealogy was totally an afterthought for 23andMe. They tacked it on as an additional potential revenue stream. The only product they have is analogous to the FF test here, plus haplogroups. They don't even offer a Y-STR test or mtDNA test you can compare against others. I don't think even a sizable minority of people who test there have the least bit of interest in genealogy.

Right now, based purely on the amount of data I've gotten from either service, 23andMe wins. Plus, they appear to be fixing some of the issues finally. I'm not real impressed with FTDNA buying out some other YDNA outfit. From my point of view, it's a waste of time/money for half their customers. Anyone want to add items to any of the lists that I use to determine who I will recommend?

From the actual e-mail the head of DNA Heritage sent out, it's pretty clear he approached FTDNA, not the other way around. The market can only support so many genetic testing companies. He felt he'd exhausted the UK market and was looking for an escape route. Most genetic testing labs don't offer any direct-to-consumer testing, but instead specialize in forensic, paternity, or research work. I'm just glad there's a little competition in the market, to keep all the companies honest.

[mkdexter]

John - 23andMe gives you your y- and mt-DNA haplogroup based on SNP analysis. I don't know the methodological details of the differences, but the 23andMe analyses seem to be more precise than what you get with an estimate based on 12 marker or HVR1 STRs. (E.g., my initial hg predictions were N (y) and L1 (mt); 23andMe called it as N1c1 (which agrees with my deep clade results at FTDNA) and L1b1a)

If you were not aware of it yes FTDNA uses SNP testing for YDNA as well. They will offer it as a separate test for those who want to confirm their "predicted haplogroup" and they offer it free when they (FTDNA) are unable to predict a haplogroup based on the first 12 YDNA markers. If you have tested 37, 67 or 111 markers your closer matches will basically be in your haplogroup and therefore a separate SNP test may not even be necessary. Actually you are probably aware of it because you mentioned deep clade, which is the FTDNA SNP yDNA test.

MTDNA testing is all SNP based at FTDNA: HVR1, HVR2 and FGS.

Of course 23andMe is not using their results for matching purposes, only informational. I've only used it to determine whether I'd consider my RF match a possiblility on the paternal lineage side. It doesn't mean they are, just they might be. To many other lines to filter out to be sure.

[wkauffman]

They do test the Y chromosome, but only to the extent so they can assign a haplogroup. They don't test any STRs at all, so you won't get the standard haplotype listing for any number of markers. It's similar for mtDNA. They test enough SNPs to assign a haplogroup, but not enough to actually compare your mtDNA to the CRS or anyone else.

They use the same chip FTDNA does for the FF, which is essentially the only service 23andMe offers. They just added a few custom SNPs to get the information I mentioned above. If you're getting DNA tests for genealogical purposes, FTDNA is the place to go, IMHO.

The extent is actually broader than just the known SNPs which are assigned to haplogroups. A large number of y-SNPs were added to the chips to provide opportunities to identify genealogically relevant SNPs. That has been somewhat successful but 23andMe needs to be more careful around how they select y-SNPs and assure that the are testable within the context of the Illumina technology. In the reported Illumina y-SNP results I have identified over 10 new SNPs. 2 of these SNPs are now defining new haplogroups. The others appear to be private to their surnames and can be utilized to confirm lineage associations. We have used one of the private SNPs to confirm the paper trail relationship between 7th cousins.

Note that the Illumina chip which is used for Family Finder DOES have y-SNPs present. FTDNA seems to be keeping that data to themselves and not providing it back to the user.

[nolnacsj]

Kasa, I think in your comparison between 23andMe RF, and FTDNA FF, you forgot to list that some people include Gedcoms with FF and RF does not.

My response rate from matches have been much better at FTDNA, but even if they do not reply, I have a name, sometimes a surname list, and sometimes a Gedcom. At RF, no answer means NADA except a haplogroup which is not very helpful to me. I have 40 unanswered 4th cousin sharing requests pending there, and 4 who replied. One of those also tested with FTDNA, and she replied to me here too. I have had fewer 4th cousin matches here, but 100% of those I have contacted, replied. I only have one 4th-distant cousin on Affy who never answered. I am waiting to see if he shows up on Illumina before I try him again.

I enjoy using the FTDNA site more than 23andMe which I find more confusing. However, the public/community forums on both sites are good.

Both sites have strong and weak points as you point out, which is why I tested with both. However, the monthly $9.00 fee 23andMe imposed did not make me very happy, and therefore I have not upgraded to the V3 chip. As long as the response rate continues to be so low there, I will not upgrade, and keep my main focus here. FTDNA upgraded me for free (thank you!)

I also think that for non-technical people just starting out with DNA testing, FTDNA is more user-friendly. I have recommended FTDNA to many people, who have now purchased kits. I always recommend that especially adoptees do both RF and FF tests, but that if they can only do one, then I recommend FTDNA FF.

Maybe I drank the Kool-aide, but that is my story and I am sticking to it!

Judy

[nolnacsj]

removed, duplicate message. Judy

[nathanm]

Note that the Illumina chip which is used for Family Finder DOES have y-SNPs present. FTDNA seems to be keeping that data to themselves and not providing it back to the user.

Yeah, they admit they're scrubbing the data before it's available for download. But they don't really say what they're scrubbing. I figured it was partly to protect themselves against a possible ruling from the FDA regarding direct-to-consumer, medical-related DNA tests. As long as they claim it's a strictly genealogical test, the bureaucrats should leave them alone.

I wish they'd release all the data, but they want people to buy more tests. At least it's pretty easy to figure out the so-called "Warrior Gene" from the X-chromosome data. Not that I would've paid for it in the first place.

[mkdexter]

Yeah, they admit they're scrubbing the data before it's available for download. But they don't really say what they're scrubbing. I figured it was partly to protect themselves against a possible ruling from the FDA regarding direct-to-consumer, medical-related DNA tests.

Yes they say what they are scrubbing, just don't give us the list. Like you say its to avoid being considered a medical test. However some of the 23andMe SNPs are custom for medical purposes and FTNDA doesn't include the custom SNPs that 23andMe does anyway.

In FTDNA FF:
First the SNPs that are not useful for matching (FF) are not used.
Second they use the remaining SNPs to match
Third they remove the remaining so called "medical" SNPs that were left in for matching in order to provide privacy and to provide a test that is not considered medical (as you stated).
Fourth the remainder is provided in the download.

FTDNA also doesn't add the custom Illumina SNPs used for Y and MT haplogroups like 23andMe does. Without the custom Illumina SNPs its better to use the tests they've been using already for MT and Y data.

MD.

[Kasandra]

Search and Filter:
FF matching lists allow us to view, filter and sort in a multitude of ways; by name, by surname, by longest block, etc., etc. making searches through the list efficient.

>OK I expect RF to be updated shortly to enable that though.

RF searches (for a surname as an example) will provide the customer's userid and are limited to the first 100. Can't sort or filter from with the list of our matches.

> True but getting 100 is better than getting none.

Chromosome Segment Comparison:
FF chromosome browser allows us to filter our relations and then compare up to 5. This is a big plus for FTDNA as it is very important to find in common segments if you have the ability to distinguish the paternal from maternal (still a plus even if the lineage is unknown because its better than not being able to compare side by side).

RF chromosome browser (equivalent) allows us to only compare ourselves and our immediate relatives to another person . Comparisons are one at a time between ourselves and/or relatives and the other person. Only large segements are shown (although I don't have an issue with this being longest blocks only, some might).

>For adoptees this is pretty much BS and I won't recommend a service because of it.

Service:
FTDNA has a full-time in office staff specifically there to answer phone calls, 23andMe does not.

>Already gave them CS kudos

Tests:
FTDNA allows matching and has databases for YDNA and MTDNA
23andME does not.
The only issue here seems to be that FF customers would like to see their FF match's YDNA or mtDNA haplogroups. That's possible. Request this in the FEEDBACK button at the top of the FTDNA page.

>I suggested it a long time ago to someone ... But for females, this is pretty useless. Especially for adoptees. Not going to get a hit off your MTDNA matches too often that is meaningful when they go back thousands of years.

Comment:
The 23andMe database is only much larger because they took their entire tested medical community and made them available for RF at its onset in Nov 2009. Those in their database at the start of RF were never there because they wanted to use 23andMe for genealogical purposes - and many still aren't. If we took just those from Nov 2009 on and then compared to FTDNA FF Feb 2010 on, we would have a much closer quantity. I still think the RF db would be a little larger but not as much as it is stated to be now though.

> How large the actual database is doesn't matter per my analysis. I compared the number of folks sharing and responding from each service. IF the customers at FTDNA were really responding like they did the first few months it would be still be 2 to 1 in favor of 23andMe. With the drop off of the response rate... it's a losing battle.

I do get your point though. I think the real solution is not here yet. We need to best of both worlds in one place.

MD.

I replied inside the quotes. The only real plus from my point of view is the ability to sort. And 'maybe' YDNA matching for males. Although, you can match the YDNA of your RF and AF matches just by downloading the spreadsheet and sorting it to your hearts content. I really don't think having the MTDNA matching across the service comes close to having 500 YDNA and FTDNA haplogroups to play with. But that's just me.

[Kasandra]

Who says the response rate at FTDNA is going down? I've been consistently running about an 80% reply rate.

>I and many others have experienced a serious drop in response rates with the conversion to Illumina. It was about 80% and now it's about 30% but as I said, I'll update that figure next week.

Haplogroups are listed for Y-DNA and mtDNA matches, where it's most appropriate. For FF matches, it's a tossup whether haplogroups would even help find how you're related. Since autosomal DNA is good for finding relatives who match ancestors within the past 5 generations, haplogroups are only good for 2 out of the 32 family lines. I think it would be a good feature for them to add, but it's not essential.

>Here I don't agree with you. I've used MTDNA and Y DNA haplogroups to good effect on 23andMe to identify which cousins are from what side of my genome. I can pretty much predict 40% of my matches with greater than 90% accuracy based on haplogroup alone. This allows me to tailor my invitations but even better I've been able to analyze what percent of my matches are from which grandparent. The overall numbers are slightly less skewed than my reply numbers because I have one whole section of my genome made up of polite Canadians .. they seem more likely to respond than most other groups.

Elsewhere on the forum, somebody (mkdexter, IIRC) previewed a personal profile type page FTDNA was working on. So it's probably coming eventually. However, that got put on the back burner while they're transitioning to the Illumina platform. I don't think many people realize how big of an undertaking that switch really is. It's not like replacing your Dell with an HP, or even a Mac. That's why they had to retest all the previous FF customers, and did it at no additional cost.

>Yeah it was nice of them to do something so that their customer base wouldn't.. you know, sue em. LOL I like them but that was a pure business decision. Not that I'm knocking it, it was nice it was free but I don't see how they could have charged. And, it's not as big a change as you make out. I've run DNA tests for years. Especially since I don't believe they've tweaked the algorithms at all, that's why so many cousins are just clumped in the 'I dunno' category of something to distant.

What does your last problem have to do with FTDNA? It's the same over at 23andMe. At least you're able to download your raw data and use 3rd party tools like those. Ancestry's the only commercial outfit I've found that allows people to import DNA info from other sources. Which is good, because apparently their in-house testing isn't doing so well, and their DNA site is down all the time. Plus, FTDNA operates free databases (Ysearch & mitosearch) so people who tested elsewhere can input their data and find matches.

"Ancestral locations for most my matches" [emphasis added] might be a pro for you, but many others have different experiences. Almost none of my dad's matches on 23andMe have locations, surnames, or respond to any contact.

>As with everything in life YMMV

Genealogy was totally an afterthought for 23andMe. They tacked it on as an additional potential revenue stream. The only product they have is analogous to the FF test here, plus haplogroups. They don't even offer a Y-STR test or mtDNA test you can compare against others. I don't think even a sizable minority of people who test there have the least bit of interest in genealogy.

>To which I reply, SO? To your first point, it's not necessary to get your deep clade testing done at the same place you get your FF/PF stuff done. And to your second point, as I pointed out, I don't really care that 'most' of their database isn't interested in genealogy. I get ten times the matches and half the response rate which ends up with MORE matches that are willing to talk to me about genealogy.

From the actual e-mail the head of DNA Heritage sent out, it's pretty clear he approached FTDNA, not the other way around. The market can only support so many genetic testing companies. He felt he'd exhausted the UK market and was looking for an escape route. Most genetic testing labs don't offer any direct-to-consumer testing, but instead specialize in forensic, paternity, or research work. I'm just glad there's a little competition in the market, to keep all the companies honest.

> OK, I just said I wasn't impressed by it. FTDNA evidently was impressed by it ergo the big press release.

[rivergirl]

Any lab test will take time, these usually take two weeks to process. FTDNA had thousands to retest (convert in other words) so yes there was a long wait.

.

Dexter, you forget that FTDNA stated in an email that those who chose the conversion would be done in 2-3 weeks with the rest of the database completed in 6-8 weeks.
FTDNA know the size of the database, knew how many kits would need converting.
They are the ones who came up with the 8 weeks.
That was back on the 11 Feb, so we are well over 8 weeks.


I think FTDNA have taken on more than they can handle with sales, 111 upgrades and now the DNA Hertiage merge and we are seeing the consequence in delays in results.