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View Full Version : Am I Positive for M343 ? Another commerical testing SNP Anomaly?



jatt2016
04-19-2016, 01:28 AM
Hi Guys :

Would be requesting you for your expertise. My Y haplo group have been recently classified as R-Z2976 and to be in this haplo, one has to be positive in the upstream SNP M343.
My Tree on FTDNA shows that I am presumed positive for it.
(Please see attachment)
https://i.gyazo.com/4022bf25910fc90ba9efb64a05485683.png

My raw Nat Geo File shows that I am CC for M343

https://i.gyazo.com/5db3e55e81b42e56b6e11c9137bd8d3a.png


and when I checked the mutation for M343 at the link below, it came out that the mutation for M343 is C->A ( Please check screenshot)

https://i.gyazo.com/875b7d267bbd901d0ca85c32dc204d53.png

Please confirm if I am positive for SNP343.


http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html

VinceT
04-19-2016, 03:03 AM
Nope, doesn't look like it at all. If you actually were in R-M343, all of the SNPs up stream of your alleged R-Z2976 haplogroup should also be colored "confirmed" green, not "implied" amber. R-M343 men should report an A at M343.

Please advise FTDNA that they have messed up yet again. If your Z2976 site shows GG, it means that either they are referencing the wrong strand, or there is a parallel mutation state of Z2976 from C to G in your real haplogroup, presumably somewhere under J2a-CTS2906 from what you list in your profile here.

The recent Geno2 "Next Gen" data have really messed up FTDNA's haplotree algorithm, and I have no confidence whatsoever that their programmers have an actual clue. Instead of assigning a haplogroup based only on the so-called "terminal" SNP, they need to be evaluating all branches for the chain of SNPs that leads up to your haplogroup.

jatt2016
04-19-2016, 03:07 AM
Nope, doesn't look like it at all. If you actually were in R-M343, all of the SNPs up stream of your alleged R-Z2976 haplogroup should also be colored "confirmed" green, not "implied" amber. R-M343 men should report an A at M343.

Please advise FTDNA that they have messed up yet again. If your Z2976 site shows GG, it means that either they are referencing the wrong strand, or there is a parallel mutation state of Z2976 from C to G in your real haplogroup, presumably somewhere under J2a-CTS2906 from what you list in your profile here.



The recent Geno2 "Next Gen" data have really messed up FTDNA's haplotree algorithm, and I have no confidence whatsoever that their programmers have an actual clue. Instead of assigning a haplogroup based only on the so-called "terminal" SNP, they need to be evaluating all branches for the chain of SNPs that leads up to your haplogroup.

First I was JCTS2906 and then reassigned as Rz976 which also looks incorrect. I feel as if this is genealogical horoscope instead of a science.:)

VinceT
04-19-2016, 03:20 AM
First I was JCTS2906 and then reassigned as Rz976 which also looks incorrect. I feel as if this is genealogical horoscope instead of a science.:)

No, Geno2 is simply a bad product that should have never reached market.

jatt2016
04-19-2016, 03:26 AM
No, Geno2 is simply a bad product that should have never reached market.

I think the same now. So basically its a Chip error? the one that they use to test SNPS?. What in your opinion is the best product that can accurately tell your Y DNA haplo and the regional(autosomal ancestry)?

VinceT
04-19-2016, 03:44 AM
I think the same now. So basically its a Chip error? the one that they use to test SNPS?. What in your opinion is the best product that can accurately tell your Y DNA haplo and the regional(autosomal ancestry)?

A combination of chip errors, clueless programmers, and a poor testing platform overall. Y-SNP chips also become outdated very quickly.

The most affordable autosomal test is probably FTDNA's Family Finder chip. DNA.Ancestry.ca and 23andMe.com follow behind.

For Y-DNA haplogroups, the appropriate SNP Packs from FTDNA, or SNP Panels from YSEQ.net would be the least expensive route, but they only test for known Y-SNPs. One is better off in the long run, financially, by skipping all that and going straight for NGS testing with Big-Y from FTDNA, or even better, the ultimate Y-Elite 2.x from FullGenomes.com (my personal preference).

If I had to do it all over again, I would simply order the WGS 30x product from Full Genomes Corp, and call it done.

wombatofthenorth
04-20-2016, 02:59 AM
Ah thanks for this post. Well, well, this is proof that is FTDNA that is totally messing up how they handle certain parts of some transfers. I am positive for M343 and on both the old and new test I get "AA" so it's definitely not a matter of this is one of the ones that needs to be read opposite strand or can't be trusted or something. I'm thinking then maybe my BY2171 might actually be positive under L20 even though FTDNA tree shows it as negative or untested!

So your M343 is definitely negative and it's not that it is really positive but need to be read opposite strand or anything.

wombatofthenorth
04-20-2016, 03:02 AM
No, Geno2 is simply a bad product that should have never reached market.

How is this the Geno 2's fault though? It's just the FTDNA transfer doing weird things.

jatt2016
04-20-2016, 03:30 AM
How is this the Geno 2's fault though? It's just the FTDNA transfer doing weird things.

Interesting to note is that Nat Genographic has reported my as J-CTS2906. I am following up with them and they have assured me that the case will be resolved in 2-3 weeks. I will keep my fingers crossed!

wombatofthenorth
04-20-2016, 03:42 AM
Actually what do you get for L21? Are you positive for that? If not for that either than the result seems dubious.
Hmm I see that I am also positive for Z2976 so I wonder if this new SNP is not a broken one, unless L20 also often have that. If so then the negative M343 would be the one to trust (unless L21 turns out positive).
Other odd ones I'm positive for on the R-branch (just going by FTDNA green and not verifying myself for the most part other than for a couple where the old test also had them) along with Z2976 are MC14, Z2983, L459 (although L21 negative), S5153, Z284, L625, CTS12976, S3207, CTS12023, Z2396. All those ones that seem odd (although perhaps it is common for L20 to have them too?) seem to be new SNPs on the new test only (other than for L625, CTS12023). Man, I hope that doesn't mean that most of the new SNPs added since the old test register false? Or maybe the new ones are all to be read opposite strand of the ones on the old test or at least some of them?

Hmm L625 I was "AA" on the old test but "TT" on the new. Same for CTS12023 where I am negative AA on the old test and seem to be positive GG on the new , so maybe it is meant to be read opposite strand on the new?

I'm curious what you got for all those I mentioned, did they all show up as green too? Maybe we can see if they possibly always come out positive implying FTDNA is either not reading those ones on the correct strand or they are stuck always positive?

wombatofthenorth
04-20-2016, 03:43 AM
Interesting to note is that Nat Genographic has reported my as J-CTS2906. I am following up with them and they have assured me that the case will be resolved in 2-3 weeks. I will keep my fingers crossed!

Maybe Geno knows which ones need to be read reverse strand or to avoid and FTDNA, for some reason, does not yet?

wombatofthenorth
04-20-2016, 03:47 AM
Interesting to note is that Nat Genographic has reported my as J-CTS2906. I am following up with them and they have assured me that the case will be resolved in 2-3 weeks. I will keep my fingers crossed!

FWIW I am R-L20 and negative at CTS2906.

wombatofthenorth
04-20-2016, 04:59 AM
I'm curious, what do you get for BY2171? I'm trying to figure out if it's to be read as is or not.

jatt2016
04-20-2016, 10:19 AM
I'm curious, what do you get for BY2171? I'm trying to figure out if it's to be read as is or not.

Hi for BY2171 I am AA in my raw data file and it is not in listed of reported positives.

ArmandoR1b
04-20-2016, 12:36 PM
Ah thanks for this post. Well, well, this is proof that is FTDNA that is totally messing up how they handle certain parts of some transfers.


How is this the Geno 2's fault though? It's just the FTDNA transfer doing weird things.


Maybe Geno knows which ones need to be read reverse strand or to avoid and FTDNA, for some reason, does not yet?
It's not only the fault of FTDNA. Geno has a lot of false positives. Geno uses an Illumina customized chip and so does 23andme and BritainsDNA. 23andme doesn't have false positives and I haven't heard of BritainsDNA having a lot of false positives and the original Geno 2.0 didn't have near the number of false positives that this chip has. So part of the cause of trouble is either how the chip was designed or what is reported to FTDNA by Geno 2.0+. Even if it is an issue of Geno 2.0+ reading the wrong strand that is not the fault of FTDNA in any way whatsoever. If an SNP is listed with the mutation of a certain allele to another certain allele the designers should know to design the chip and the primers to look for it correctly or not include it in the list of reported SNPs at al. Maybe a better term for the false positives is invalid test result because it the end that is what a false positive is and that is what a read of the reverse strand is.


I'm curious, what do you get for BY2171? I'm trying to figure out if it's to be read as is or not.
BY2171 is T to A (http://ybrowse.org/gb2/gbrowse_details/chrY?ref=ChrY;start=23615856;end=23615856;name=BY2 171;class=Sequence;feature_id=94170;db_id=chrY%3Ad atabase) so an A should be a positive but as you can see he has A and so do other people that are not U152. If it is listed as T to A then that is how it is supposed to be read. So it is an invalid test result.

Geno 2.0+ should be providing a list of the SNP, the position, the listed mutation of the SNP, and the positive and negatives test results to all customers. They don't provide any of that anymore unless they do an FTDNA transfer, and only some of the info is supplied after the transfer, and it doesn't make sense.

jatt2016
04-20-2016, 11:35 PM
No, Geno2 is simply a bad product that should have never reached market.


A combination of chip errors, clueless programmers, and a poor testing platform overall. Y-SNP chips also become outdated very quickly.

The most affordable autosomal test is probably FTDNA's Family Finder chip. DNA.Ancestry.ca and 23andMe.com follow behind.

For Y-DNA haplogroups, the appropriate SNP Packs from FTDNA, or SNP Panels from YSEQ.net would be the least expensive route, but they only test for known Y-SNPs. One is better off in the long run, financially, by skipping all that and going straight for NGS testing with Big-Y from FTDNA, or even better, the ultimate Y-Elite 2.x from FullGenomes.com (my personal preference).

If I had to do it all over again, I would simply order the WGS 30x product from Full Genomes Corp, and call it done.


How is this the Geno 2's fault though? It's just the FTDNA transfer doing weird things.


It's not only the fault of FTDNA. Geno has a lot of false positives. Geno uses an Illumina customized chip and so does 23andme and BritainsDNA. 23andme doesn't have false positives and I haven't heard of BritainsDNA having a lot of false positives and the original Geno 2.0 didn't have near the number of false positives that this chip has. So part of the cause of trouble is either how the chip was designed or what is reported to FTDNA by Geno 2.0+. Even if it is an issue of Geno 2.0+ reading the wrong strand that is not the fault of FTDNA in any way whatsoever. If an SNP is listed with the mutation of a certain allele to another certain allele the designers should know to design the chip and the primers to look for it correctly or not include it in the list of reported SNPs at al. Maybe a better term for the false positives is invalid test result because it the end that is what a false positive is and that is what a read of the reverse strand is.


BY2171 is T to A (http://ybrowse.org/gb2/gbrowse_details/chrY?ref=ChrY;start=23615856;end=23615856;name=BY2 171;class=Sequence;feature_id=94170;db_id=chrY%3Ad atabase) so an A should be a positive but as you can see he has A and so do other people that are not U152. If it is listed as T to A then that is how it is supposed to be read. So it is an invalid test result.

Geno 2.0+ should be providing a list of the SNP, the position, the listed mutation of the SNP, and the positive and negatives test results to all customers. They don't provide any of that anymore unless they do an FTDNA transfer, and only some of the info is supplied after the transfer, and it doesn't make sense.

Hi guys,

Thank you all for your input. FTDNA was contacted today, the problem was explained to them and they have sincerely accepted that there is a general issue with the data transfer from genographic to FTDNA site. The customer service expert assured that their engineers are working on it and likely in two weeks the problem will be solved. The raw data files available on FTDNA site are not correct and should not be used for making any inference at this point in time. The Nationalal Genographic is also aware of the situation and the result showed at Nat Geo site is the correct one i.e. J -CTS2906.

Thanks and regards,

Jatt

dp
04-20-2016, 11:53 PM
Jatt,
hope you don't mind the following project plug.
dp :-)

For those men who are members of R1b-Z2976, please join:
https://www.familytreedna.com/public/R-DF49
The path is DF49>Z2980>Z2976.
I am Sanger certified Z2976+.
from there to my tip the path goes Z2976>DF23>Z2961>ZZ30>ZP106.
I believe I am correct in saying that Z2976xDF23 is a very small group.
dp :-)

leo76
04-21-2016, 03:25 AM
[QUOTE=jatt2016;152119]The National Genographic is also aware of the situation and the result showed at Nat Geo site is the correct one i.e. J -CTS2906.

Thank you for your efforts on this, Jatt, and for the update.

I have to say that I think Geno 2.0 Next Generation is a BIG disappointment. At least, the quality control that was conducted on the product before release was extremely poor. Like it was rushed out for the Christmas 2015 season.

It's no secret that their sales have been slowly declining over the past few years. Geno 2.0+ might partially have been an attempt to reverse this and regain some market share, but ironically, with the utter MESS of a product they've shoved out the door now, their once-fine reputation might have been irreversibly tarnished.

There is NO excuse that so many people should have false positives, misassigned haplogroups, etc. In my case Geno 2.0+ was largely correct (even though it missed my terminal y-SNP because it no longer tests for it!), but I was lucky. A lot of other folks were not.

I think Nat'l Geno owes their customer base an apology and a re-release of the product.

jatt2016
04-21-2016, 10:22 AM
[QUOTE]

Thank you for your efforts on this, Jatt, and for the update.

I have to say that I think Geno 2.0 Next Generation is a BIG disappointment. At least, the quality control that was conducted on the product before release was extremely poor. Like it was rushed out for the Christmas 2015 season.

It's no secret that their sales have been slowly declining over the past few years. Geno 2.0+ might partially have been an attempt to reverse this and regain some market share, but ironically, with the utter MESS of a product they've shoved out the door now, their once-fine reputation might have been irreversibly tarnished.

There is NO excuse that so many people should have false positives, misassigned haplogroups, etc. In my case Geno 2.0+ was largely correct (even though it missed my terminal y-SNP because it no longer tests for it!), but I was lucky. A lot of other folks were not.

I think Nat'l Geno owes their customer base an apology and a re-release of the product.

I agree that they should address the issue publicly and save the customers from frustration and inconvenience. I understand that this is an emerging science and glitches are expected but then again it is the duty of the vendor to let buyers know of any shortcomings of the product and uncertainties involved.

wombatofthenorth
04-22-2016, 02:42 AM
Hi for BY2171 I am AA in my raw data file and it is not in listed of reported positives.

HMm that suggests that either it is one to be read strand reversed or, worse, that it's a broken one.

EDIT: with your note from FTDNA that the data as transferred can't be trusted maybe that tends to give more hope that much of this stuff is strand reversal. Geno knows what strand for each SNP but apparently something got lots in the communication back to FTDNA? Hopefully.

I also wonder if this is why full FTDNA transfers seem to be stuck. I was told that people often got them complete in hours, but for those who tried this a few days ago, the transfers seem to be still pending. Maybe they are waiting to get this transfer mess fixed up first.

(also we should note that a lot of those who got false results at FTDNA after any sort of transfer were given the correct on at the Geno site itself)

I should also note that FTDNA seems to have had some sloppy quality control lately though as they did seem to bungle up my dad's mtDNA result, leaving him a number of branches upstream of what the test should be able to do. Trying to get them to re-run it. It might not even be universal, just one or two very unfortunately placed no calls, but such calls so far upstream should have triggered an FTDNA quality review for his test IMO. It's not like even just the last SNP, we are talking a few levels upstream and I don't believe that should be let through quality control. (interestingly he never even received a message about it having even entered quality control, he got one for each early stage and then suddenly results in and never got the quality control stage message this time).

jatt2016
04-22-2016, 12:14 PM
HMm that suggests that either it is one to be read strand reversed or, worse, that it's a broken one.

EDIT: with your note from FTDNA that the data as transferred can't be trusted maybe that tends to give more hope that much of this stuff is strand reversal. Geno knows what strand for each SNP but apparently something got lots in the communication back to FTDNA? Hopefully.

I also wonder if this is why full FTDNA transfers seem to be stuck. I was told that people often got them complete in hours, but for those who tried this a few days ago, the transfers seem to be still pending. Maybe they are waiting to get this transfer mess fixed up first.

(also we should note that a lot of those who got false results at FTDNA after any sort of transfer were given the correct on at the Geno site itself)

I should also note that FTDNA seems to have had some sloppy quality control lately though as they did seem to bungle up my dad's mtDNA result, leaving him a number of branches upstream of what the test should be able to do. Trying to get them to re-run it. It might not even be universal, just one or two very unfortunately placed no calls, but such calls so far upstream should have triggered an FTDNA quality review for his test IMO. It's not like even just the last SNP, we are talking a few levels upstream and I don't believe that should be let through quality control. (interestingly he never even received a message about it having even entered quality control, he got one for each early stage and then suddenly results in and never got the quality control stage message this time).

National Geongraphic and Family Tree DNA are both reputable organizations and I hope they fix this glitch soon. It takes 8-9 weeks before you get your DNA results. I bought the kit in December and got my results in February 2016 , found out discrepancies in my raw data. The errors/findings were communicated via email to genographic and was assigned a ticket number, did multiple follow ups and its been additional 8 weeks on top of the regular 8 week , the issue is still to be resolved. I hope that it gets resolved as per their assurance i.e. 2 more weeks.:)

ArmandoR1b
04-22-2016, 12:53 PM
HMm that suggests that either it is one to be read strand reversed or, worse, that it's a broken one.

EDIT: with your note from FTDNA that the data as transferred can't be trusted maybe that tends to give more hope that much of this stuff is strand reversal. Geno knows what strand for each SNP but apparently something got lots in the communication back to FTDNA? Hopefully.
Even if it is strand reversal it is an invalid test result so I don't know why you have hope for it being a strand reversal.


(also we should note that a lot of those who got false results at FTDNA after any sort of transfer were given the correct on at the Geno site itself)
There are also people that did not get the correct terminal SNP at the Geno site. A person that is positive for Z2105, CTS1843, and S12460 was told by Geno 2.0+ that his terminal SNP was farther upstream. DF27 people have been put into a U152 subclade or an incorrect DF27 subclade by Geno 2.0+. So even the Geno 2.0+ site has problems.


I should also note that FTDNA seems to have had some sloppy quality control lately though as they did seem to bungle up my dad's mtDNA result, leaving him a number of branches upstream of what the test should be able to do. Trying to get them to re-run it. It might not even be universal, just one or two very unfortunately placed no calls, but such calls so far upstream should have triggered an FTDNA quality review for his test IMO. It's not like even just the last SNP, we are talking a few levels upstream and I don't believe that should be let through quality control. (interestingly he never even received a message about it having even entered quality control, he got one for each early stage and then suddenly results in and never got the quality control stage message this time). That is from Geno 2.0+ transfer though correct? Geno 2.0+ doesn't provide raw data to it's customers. Why not? The FMS test from FTDNA is very good although the extra mutations report on the site has a bug but there is not a problem with the raw data and the subclade is as accurate as the older phylotree that they use.

jatt2016
04-22-2016, 04:06 PM
Even if it is strand reversal it is an invalid test result so I don't know why you have hope for it being a strand reversal.


There are also people that did not get the correct terminal SNP at the Geno site. A person that is positive for Z2105, CTS1843, and S12460 was told by Geno 2.0+ that his terminal SNP was farther upstream. DF27 people have been put into a U152 subclade or an incorrect DF27 subclade by Geno 2.0+. So even the Geno 2.0+ site has problems.

That is from Geno 2.0+ transfer though correct? Geno 2.0+ doesn't provide raw data to it's customers. Why not? The FMS test from FTDNA is very good although the extra mutations report on the site has a bug but there is not a problem with the raw data and the subclade is as accurate as the older phylotree that they use.

Hi Armando,

You have raised an interesting point, if they know that this is data transfer problem then why not provide the raw file locally on Nat Geo site? What are your takes on that?

Regard,
Jatt

Ali16
05-13-2016, 01:07 PM
Because it is not a data transfer problem. The data originates with FTDNA. How is it possible you have not understood this after all these months?