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aistea
05-04-2016, 10:09 PM
Hi folks,

Does anyone know if the raw data for the latest Geno 2.0 NextGen is really complete? isogg.org claims that approximately 3000 medically related SNPs are removed. I called The Geno Project and familytreedna and both told me that the raw data is untouched. They said that the raw data is exactly the same which they use for their analysis.

Has anyone of you downloaded the raw data for Geno 2.0 NextGen? Does it include all 750.000 SNPs?

dnoone
05-05-2016, 07:56 PM
Did the test but they have no download link and give some insolence about transferring to ftdna and paying more if you want to get your raw file. Not impressed. Also their website is mainly about pushing the " out of africa" theory than anything . Something that seems more a media phenomenon than anything with scientific proof behind it. I managed to get small files for ysnps and mtdna on ftdna when I did the transfer.

aistea
05-05-2016, 10:24 PM
Would you be able to tell me how many ysnps and mtdna there are on those two files?

ArmandoR1b
05-05-2016, 11:54 PM
Would you be able to tell me how many ysnps and mtdna there are on those two files?

Every test has a different number of Y-DNA SNPs in the file that available to download after the transfer to FTDNA. They can range from 13,532 to 13,630 SNPs. They claim they examine more than 15,000 markers on the Y chromosome (https://genographic.nationalgeographic.com/faq/about-project/#difference-between-1-geno2) but they are counting the redundant names. A major problem is a large number of false positive and false negatives in the transferred file. FTDNA is still working on a fix that should have been fixed 6 months ago. Just read some of the other threads in the Geno 2.0 section.

The mtDNA file has just a short list of SNPs and they can't be used reliably with the James Lick predictor at http://dna.jameslick.com/mthap/ A Full Sequence mtDNA test from FTDNA is much better.

aistea
05-06-2016, 04:36 AM
Every test has a different number of Y-DNA SNPs in the file that available to download after the transfer to FTDNA. They can range from 13,532 to 13,630 SNPs. They claim they examine more than 15,000 markers on the Y chromosome (https://genographic.nationalgeographic.com/faq/about-project/#difference-between-1-geno2) but they are counting the redundant names. A major problem is a large number of false positive and false negatives in the transferred file. FTDNA is still working on a fix that should have been fixed 6 months ago. Just read some of the other threads in the Geno 2.0 section.

The mtDNA file has just a short list of SNPs and they can't be used reliably with the James Lick predictor at http://dna.jameslick.com/mthap/ A Full Sequence mtDNA test from FTDNA is much better.

Shouldn't there be three files:

1. 3500 Mitochondria
2. 15,000 Y chromosome
3. 700,000 Collection of other SNPs

???

ArmandoR1b
05-06-2016, 05:35 AM
Shouldn't there be three files:

1. 3500 Mitochondria
2. 15,000 Y chromosome
3. 700,000 Collection of other SNPs

???

1. Like I said, it is a short list of SNPs in the file. They obviously think that you only need to see the mtDNA mutations that are pertinent to your subclade and that isn't even enough because the subclade is better defined with the Full Sequence test from FTDNA or a FullGenomes Corp test.

2. Like I said, over 13,000 Y chromosome SNPs but some of them have redundant names so Nat Geo counts them too to make it look like more than 15,000 Y chromosome SNPs.

3. You don't get the autosomal DNA file unless you pay for a Family Finder test which is $39 with the Geno2+ transfer. I doubt that the Geno 2.0 NextGen includes medically relevant SNPs but you would have to ask someone that has paid for the Family Finder test and knows how to determine which, if any, medically related SNPs are included.