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XooR
02-17-2016, 01:57 PM
Does anyone has any experience with this study? It seems interesting and free.

Participants in Genes for Good have a unique opportunity to learn about their health, behavior, and ancestors. Any information you provide to the study is yours to visualize using plotting tools available in the App itself. If you like, you can also download the information. After all, it's your information and you should be able to do with it what you wish.

https://genesforgood.sph.umich.edu/
http://apps.facebook.com/genesforgood

Varun R
02-18-2016, 12:34 AM
Xoor,

My mom and I tested with Genes for Good. Below is a list of files you are sent:

I. What Is In Your Download
---------------------------

You have just downloaded a ZIP archive containing the following 9 files:

1. GFG_filtered_unphased_genotypes.vcf.gz
2. GFG_filtered_unphased_genotypes.vcf.gz.tbi
3. GFG_filtered_unphased_genotypes_23andMe.txt
4. GFG_filtered_unphased_genotypes_vcf.txt
5. GFG_filtered_imputed_genotypes_noY_noMT.vcf.gz
6. GFG_filtered_imputed_genotypes_noY_noMT.vcf.gz.tbi
7. GFG_filtered_imputed_genotypes_noY_noMT_23andMe.tx t
8. GFG_filtered_imputed_genotypes_noY_noMT_vcf.txt
9. README.txt

Roughly 500,000 SNPs are tested. Although they send you two files with genotypes in 23andMe format, some of the SNPs use different identifying nomenclature than what is used by 23andMe. Having not looked at the .txt files extensively, I can't say how many SNPs are identified differently, (although I believe some have discussed the matter in the 23andMe forums). Also, I don't know how to quickly change the differing SNP identifiers to standard 23andMe format.

They also provide a pie chart with rudimentary (broad) ethnic breakdown (like Ancestry Comp), a chromosome painting and a PCA showing your position relative to academic samples. The admixture analysis seemed reasonable- I scored 98% C and S Asia and 2% Oceania while my mom scored 96% C and S S Asia and 4% Oceania.

I haven't contacted J. Olson to ask whether the 23andMe files would be accepted by Gedmatch, but that is something I plan to do soon. I had a positive experience with GenesforGood overall.

Ann Turner
02-18-2016, 01:41 PM
Varun R or others with Genes for Good data --

That could be a very informative set of files. I'd be very interested in seeing how the phased and imputed files compare with the genotype data for segment matching purposes. DNA.Land will provide a phased and imputed file (39,000,000 SNPs) based on an upload from the big three autosomal tests, but it doesn't separate the two processes. The final result is not really satisfactory: phase switch and/or imputation errors seem to fragment the segments too much. I'll see if I can locate the thread where I reported on that.

If you wouldn't mind sharing your data, I could take a look at it (and collaborate with John Olson on whether the results would be satisfactory for GEDmatch). The files are probably too big to e-mail, but if you'd like to send them via MailBigFile or a similar service, my e-mail is [email protected]

EDIT to add link to thread: http://www.anthrogenica.com/showthread.php?5601-DNA-Land-imputed-VCF-file&p=122298&viewfull=1#post122298

psaglav
02-18-2016, 05:06 PM
Ann, can the imputed dnaland data be uploaded to gedmatch as a kit? (sorry if I misunderstood.)

Ann Turner
02-18-2016, 08:17 PM
Ann, can the imputed dnaland data be uploaded to gedmatch as a kit? (sorry if I misunderstood.)
No, I did quite a bit of finagling to get the imputed file in a format accepted at GEDmatch. It turned out not to be worth the effort -- it's far better just to upload whatever file you uploaded to DNA.land in the first place -- but it gave me some insights into the limitations of phasing/imputation.

crossover
05-06-2016, 03:02 PM
i decided to experiment with this dna analysis
9174
9175

Sikeliot
05-06-2016, 04:26 PM
i decided to experiment with this dna analysis
9174
9175

What is your ancestry?

XooR
05-06-2016, 05:02 PM
Here is my results,

9178
9179
9180

Sikeliot
05-06-2016, 07:18 PM
Here is my results,

9178
9179
9180

How long did it take for these to come in?

XooR
05-06-2016, 07:24 PM
How long did it take for these to come in?

Including initial process it took almost 2 months.

Sikeliot
05-06-2016, 07:27 PM
Including initial process it took almost 2 months.


I just got my mother's result in. My question is why the pie chart and the chromosome painting look so different?

crossover
05-06-2016, 11:33 PM
How long did it take for these to come in?

mines took a little over a month

crossover
05-06-2016, 11:35 PM
What is your ancestry?

my dad is white, mom is mexican-american(her parents are from mexico)

sbtoloc
05-24-2016, 06:09 PM
Any updates on downloading Genes for Good data to Gedmatch or Dna land?

crossover
05-25-2016, 05:13 PM
not yet, but i think they are still working on it, but genesforgood customers may only be allowed to use one-to-many with other genes for good kits since they use different snps than the main three.

Surreal
08-30-2016, 05:22 AM
Here are mine, my mother's, and my brother-in-laws:

Mine:

23andMe gives me 73% SSA, 24.3% European, 2.5% Native American and East Asian, 0.3% Unassigned
FamilytreeDNA gives me 73% SSA, 24% European, 3% Middle Eastern, 1% Central Asian
AncestryDNA gives me 72% SSA, 23% European, 3% West Asian, 2% South Asian
DNALand gives me 71% African, 29% West Eurasian
Wegenes gives me 68.53% SSA, 28.14% European, 2.96% Southern Asian, 0.34% Austronesian, 0.03% Other


http://i.imgur.com/ODOBRNH.png
http://i.imgur.com/dpLKOBc.png

Here's a comparison of my Gedmatch results using Genes for Good, 23andMe, and AncestryDNA on the Eurogenes K36 calculator:
http://i.imgur.com/vhlHP9S.png


My Mother's:

http://i.imgur.com/egmduU1.png
http://i.imgur.com/eFwElvv.png

Gedmatch:
http://i.imgur.com/xDG99ze.png
http://i.imgur.com/YLevHqV.png
http://i.imgur.com/KT8cjoV.png



My Brother-In-Laws:
He's African American. His mother is 3/4th African American, 1/4th European American (his great-grandfather), and his father is of Louisiana Creole descent:

http://i.imgur.com/0TbJ36v.png
http://i.imgur.com/kTcIblS.png

Gedmatch Results:



Eurogenes:
http://i.imgur.com/Z0MC9xM.png
http://i.imgur.com/SaRz673.png
http://i.imgur.com/pXmOsNh.png

HarrapaWorld:
http://i.imgur.com/z0eSbwq.png
http://i.imgur.com/teTPhDi.png

MDLP:
http://i.imgur.com/6LjtgDs.png
http://i.imgur.com/Hs4OzW0.png

puntDNAL:
http://i.imgur.com/M3x5WHF.png
http://i.imgur.com/Gh5r9xb.png
http://i.imgur.com/NBa2cVt.png