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Of course, they're just calling SNPs and using published GWAS studies to estimate disease risk. You can get your "raw genome" text file from 23andMe and convert

Of course, they're just calling SNPs and using published GWAS studies to estimate disease risk. You can get your "raw genome" text file from 23andMe and convert to e.g. VCF format for use in a bioinformatics tool like the variant effect predictor. Besides, really the most interesting health-related alleles are the simplest: ApoE, BRCA1 — no complicated algo is needed to interpret those associations.

nutmeg 12y ago
Is there an easy way (or introductory guide) for someone not familiar with bioinformatics tools?
- citricsquid 12y ago
  http://www.snpedia.com/index.php/Promethease http://www.snpedia.com/index.php/Promethease
- heuermh 12y ago
  I've written a free/libre open source java client for the 23andMe API here https://github.com/heuermh/personal-genome-client https://github.com/heuermh/personal-genome-client Let me know if you would like any help with the analysis.
bentcorner 12y ago
Thanks for the comment - my wife and I submitted 23andme kits for fun and learned some of our history, but I was disappointed we weren't able to get any health information from it. I didn't know you could get your genome info from 23andme and get it interpreted by someone else!
jessriedel 12y ago
> You can get your "raw genome" text file from 23andMe Well, not your full genome. You can get the raw SNPs that 23andMe test for, and if you're in their pilot program that sequences the exome (which is a superset of the SNPs but a subset of the full genome) then you can presumably get the raw data on that.
- jebus989 12y ago
  That's their terminology I believe (hence quotes). However, for fun you can have a go at imputing a full genome from these SNPs (e.g. http://genomesunzipped.org/2013/03/learning-more-from-your-23andme-results-with-imputation.php http://genomesunzipped.org/2013/03/learning-more-from-your-2...). SNPs aren't necessarily exonic either so exome-seq isn't a superset of SNPs (I am a bioinformatics PhD student so while this isn't precisely my day job I'm not speaking from a position of ignorance).
  - jessriedel 12y ago
    Thanks for the correction.

nutmeg 12y ago

Is there an easy way (or introductory guide) for someone not familiar with bioinformatics tools?

citricsquid 12y ago
http://www.snpedia.com/index.php/Promethease http://www.snpedia.com/index.php/Promethease
heuermh 12y ago
I've written a free/libre open source java client for the 23andMe API here https://github.com/heuermh/personal-genome-client https://github.com/heuermh/personal-genome-client Let me know if you would like any help with the analysis.

bentcorner 12y ago

Thanks for the comment - my wife and I submitted 23andme kits for fun and learned some of our history, but I was disappointed we weren't able to get any health information from it. I didn't know you could get your genome info from 23andme and get it interpreted by someone else!

jessriedel 12y ago

> You can get your "raw genome" text file from 23andMe Well, not your full genome. You can get the raw SNPs that 23andMe test for, and if you're in their pilot program that sequences the exome (which is a superset of the SNPs but a subset of the full genome) then you can presumably get the raw data on that.

jebus989 12y ago
That's their terminology I believe (hence quotes). However, for fun you can have a go at imputing a full genome from these SNPs (e.g. http://genomesunzipped.org/2013/03/learning-more-from-your-23andme-results-with-imputation.php http://genomesunzipped.org/2013/03/learning-more-from-your-2...). SNPs aren't necessarily exonic either so exome-seq isn't a superset of SNPs (I am a bioinformatics PhD student so while this isn't precisely my day job I'm not speaking from a position of ignorance).
- jessriedel 12y ago
  Thanks for the correction.