Comments on: My genome, unzipped http://www.genomesunzipped.org/2012/12/my-genome-unzipped.php public personal genomics Fri, 24 May 2013 15:46:39 +0000 hourly 1 http://wordpress.org/?v=3.5.1 By: Twelve Developments on 12/12/12 « Homologushttp://www.genomesunzipped.org/2012/12/my-genome-unzipped.php#comment-453120 Twelve Developments on 12/12/12 « Homologus Wed, 12 Dec 2012 20:17:54 +0000 http://www.genomesunzipped.org/?p=5253#comment-453120 [...] (ix) My Genome, Unzipped. [...]

]]> By: razibhttp://www.genomesunzipped.org/2012/12/my-genome-unzipped.php#comment-445837 razib Mon, 10 Dec 2012 21:34:40 +0000 http://www.genomesunzipped.org/?p=5253#comment-445837 my working assumption is that it will only go beyond ‘for entertainment purposes only’ (at least as more than thick-snp-chip value added) once we get familial pedigrees with deep coverage. pick up loss of function and what not with high degree of confidence. am i wrong?

(i plan to have this done soon too btw, even if i don’t plan to find anything super interesting)

]]> By: Joe Pickrellhttp://www.genomesunzipped.org/2012/12/my-genome-unzipped.php#comment-445691 Joe Pickrell Mon, 10 Dec 2012 20:15:30 +0000 http://www.genomesunzipped.org/?p=5253#comment-445691 Hi Madeleine,

Thanks for the note! I’ll definitely update GET-Evidence if I see anything interesting on these variants.

]]> By: Madeleine Ballhttp://www.genomesunzipped.org/2012/12/my-genome-unzipped.php#comment-445246 Madeleine Ball Mon, 10 Dec 2012 16:11:42 +0000 http://www.genomesunzipped.org/?p=5253#comment-445246 Thank you for participating in our project! While you may find nothing now, that’s in large part because we know so little — there’s a potential for discoveries in the future. I’m sure that contributions of public genomes like your own get us there sooner.

There is definitely a high risk of false negatives. Our GET-Evidence review system is limited to variants that it knows about, and that is in turn limited to what gets shared with the public databases it uses (e.g. OMIM).

There’s undoubtedly many “known” pathogenic variants we’re missing. Genetic testing groups (e.g. experts in genetic testing for Brugada syndrome) don’t typically share all their variants publicly, and even if they do (e.g. via publications) those might not make it into a curated OMIM page or other central database.

There are some efforts to organize these into a single source (e.g. ClinVar and MutaDataBase), but testing companies may also wish to retain them as private “trade secrets” for business purposes. Dan Vorhaus’s recent post is useful on this topic: http://www.genomicslawreport.com/index.php/2012/11/28/myriad-updates-clinical-data-as-trade-secrets-and-a-pending-certiorari-decision/

I try to briefly review all new PGP genomes to see if anything new is flagged and should get in depth review before being return. , but GET-Evidence is still extremely new and unused — very much “in development”. Most variants are “insufficiently evaluated” and so lack an interpretation on the main report page. Having genomes like yours is critical for that development though. Since it’s freely editable (and freely shared as CC0), anyone can add something as soon as they realize it’s missing.

If you click on the “insufficiently evaluated” tab in your report, you’ll see there’s currently two highly ranked variants. I believe I looked at them long enough to conclude they seem to be recessives (assuming they’re real… the literature has many false positives as well) and thus are unlikely to be an immediately health concern. I think they’re worth reviewing, but I don’t have much time these days. If you’re interested in following the breadcrumbs you can click on those variants and find out more about them. Please feel free to edit as well!

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