As part of the Personal Genome Project (PGP), my genome was recently sequenced by Complete Genomics. My PGP profile, including the sequence, is here, and their report on my genome is here. As I play around with the best ways to analyze these data, I’ll write additional posts, but for now I’ve noticed only one thing: I’m almost surprised by how unsurprising my full genome sequence is.
According the the PGP’s genome annotator, I have two variants of “high” clinical relevance. The first is the APOE4 allele, which Luke had already reported that I carry. The second is a variant that causes alpha-1-antitrypsin deficiency, which is also typed by 23andMe.
Of course, this is all quite reassuring. Long-time readers will remember that last year I was briefly worried that I might have Brugada syndrome. I do not carry any of the known pathogenic mutations (modulo worries about false negatives); this of course is now unsurprising, but would have been really nice information to have, say, when I was talking with a cardiologist last year.
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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!
Hi Madeleine,
Thanks for the note! I’ll definitely update GET-Evidence if I see anything interesting on these variants.
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)