Complete Genomics user

[rworthi]

I teach pharmacogenomics at Southern Illinois University and I am a subject of the Personal Genomes Project. I got a seed grant from my university an my genome is being sequenced by Complete Genomics, while my exome is being sequenced by Otogenetics using the Niblegen v2 capture. I have annotated the mouse and human genomes at the Washington University Genome Sequencing Center, and nematode genomes with Divergence, Inc.

[gtyrelle]

SNPedia may be of interest. See here for a report generated from CG data.

[rworthi]

SNPedia

Thanks for the tip. I use Promethease for my 23andme data, but I was not aware that they have incorporated CGI data analysis as well.

[cariaso]

SNPedia + Promethease + Complete Genomics =

Hello, I'm the author of Promethease.

http://www.snpedia.com/index.php/Promethease

It does have support for Complete Genomics formatted files, and I'll be curious for you to confirm that it works for you as easily as your previous 23andMe data. ... albeit a bit more slowly due to the size.


There are 2 files available from CGI, one is the 'masterVarBeta', and I expect they intend to give that to you. However there is another file, the 'dbSNP' file which may or may not be included. That file will help to give you the most comprehensive Promethease report possible.



Assuming the Nimblegen format includes rs#s, I'd be willing to add support for that as well. That would allow you to pool all 3 platforms and immediately highlight rs#s at which they disagree.


The combination of 23andMe + CGI dbSNP + Nimblegen file would probably make you the new leader for the title 'most genotyped' among SNPedia. Without it your data would be most comparable to the current leader who has combined 23andMe with CGI masterVarBeta. Still it's a good example of what you can expect.

http://www.snpedia.com/index.php/User:David_Ewing_Duncan

is the person, and there you can find various platform specific reports, but the combined everything version is at

http://files.snpedia.com/reports/genome_David_Duncan_pooled.html

The part that I think is of most interest to you is
(Warning Large File URL)

http://files.snpedia.com/reports/promethease_data/genome_David_Duncan_pooled_Topic.html

PharmGKB is one of the largest Topics in SNPedia. David Duncan here shows 2015 PharmGKB snps as I write this. As you scroll past the first 100 the color gets lighter, and then suddenly jumps back to bright red. This marks the end of the genotypes with an assigned magnitude.

http://snpedia.com/index.php/Magnitude

and the beginning of the section where we know only the HapMap frequency. At present David Duncan here shows 2 with 0.0% frequency one of which seems quite interesting.

http://www.snpedia.com/index.php/Rs12272004

rs12272004(A;A) is well replicated as having some sort of effect. But I nor SNPedia can yet say much more about it.


He has many other SNPs. If you quickly scroll the rest of the report you'll see the colors gradually fade then jump at new sections. Down at the very bottom are the green snps, where we've already concluded you have the normal form.

Your own report will substantially overlap with his. If you or your students would annotate any part of your genome in SNPedia in this way, it would immediately benefit David Duncan's report.

Similarly, improving his report today would improve the Promethease report you'll make when your CGI data arrives. Obviously you'd be helping to improve many other people's genomes at the same time.

[scordes]

The dbSNPAnnotated file is a standard deliverable that is included in the ASM folder for all genome assemblies.