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.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Complete Genomics user
Professor of Pharmaceutical Sciences at Southern Illinois University. Subject of the Personal Genomes Project with CGI genome sequencing, funded by a university seed grant. Annotated human and mouse genomes at the Washington University (St. Louis) GSC during Bob Waterston's tenure. Worked in nematode gene discovery at Divergence, Inc. Recent NSF grant in yeast recombinant genetics. Teach pharmacogenomics, human genomics and pharmaceutical biotechnology.Tags: None
-
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.Professor of Pharmaceutical Sciences at Southern Illinois University. Subject of the Personal Genomes Project with CGI genome sequencing, funded by a university seed grant. Annotated human and mouse genomes at the Washington University (St. Louis) GSC during Bob Waterston's tenure. Worked in nematode gene discovery at Divergence, Inc. Recent NSF grant in yeast recombinant genetics. Teach pharmacogenomics, human genomics and pharmaceutical biotechnology.
Comment
-
SNPedia + Promethease + Complete Genomics =
Hello, I'm the author of 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.
is the person, and there you can find various platform specific reports, but the combined everything version is at
The part that I think is of most interest to you is
(Warning Large File URL)
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.
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.
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.
Comment
-
The dbSNPAnnotated file is a standard deliverable that is included in the ASM folder for all genome assemblies.Shaun Cordes, PhD | Customer Support Scientist | Complete Genomics, Inc.
Toll-free: (855) 267-5358 | Direct: (650) 943-2651
[email protected]
Comment
Latest Articles
Collapse
-
by seqadmin
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
Channel: Articles
07-08-2024, 03:19 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 07-25-2024, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
07-25-2024, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
161 views
0 likes
|
Last Post
by seqadmin
07-19-2024, 07:20 AM
|
||
Started by seqadmin, 07-16-2024, 05:49 AM
|
0 responses
127 views
0 likes
|
Last Post
by seqadmin
07-16-2024, 05:49 AM
|
Comment