[ensembl-dev] new chips on BioMart's filter Variation Set Name

[Neil Walker]

Hi all (and sorry if this thread is chasing various folk around)

I sit on several Data Access Committees in a technical capacity 
(including for the 1958 Birth Cohort) - and one question that comes up 
often is:

/    Can I have data for my current favourite SNPs x, y and z? /

This kinda assumes that data will exist for any arbitrary SNP that is 
named, which is, of course, not the case.  So first we check whether 
these appear in any of the datasets that are deposited in the EGA, or 
locally, or whether new typing will have to be commissioned.

As I discovered from my colleague, Olly Burren, one good way of allowing 
people to answer the same question for themselves, is to point them 
first to Ensembl Mart to at least check whether SNPs appear on one of 
the big SNP chips used by e.g. WTCCC2.

Excellent!

So, my question is:

*    How do I ask for more chips to be added to the Variant Set Name 
pull-down? *

The two I would especially keen to see are:

     Illumina Exome-chip
http://diagram-consortium.org/uk-exome-chip/

     Illumina Immunochip
http://www.nature.com/nrg/journal/v14/n9/box/nrg3502_BX1.html

For the future, the heuristic I'm reaching for is - if a large dataset 
using a commodity chip is deposited in the EGA, it would be good to be 
able to filter on the SNPs that were on that chip in Ensembl Mart.  
Obviously in an ideal world, one would reference the exact name of the 
chip as appears in the Ensembl Mart filter in the README that comes with 
the dataset, so people would know what to look for.

Cheers
Neil

-- 
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Neil Walker                         email:neil.walker at cimr.cam.ac.uk
JDRF/WT Diabetes and Inflammation   tel: +44 (0)1223 763210
     Laboratory                      fax: +44 (0)1223 762102
Cambridge, UKhttp://www-gene.cimr.cam.ac.uk/todd/
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