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

Sarah Hunt seh at ebi.ac.uk
Tue Dec 10 11:03:02 GMT 2013


Hi Neil,

I hope all goes well with you!

We are keen to support the popular chips, especially those with data
in EGA. The Exome chip will be in our next release due in February -
we'll try to get the ImmunoChip loaded for this release too.

All the best,

Sarah

On Mon, Dec 9, 2013 at 2:12 PM, Neil Walker <neil.walker at cimr.cam.ac.uk> wrote:
> 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
>
> --
> ---------------------------------------------------------------------
> 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, UK                       http://www-gene.cimr.cam.ac.uk/todd/
> ---------------------------------------------------------------------
>
>
>
>
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