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Hi all (and sorry if this thread is chasing various folk around)<br>
<div class="moz-forward-container"> <br>
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: <br>
<br>
<i> Can I have data for my current favourite SNPs x, y and z?
</i><br>
<br>
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. <br>
<br>
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.<br>
<br>
Excellent!<br>
<br>
So, my question is: <br>
<br>
<b> How do I ask for more chips to be added to the Variant Set
Name pull-down? </b><br>
<br>
The two I would especially keen to see are: <br>
<br>
Illumina Exome-chip <br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://diagram-consortium.org/uk-exome-chip/">http://diagram-consortium.org/uk-exome-chip/</a>
<br>
<br>
Illumina Immunochip <br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.nature.com/nrg/journal/v14/n9/box/nrg3502_BX1.html">http://www.nature.com/nrg/journal/v14/n9/box/nrg3502_BX1.html</a>
<br>
<br>
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. <br>
<br>
Cheers <br>
Neil<br>
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Neil Walker email: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:neil.walker@cimr.cam.ac.uk">neil.walker@cimr.cam.ac.uk</a>
JDRF/WT Diabetes and Inflammation tel: +44 (0)1223 763210
Laboratory fax: +44 (0)1223 762102
Cambridge, UK <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www-gene.cimr.cam.ac.uk/todd/">http://www-gene.cimr.cam.ac.uk/todd/</a>
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