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Hi Catherine<br>
<br>
When data goes into the GWAS catalogue, it is defined just by the
region where the GWAS study was carried out, in this case Europe. In
Ensembl, we have data from specific experiments, working with
particular populations. We calculate the LD from the experiments we
have in our databases. We can't claim to have all the variation and
LD for everybody in Europe, only for the group studied, so we define
our population names as the experiments. You can then look at the
experiments themselves to see whether they are representative for
your purpose or not.<br>
<br>
Here's a sum up of the samples used in 1000 Genomes. <br>
<a class="moz-txt-link-freetext" href="http://www.1000genomes.org/about#ProjectSamples">http://www.1000genomes.org/about#ProjectSamples</a><br>
<br>
As you can see, the European (EUR) super-population is made up of
British (GBR), Finnish (FIN), Spanish (IBS), Italian (TSI) and
American (CEU) subpopulations. If you think this is representative
for what you're doing then the 1000 Genomes EUR population is the
one you want to use to get your LD. The name for this population in
the database is 1000GENOMES:phase_1_EUR, telling us it comes from
1000 Genomes, it's the data from phase 1 and it's the European
population (watch out for phase 3 with more variants coming soon).
We don't currently have a more representative population for Europe
as a whole.<br>
<br>
All the best<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 20/02/2015 16:50, Catherine Leroy
wrote:<br>
</div>
<blockquote
cite="mid:B70374BB-31B9-4707-A468-90AE54549F19@ebi.ac.uk"
type="cite">
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I get my snp and ethnicity from the gwas catalog database. The
specific example I gave earlier is pubmed : <span
style="background-color: rgb(255, 255, 255);"><i>23128233. So I
won’t have much more then what I have put in my script. </i></span>
<div><span style="background-color: rgb(255, 255, 255);"><i>So
there’s no such thing as r2 data for ‘European population’?<br>
</i></span>
<div><br>
</div>
<br>
<div>
<div>On 20 Feb 2015, at 14:36, Emily Perry <<a
moz-do-not-send="true" href="mailto:emily@ebi.ac.uk">emily@ebi.ac.uk</a>>
wrote:</div>
<br class="Apple-interchange-newline">
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<div bgcolor="#FFFFFF" text="#000000"> Hi Catherine<br>
<br>
You need to use the names that the populations are called
in the database, so to get 1000 genomes Europeans you
would use 1000GENOMES:phase_1_EUR.<br>
<br>
All the best<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 20/02/2015 13:32,
Catherine Leroy wrote:<br>
</div>
<blockquote
cite="mid:D073601E-A2C7-4B25-931B-8E33DEA263EC@ebi.ac.uk"
type="cite">
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Hello,
<div><br>
</div>
<div>I am trying to work my head around LD. As you might
see from my questions it is all quite new to me.</div>
<div><br>
</div>
<div>I have the following snp : <span
style="background-color: rgb(255, 255, 255);">rs11010067</span></div>
<div><span style="background-color: rgb(255, 255, 255);">and
I am trying to get the r2 value using the script
I’ve copied past below.</span></div>
<div><span style="background-color: rgb(255, 255, 255);"><br>
</span></div>
<div><span style="background-color: rgb(255, 255, 255);">If
I enter as population : Europe </span></div>
<div><span style="background-color: rgb(255, 255, 255);">then
I don’t get anything back. </span></div>
<div><span style="background-color: rgb(255, 255, 255);"><br>
</span></div>
<div><span style="background-color: rgb(255, 255, 255);">If
I enter as population : </span><span
style="background-color: rgb(255, 255, 255);">CSHL-HAPMAP:HapMap-CEU</span></div>
<div>
<div>Then I get back a list of variation1, variation2
and r2. </div>
</div>
<div><br>
</div>
<div>I don’t understand why I don’t get anything with
Europe. </div>
<div>Could somebody explain that to me or point me to
some documentation about LD I could read. </div>
<div><br>
</div>
<div>I would want to use r2 to determine if a snp I have
is in the same LD Block then the gene I’m supposing it
is linked to using a threshold for r2 (which I haven’t
determine yet, I’ve just started working on that). The
problem is that the indication I have as population
for this snp in my data (Gwas catalog) is Europe which
doesn’t return anything. </div>
<div><br>
</div>
<div>Thanks for your help,</div>
<div>Catherine</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<pre style="background-color: rgb(255, 255, 255);"><font face="Helvetica">use strict;
use warnings;
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => '<a moz-do-not-send="true" href="http://ensembldb.ensembl.org/">ensembldb.ensembl.org</a>',
-user => 'anonymous',
);
my $rs_id = "rs11010067";
my $variation_adaptor = $registry->get_adaptor( 'human', 'variation', 'variation' );
my $variation = $variation_adaptor->fetch_by_name($rs_id);
my $population_adaptor = $registry->get_adaptor('human', 'variation', 'population'); <span style="font-style: italic;">#get adaptor for Population object
</span>my $population = $population_adaptor->fetch_by_name("CSHL-HAPMAP:HapMap-CEU");
<span style="font-style: italic;">#my $population = $population_adaptor->fetch_by_name("Europe");
</span><span style="font-style: italic;">
</span>foreach my $variation_feature (@{$variation->get_all_VariationFeatures()}) {
print $variation_feature->seq_region_name(),':', $variation_feature->seq_region_start(), '-', $variation_feature->seq_region_end(),"\n";
my $ldFeatureContainerAdaptor = $registry->get_adaptor('human', 'variation', 'ldfeaturecontainer'); <span style="font-style: italic;">#get adaptor for LDFeatureContainer object
</span><span style="font-style: italic;"> </span>my $ldFeatureContainer = $ldFeatureContainerAdaptor->fetch_by_VariationFeature($variation_feature, $population);
my $r_square_values = $ldFeatureContainer->get_all_r_square_values();
foreach my $r_square_value (@{$r_square_values}){
my $variation_feature_1 = $r_square_value->{variation1};
my $variation1_name = $variation_feature_1->name();
<span style="font-style: italic;">#$variation1
</span><span style="font-style: italic;"> </span>my $variation_feature_2 = $r_square_value->{variation2};
my $variation2_name = $variation_feature_2->name();
my $r2 = $r_square_value->{r2};
print "variation1 = " , $variation1_name, "variation1_region_name = ", $variation1_name, " \n";
print "variation2 = " , $variation2_name, "variation2_region_name = ", $variation2_name, " \n";
print "r2 = " , $r2 , "\n\n";
}
}
</font></pre>
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<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Officer
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Officer
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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