[ensembl-dev] LD/population questions

[Catherine Leroy]

Hello, 

I am trying to work my head around LD. As you might see from my questions it is all quite new to me.

I have the following snp : rs11010067
and I am trying to get the r2 value using the script I’ve copied past below.

If I enter as population : Europe 
then I don’t get anything back. 

If I enter as population : CSHL-HAPMAP:HapMap-CEU
Then I get back a list of variation1, variation2 and r2. 

I don’t understand why I don’t get anything with Europe. 
Could somebody explain that to me or point me to some documentation about LD I could read. 

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. 

Thanks for your help,
Catherine




use strict;
use warnings;
use Bio::EnsEMBL::Registry;


my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
-host   => 'ensembldb.ensembl.org',
-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'); #get adaptor for Population object
my $population = $population_adaptor->fetch_by_name("CSHL-HAPMAP:HapMap-CEU");
#my $population = $population_adaptor->fetch_by_name("Europe");

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'); #get adaptor for LDFeatureContainer object
    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 = $variation_feature_1->name();
        #$variation1
        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";

    }
}




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