[ensembl-dev] GTEx REST data

[Thomas Juettemann]

Hello Andrew,

Thank you for your email. Having the allele’s added is a good idea, it is unfortunately not a quick thing to do and won’t be added quickly. We are currently working on a much more comprehensive eQTL resource which will contain all of GWAS and GTEx. It  should be available within 2 years, therefore we keep developing the current resource to a minimum. That said, we are committed to update our DB with GTEx v8, which should come out this summer.

In order to get the alleles for your rsids you could use the variation ID endpoint from GRCh37 (which was used by GTEx):
http://grch37.rest.ensembl.org/variation/human/rs6691927?content-type=application/json <http://grch37.rest.ensembl.org/variation/human/rs6691927?content-type=application/json> 

I hope this helps, please let me know if you have further questions or comments.

All the best,
Thomas

—
Thomas Juettemann, PhD
Senior Technical Officer 
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom


On 20 Feb 2018, at 07:10, andrew126 at mac.com wrote:

Hi,

I am writing to inquire about the v6 GTEx eQTL data served by REST.

eQTL results in the original v6 GTEx downloads are of this format:
	gene: ENSG00000228327.2
	SNP: 1_1584002_A_G_b37
		(where, SNP is chr_position_ref_alt_assembly)
	beta: -0.167152
	t-test: -1.15677
	p-value: 0.252864

The beta is the eQTL effect relative to the alternate allele.  That is, in the above example, the G allele results in lower transcription of ENSG00000228327.

GTEx also released an rs# lookup for the v6 data:
	1       1584002 1_1584002_A_G_b37       A       G       1       rs6691927

The above data are returned by REST for Brain_Anterior_cingulate_cortex_BA24 via:
	https://rest.ensembl.org/eqtl/id/homo_sapiens/ENSG00000228327?content-type=application/json;tissue=Brain_Anterior_cingulate_cortex_BA24;variant_name=rs6691927

The returned data are:
	[{"statistic":"beta","value":-0.167152125808732},{"statistic":"p-value","minus_log10_p_value":0.597112188559852,"value":0.252864470319954}]

The data make no mention of the effect allele.  Is there a method by which the effect allele (alternate allele as declared in the GTEx analysis) can be determined and/or returned?

Direct interpretation seems complicated by 800k of the 11m v6 variants currently having more than 1 alternate allele in v90 Ensembl.
Another 140k of the variants have non-matching ref and alt alleles in the v90 assembly .. some appear to be simple strand flips, while others are less obvious .. for example, rs6691927 has changed from being an A/G variant to being a G/A variant (so one would need to know to grab the current alternate allele and change the sign of the beta value for correct interpretation).

Thank you for any guidance.

In addition, are there plans to update the eQTL data to v7?

Best,

Andrew



_______________________________________________
Dev mailing list    Dev at ensembl.org
Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20180220/8701a83a/attachment.html>