eye eQTL

[Guoqiang Zhang]

Dear Kyoko,

Is it possible to include eye eQTL in SNP2GENE searches?

https://gtexportal.org/home/datasets -> external datasets -> Eye Genotype Expression (EyeGEx) Database

Thanks!

Best,

Guoqiang

[Kyoko Watanabe]

Hi Guoqiang,

Sure I'll make sure to include in the next release (planning end of May).

Thank you for the information!

Best,

Kyoko

[Guoqiang Zhang]

Hi Kyoko,

Is the GTex eye eQTL available in the FUMA May 2019 release? I couldn't find it in the eQTL mapping Tissue Types list.

Thanks.

Best,

Guoqiang 

[Kyoko Watanabe]

Hi Guoqiang,

Sorry I was going to tell you sooner.

We tried to include eyeGEx but something was wrong about the SNP position.

They reported GRCh38 but when I converted to hg19, only few positions were converted.

We did some manual check and there were couple of SNPs that have position doesn't match with the dbSNP as well.

We were not able to figure out what's exactly going on so excluded from the current release.

Do you know more about this eQTL data?

Could you maybe let me know if you know anything about the eQTL position?

Best,

Kyoko

[Guoqiang Zhang]

Hi Kyoko,

Thank you. Sorry I don't know either. Maybe write to the author?

Thanks.

Best,

Guoqiang

[Guoqiang Zhang]

Hi Kyoko,

I had a better look at the eQTL file GTex website provided (Retina.nominal.eQTLs.with_thresholds.tar). 

Seems that columns 9, 10, 11 agree with the GRCh38 (hg19) coordinates in dbsnp. Although column 9,10,11 don't agree with column 8. 

So we can just use column 9, 10 and 11?

Could you have a look?

Thank you very much.

Best,

Guoqiang

[Kyoko Watanabe]

Well that's what we did.

Looks mostly fine but liftOver only convert less than half of input.

I can't quite figure out why they are not mapping to hg19.

If you look into more SNPs, you actually see SNPs on different location (on hg38) than what reported in dbSNP, and not sure why they mismatch...

Best,

Kyoko

[Guoqiang Zhang]

It appears that most if not all the mismatches are the ones that are not simple SNP but indels. I have reached out to the author and see if they can fix this.

Thanks.

Best,

Guoqiang

[Nik Tz]

Hi, thanks for the great work on FUMA.

Just wondering how this issue was resolved in the end? 

Were any changes needed to data shared on the EyeGex Ratnapriya 2019 Nat Genet paper?

Is there a new link to replace the 404 error on the website:

The file containing the cis-eQTLs can be downloaded from https://storage.googleapis.com/gtex_external_datasets/eyegex_data/single_tissue_eqtl_data/Retina.nominal.eQTLs.with_thresholds.tar
Many thanks, Nik

[Jiajun Xu]

Hi Nik,

I am currently facing the same challenge in downloading these files(404 error).  I’ve also tried the GTEx Portal website, where I couldn't find the download link.

I was wondering if you have managed to find a new link since your last post? 

Best regards,

Jiajun Xu