Duplication of SNPs when uploading template in Curation app for GCST90085780

[ar-ibrahim]

SNP entries are duplicated when uploading template in Curation app. This consistently occurs even when using a new template for the upload.

https://www.ebi.ac.uk/gwas/curation/studies/95477043/associations

[ljwh2]

@ar-ibrahim does this still need attention or did you manage to resolve it?

[ar-ibrahim]

I tried uploading a new template. I also tried entering the association manually. It's still duplicated every time. I checked the other studies in this PMID. This seems to happen only with this study. I tried to manually edit the row after uploading the association but the page keeps timing out.

Would it be possible to delete this study and make a new submission?

[ar-ibrahim]

Might be a mapping issue. L.H. suggested that it might be an out-of-date variant.

[ljwh2]

Seems this particular variant produces duplicate mappings. Noting this is a variant ID that was merged a long time ago, although this doesn't normally cause a problem as far as I know https://www.ncbi.nlm.nih.gov/snp/rs115094736 @sprintell could you please check what is going on in the mapping pipeline for this variant?

[eks-ebi]

This issue also affected a second example: rs199679345

[eks-ebi]

It seems that the variants that cause problems also have alternative rsIDs that point to the same variant.

These appear like this in the GWAS Catalog search results:

Could this be somehow causing the variant to be retrieved twice?

[ljwh2]

Note, this study is now published and available in production, with the SNP duplicated