Format of genomic data in the ClinVar widget

Feature requests Platform feature requests
,
1

Good day Open Targets!

I am seeing that ClinVar widget genomic data has been converted from HGVS to some other format rather than HGVS format. The display of large insertions in columns are problematic in this kind of format.

ClinVar
ClinVar2506×1064 402 KB

Is there a plan to express genomic data in HGVS format in any upcoming new data releases? What was the reason not to use HGVS?

Thank you very much in advance for your help.

This question was sent to the Open Targets helpdesk and has been posted here so that the answer can benefit the whole Community.

2

Hi @wintercl, and welcome to the Open Targets Community! :tada:

Thank you for your feedback. The information in the ClinVar widget has never been in HGVS format, but there are ongoing discussions in the team about the best format to use to best represent possible mutations. We’ll keep you posted!

3

Hi @wintercl, until this day we have been importing SNPs and small indels from ClinVar exclusively. The consideration behind identify variants by chromosome_position_ref_alt was to increase consistency between the Platform and the Genetics Portal.

Currently, we are in the process of ingesting structural variants as disease/target evidence from ClinVar, for which (as you have pointed out) the above annotation is not suitable. To accommodate the requirements of the new variant set, we will provide the HGVS identifiers as well.

4

Thank you dsuveges! Will you incorporate this soon? Will you broadly apply the HGVS identifiers to SNVs etc, in addition to the structural variants of the ClinVar ingest?

Cindy

5

Yes, once the HGVS is available, it will be there for all variants not only for structural variants. We are aiming to get this feature ready with the 22.04 release, however this timeline depends on our data providers as well.

1 Like
6

Hi @wintercl!

Our latest update is out today, and among the new features is the inclusion of HGVS notation. :partying_face:

Find our more on our blog: Open Targets Platform 22.04 has been released!

7

Whoohoo!! This is great news:). Thanks so much for updating me, Helene:). Congratulations on your latest release!

Have a wonderful day!

Cindy

1 Like