Change gene symbol for ENSG00000286219

[Caustint]

Describe the bug seqr lists the gene symbol for ENSG00000286219 as AC242843.1, but the correct symbol should be NOTCH2NLC. AC242843.1 doesn't seem to be listed as an alias in any of the databases I've checked (HGNC, ensembl, NCBI). This is a disease-associated gene in which we expect to return a pathogenic variant, so it would be nice to have the correct symbol.

Link to page(s) where bug is occurring https://seqr.broadinstitute.org/summary_data/gene_info/ENSG00000286219

Scope of the bug

Screenshots

[hanars]

This is the gene name for that ensembl ID in the gencode 31 release, which is the latest gencode release seqr has, so its not really a bug. Do you want me to update seqr to a more recent gencode release?

[Caustint]

Ah, got it. I assume upgrading gencode releases is a non-trivial amount of work. Is it something you do at a regular cadence?

Christina Austin-Tse, PhD, FACMG Analysis Team Lead, Rare Disease Group, Broad Institute of MIT and Harvard Clinical Molecular Geneticist, Center for Genomic Medicine, Massachusetts General Hospital Instructor in Pathology, Harvard Medical School Pronouns: She/her

On Tue, Nov 16, 2021 at 4:13 PM hanars @.***> wrote:

This is the gene name for that ensembl ID in the gencode 31 release, which is the latest gencode release seqr has, so its not really a bug. Do you want me to update seqr to a more recent gencode release?

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[hanars]

It's not trivial, especially because every time I've done it I immediately get a bunch of complaints that variants are now being listed in the "wrong" gene - there's always at least a couple discovery variants that change name. That said, it is objectively necessary to periodically update. We don't have any sort of regular cadence for it, and it looks like we haven't updated since 2019 so we are probably overdue. So I think this is a call you and Anne need to make

[Caustint]

Got it, thanks for the context! I will discuss with Anne and get back to you.

On Wed, Nov 17, 2021 at 10:37 AM hanars @.***> wrote:

It's not trivial, especially because every time I've done it I immediately get a bunch of complaints that variants are now being listed in the "wrong" gene - there's always at least a couple discovery variants that change name. That said, it is objectively necessary to periodically update. We don't have any sort of regular cadence for it, and it looks like we haven't updated since 2019 so we are probably overdue. So I think this is a call you and Anne need to make

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/seqr/issues/2301#issuecomment-971699080, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQEFBFI7MLPVJGFCHXGZN5TUMPD4VANCNFSM5IFHKUFQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[hanars]

@Caustint did we decide if we want to update gencode in seqr?

[Caustint]

Sorry for not following up! Anne recommended waiting for the next release of gnomAD and then matching what they use.

Christina Austin-Tse, PhD, FACMG Analysis Team Lead, Center for Mendelian Genomics, Broad Institute of MIT and Harvard Clinical Molecular Geneticist, Center for Genomic Medicine, Massachusetts General Hospital Instructor in Pathology, Harvard Medical School Pronouns: She/her

On Wed, Jan 12, 2022 at 4:37 PM hanars @.***> wrote:

@Caustint https://github.com/Caustint did we decide if we want to update gencode in seqr?

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[lynnpais]

Closing this ticket as it will be done with the next gencode release/ gnomAD update