[ensembl-dev] Gene VARS mysteriously moved from CHR_HSCHR6_MHC_APD_CTG1 to HSCHR6_MHC_APD_CTG1 in release 110

[Natalie Willhoft]

Hi Hervé,

Thanks for your email.

In previous releases, genes on patches were projected from their scaffold sequences (e.g. HSCHR6_MHC_APD_CTG1) and stored onto chromosome-based sequences (e.g. CHR_HSCHR6_MHC_APD_CTG1). Therefore in this case, the gene(s) on this example patch had been projected onto a sequence with coordinate positions in the context of human chromosome 6. Historically, the Ensembl Core Perl API was built to support genes on patches based on these chromosome-based sequences, which were ultimately used to visualise a given patch on the Ensembl Browser with all its associated features.

As you mentioned, this has changed as of Release 110 so that we now keep the genes (and their associated features) on their original scaffold patch sequence. I should also clarify that this work only relates to human.

Please do let us know if you have any more questions on this topic.

Thanks and best wishes,
Natalie

Natalie Willhöft (Dawson)
Ensembl Infrastructure Team
EMBL-EBI 
nwillhoft at ebi.ac.uk

> On 23 Aug 2023, at 06:30, Hervé Pagès <hpages.on.github at gmail.com> wrote:
> 
> Hi,
> 
> Looks like starting with Ensembl 110 (now based on GRCh38.p14), human gene ENSG00000231116 (VARS) is now reported to be located on sequence HSCHR6_MHC_APD_CTG1 after being reported to be on sequence CHR_HSCHR6_MHC_APD_CTG1 for many years (at least since Ensembl release 85, based on GRCh38.p7).
> 
> Anybody knows what sequence CHR_HSCHR6_MHC_APD_CTG1 was actually supposed to be? Was never a valid GRCh38 sequence name. At least the new sequence name belongs to GRCh38.
> 
> Thanks,
> 
> H.
> 
> -- 
> Hervé Pagès
> 
> Bioconductor Core Team
> hpages.on.github at gmail.com <mailto:hpages.on.github at gmail.com>
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