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

[Hervé Pagès]

Thanks Natalie for the explanation.

This is a BIG change that has the potential to break or hurt the 
reproducibility of lots of code that makes use of these annotations. Was 
this announced somehow or is there a document somewhere on the Ensembl 
website that describes these changes? Sorry in advance if I missed it.

Thanks again,

H.

On 8/24/23 01:57, Natalie Willhoft wrote:
> 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
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>
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github at gmail.com
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