[ensembl-dev] Variation differences in NCBI vs Ensembl

[Oliver, Gavin]

That's perfect Will - more than anything I just needed a pointer as to the nature of these things and how to investigate them!

Best, 

Gavin

-----Original Message-----
From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will McLaren
Sent: 01 March 2011 11:05
To: Oliver, Gavin
Cc: dev
Subject: Re: [ensembl-dev] Variation differences in NCBI vs Ensembl

Hi Gavin,


On 1 March 2011 10:49, Oliver, Gavin <gavin.oliver at almacgroup.com> wrote:
> Hi all,
>
>
>
> Why would differences occur between NCBI and Ensembl in terms of variations
> existing for a transcript.
>
>
>
> For example NCBI sequence NM_006712 corresponds to Ensembl transcript
> ENST00000297532.
>
>
>
> When I retrieve related SNPs via NCBI and Ensembl separately the results are
> broadly similar however there are a few differences.
>
>
>
> For example NCBI shows rs1130560 but Ensembl does not.

This SNP has been failed by the Ensembl QC process, as you can see if
you search for the SNP identifier:

http://www.ensembl.org/Homo_sapiens/Variation/Summary?r=7:150773617-150774690;v=rs1130560;vdb=variation;vf=2124870

Failed SNPs do not appear by default; you can view them by searching
for their identifiers, or by turning on the "Failed variations" track
on the location view.

>
>
>
> Whereas Ensembl shows rs117650642 whereas NCBI does not.
>

I can't answer this - the dbSNP page shows a consequence for this SNP
and transcript:

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=117650642

You'd have to ask NCBI why it doesn't appear in the view you are using!

Thanks

Will McLaren
Ensembl Variation

>
>
> Looking at variations is pretty new to me so I'm just trying to gain an
> understanding of why these differences might arise and how I should deal
> with them.
>
>
>
> Thanks in advance,
>
>
>
> Gavin
>
>
>
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The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.

Almac Group (UK) Limited, registered no. NI061368.  Almac Sciences Limited, registered no. NI041550.  Almac Discovery Limited, registered no. NI046249.  Almac Pharma Services Limited, registered no. NI045055.  Almac Clinical Services Limited, registered no. NI041905.  Almac Clinical Technologies Limited, registered no. NI061202.  Almac Diagnostics Limited, registered no. NI043067.  All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK.  

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Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation.  More information on the Almac Group can be found on the Almac website: www.almacgroup.com