[ensembl-dev] DNV annotation problem?

[Will McLaren]

Dear Ken,

When you encode variants on the negative strand, the sequence should still
read 5' to 3', but on the negative strand the 5' end is the higher
coordinate. This can be a little confusing!

+ strand: 5' >> AC >> 3'
- strand: 3' << TG << 5'

This is what is causing the problem as the GT becomes TG which changes GTg
(V) to TGg (W).

so your encoding should be (in default VEP format):

7       140453136       140453137       GT/AA    -

or on the forward strand:

7       140453136       140453137       AC/TT    +

or, in VCF:

7       140453136       .       AC      TT

For reference the same variant is found in COSMIC:

http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=7:140452636-140453637;v=COSM473;vdb=variation;vf=68925947

Regards

Will McLaren
Ensembl Variation


On 16 January 2014 21:28, Chen,Ken <KChen3 at mdanderson.org> wrote:

> Dear VEP developers,
>
> First of all, thank you for offering this wonderful resource.  We really
> appreciate it.
> In our analysis, we found this DNV (hg19, negative strand) in BRAF
> 7       140453136       140453137       TG      AA
>
> The correct HGVS annotation should be BRAF.V600K
>
> However, VEP returned BRAF.W600K
>
> It is important for us to fix this problem but we analyze data from real
> patient.
> Please let us know how to do it.
> Thanks.
>
> -Ken
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