[ensembl-dev] Change in SIFT and PolyPhen score

[Wallace Ko]

Hi Sarah,

Thanks for your explanation.
Does it mean that SIFT and PolyPhen2 scores for RefSeq transcript for
GRCh37 are now also calculated (instead of mapping from Ensembl transcript)
but at a longer update interval?

Best,
Wallace


On Thu, Jan 3, 2019 at 1:09 AM Sarah Hunt <seh at ebi.ac.uk> wrote:

>
> Hi Wallace,
>
> Apologies for the partial response.
>
> Prior to release 90, we did not calculate SIFT and PolyPhen2 scores for
> RefSeq transcripts, though they were available for those with translations
> identical to an Ensembl transcript. Although the GRCh37 transcript sets
> have been frozen for some time, we update our GRCh37 variation data roughly
> annually, and results from the analysis of new Ensembl GRCh38 translations
> would be made available then.
>
> The difference in SIFT results - the change from no data to a prediction
> -  will be due to results for a transcript matching NM_000540.2 becoming
> available in release 88.
>
> We re-ran our PolyPhen pipeline for e!90 when we noticed slightly lower
> missingness rates after a change of hardware. We suspected changes in the
> cluster set up led to less high-memory alignment failures, but were not in
> a position to test this.
>
> We now routinely calculate SIFT and PolyPhen2 scores for RefSeq
> transcripts for our GRCh38 releases, which happen roughly quarterly. Due to
> the scheduling of when RefSeq transcript data becomes available in our
> release process, these scores are available in VEP the release after the
> transcripts are available.
>
> Best wishes,
>
> Sarah
>
> On 28/12/2018 11:12, Wallace Ko wrote:
>
> Hello,
>
> For the variant chr19:g.39075695C>T, the SIFT and PolyPhen score are
> changed in recent versions of VEP.
>
> VEP HGVSc SIFT PolyPhen
> 87 NM_000540.2:c.14759C>T - unknown(0)
> 88 NM_000540.2:c.14759C>T deleterious(0) unknown(0)
> 89 NM_000540.2:c.14759C>T deleterious(0) unknown(0)
> 90 NM_000540.2:c.14759C>T deleterious(0) probably_damaging(0.998)
>
> The above table shows that for NM_000540.2:c.14759C>T, SIFT is changed
> from  '-' to 'deleterious(0)' since VEP 88 and PolyPhen is changed from
> 'unknown(0)' to 'probably_damaging(0.998)'  since VEP 90.
>
> There is no change in software version of SIFT (sift5.2.2) and PolyPhen
> (2.2.2) in these versions of VEP, so I wonder what causes to the change in
> the prediction scores.
>
> Thank you.
>
> Regards,
> Wallace Ko
>
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