[GET-dev] Autoscoring

[Alexander Wait Zaranek]

On Thu, May 20, 2010 at 2:20 PM, Madeleine Price Ball <meprice at gmail.com> wrote:
> The current plan is to have an autoscoring tool that it produces up to
> 6 points for a variant. Although we thought we'd initialize the
> scoring on the GET-Evidence pages themselves, I think (at least at the
> moment) we should not plan on this -- but we still want to generate a
> score within the system associated with the variant. We can use that
> score to sort variants that have insufficient evaluation for further
> attention.
>
How about putting the autoscore into the "Other in silico analyses"
section?  The GET-Evidence dump should also have an autoscore column.

> The plan:
>
> Autoscoring is split into three sections: computational,
> variant-specific, and gene-specific, each 2 points for a max of 6
> points.
>
> Computational (max of 2 points):
> If an non-synonymous substitution:
> +1 for NBLOSUM >= 3,
> another +1 (+2 total) if NBLOSUM = 10 (a nonsense mutation)
> For all variants:
> +1 if within 1 base of a splice site
> (Trait-o-matic has splicing data, presumably it could spot these?)
> Indels:
> +1 for indel in coding region
> another +1 (+2 total) if causes a frameshift (not a multiple of 3 in
> coding region)
>
> Variant-specific lists (max of 2 points):
> +2 if in OMIM
> +1 if in PharmGKB
> +1 if in HuGENet
> another +1 (+2 total) if HuGENet's OR >= 1.5
>
> Gene-specific lists (max of 2 points):
> +1 if in GeneTests
> another +1 (+2 total) if in a GeneReviews gene
>
Sounds great!

Thanks for summarizing,
Sasha