[GET-dev] Autoscores + Counsyl variants

[Abraham Rosenbaum]

To help in troubleshooting:
CFTR Ser1255Stop should have 6 stars (stop codon, OMIM, GeneReviews).
Some of the ACADM genes have 0 stars; this gene has a Genetests entry,
is available for testing and is present in OMIM.
According to the latest download we have >80,000 nsSNPs in our
database (we should emphasize this point) but the variant_flat does
not produce a list of splice variants or all synonymous entries. I
think that it would be a good idea to get this data so that we can
further de-emphasize our reliance on exons.
-Abraham

On Fri, May 21, 2010 at 8:53 AM, Madeleine Price Ball <meprice at gmail.com> wrote:
> I've uploaded a new copy of the counsyl variants list, there were some
> ^M's in there, invisible to us when making the google spreadsheet.
> http://mad.printf.net/counsyl_variants.csv
>
> I guess LAMB3-R635X should have at least 5 points?
> 2 for nonsense mutation
> 2 for being in OMIM
> 1 for being a GeneTests testable gene
>
> I don't know if we should worry about how "lumpy" the database data
> is. Since much of the database is imported from OMIM we expect it to
> have a lot of 2's -- the profile for an individual will look
> different. Here's the list for PGP1:
> http://mad.printf.net/PGP1_nsSNPs.csv
>
> It's strange for the counsyl list to have any 0's, Sasha pointed out
> yesterday that almost by definition these are genes that "have testing
> available". Maybe the names aren't matching, or maybe Counsyl tests
> them but they don't have per-gene testing available as listed on
> GeneTests.
>
> Should we worry about how "lumpy" the Counsyl list looks? Sasha--any
> luck on getting an HCM list from Heidi?
>
>     - Madeleine
>
> On Fri, May 21, 2010 at 12:41 AM, Tom Clegg
> <tom at scalablecomputingexperts.com> wrote:
>> Autoscores for all of the Counsyl variants are attached.
>>
>> There were a few lines that look like they were corrupted by some
>> translation process (I ignored them):
>>
>> ",nsSNP8S
>> ",nsSNP58Q
>> ",nsSNP52W
>>
>> Distribution of autoscores for counsyl variants:  (select
>> autoscore,count(variant_id) from counsyl_autoscore group by autoscore)
>>
>> +-----------+-------------------+
>> | autoscore | count(variant_id) |
>> +-----------+-------------------+
>> | 0         |                33 |
>> | 1         |                 4 |
>> | 2         |               119 |
>> | 3         |                 4 |
>> | 4         |               129 |
>> +-----------+-------------------+
>>
>> Distribution of autoscores for all variants:  (cut -f40 latest-flat.tsv |
>> tail -n +2 | sort -n | uniq -c)
>>   62304 0
>>    3993 1
>>   10473 2
>>    1512 3
>>    3378 4
>> Presumably *some* variants should be getting scores >4 -- I'll have to look
>> at this tomorrow (examples welcome).
>> The "in genetests?" contribution to the above autoscores is based on whether
>> the gene is *listed* in genetests, not whether its record indicates "test
>> available"... contrary to what I told Madeleine today.  I've fixed that just
>> now, and the scores are being recalculated.  (64 of the 836 genes in
>> genetests are "no test available")
>> Tom
>>
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