Re: [genome-www] INFORMATION REGARDING HOTSPOT MUTATION

[Maximilian Haeussler]

Hi,

in tumors or the germline?

best

Max

On Wed, Jul 3, 2024 at 6:43 AM Shrinka Sen <shrinka....@gmail.com> wrote:

Hello

           How can I know from UCSC that exons or introns of a gene have hotspot mutation? I am interested in Human SERPING1 gene.

Waiting for your reply

Thanks, and Regards

Shrinka Sen

Project Scientist

CDFD, Hyderabad, India

[Maximilian Haeussler]

Hi Shrinka,

we're a software group that writes a genome browser interface, we're not experts in clinical diagnostics. It would be best to talk to someone who knows more about diagnostics than we do. We can add data if you tell us the database, but it's hard for us to suggest a database for you to use in diagnostics, for a particular gene.

 

ClinGen VCEPs contain hotspot information, but I cannot find a VCEP for the SERPING1 gene, there is a working group (who you could reach out to), but no guidelines yet:

https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_bb571a69-47a6-4e28-a837-b9df492526c9-2022-12-15T170000.000Z?page=1&size=25&search=

A quick pubmed and scholar search finds papers who describe the SERPING1 hotspots, e.g. around intron 4, due to the Alus. I cannot say more, reading these papers is outside of what this email list can provide.

You can filter our ClinVar track to show only pathogenic variants and put it into coverage density mode and then look for hotspots, I did that in the following "session" link:

https://genome.ucsc.edu/s/Max/serping1PathogenicDensity

There is a cancer hotspots database at https://www.cancerhotspots.org/#/home, I converted that a while ago and put it onto the genome browser, and then no one I asked was interested in this track, but feel free to have a look:

https://genome.ucsc.edu/s/Max/hotspots

I'm curious if there is another database with hotspots, if you find one, please don't hesitate to let us know, I know this question has come up a few times, but so far we have not found a systematic way where someone curated hotspots in genes. 

Max

On Wed, Jul 3, 2024 at 2:03 PM Shrinka Sen <shrinka....@gmail.com> wrote:

Yes, both. Sorry I missed. I mean germline and somatic, both.