[ensembl-dev] Dev Digest, Vol 39, Issue 2

[Jun Dai]

Hi Jamie,

Thank you so much for the information.

Best,
Jun

>
> Date: Thu, 5 May 2022 16:53:30 +0100
> From: Jamie Allen <jma at ebi.ac.uk>
> To: dev at ensembl.org
> Subject: Re: [ensembl-dev] Clinical Applications of SIFT/PolyPhen
>         score(s)
> Message-ID: <5F672611-708B-4F5C-AAD7-A2AA82DD361A at ebi.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> >>
> >> From: Jun Dai <jun.d at ayassbioscience.com <mailto:
> jun.d at ayassbioscience.com>>
> >> Subject: Re: [ensembl-dev] Clinical Applications of SIFT/PolyPhen
> score(s)
> >> Date: 4 May 2022 at 20:37:56 BST
> >> To: dev at ensembl.org <mailto:dev at ensembl.org>
> >> Reply-To: Ensembl developers list <dev at ensembl.org <mailto:
> dev at ensembl.org>>
> >>
> >> Hi All,
> >>
> >> Greetings! I am working on a cancer predicting system based on genetic
> testing results  (for example, a few mutated genes detected, such as BRCA2
> deletion, PTEN mutation, etc.). Specifically, I want to provide prognostic
> information regarding the detected genetic alterations. I noticed SIFT or
> PolyPhen among many others could provide information about each of the
> genetic alterations. Does anyone have any experience to predict the
> prognostics or something similar, for example, the correlation or causal
> relationship with invasion or metastasis .
> >>
> >> Thank you!
> >> JD
> >> _______________________________________________
> >> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
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> >> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
> >
> >
>
>
> Hi Jun Dai,
>
> Approaches that groups often take when assessing the potential correlation
> of missense variants are usually through some form of burden testing across
> a gene of interest in large numbers of samples where case / control status
> is known. There are quite a few papers out there on the topic. While
> PolyPhen and SIFT are good missense scoring tools, there are many newer
> scoring tools (most of which are usable through VEP plugins -
> https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html <
> https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html>)
> which may be provide better results.
>
> Cheers,
> Jamie.
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> End of Dev Digest, Vol 39, Issue 2
> **********************************
>


-- 
Jun Dai, Ph.D
*Bioinformatics Scientist*
*Ayass Bioscience, LLC*
*8501 Wade Blvd, Building 9*
*Frisco, TX, 75034*
*jun.d at ayassbioscience.com* <jin.z at ayassbioscience.com>
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