[ensembl-dev] Clinical Applications of SIFT/PolyPhen score(s)

Jamie Allen jma at ebi.ac.uk
Thu May 5 16:53:30 BST 2022

>> 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
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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.

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