Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2

Ivan Adzhubei1, Daniel M. Jordan2, Shamil R. Sunyaev1

1 Division of Genetics, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, 2 Program in Biophysics, Harvard University, Cambridge, Massachusetts
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 7.20
DOI:  10.1002/0471142905.hg0720s76
Online Posting Date:  January, 2013
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Abstract

PolyPhen‐2 (Polymorphism Phenotyping v2), available as software and via a Web server, predicts the possible impact of amino acid substitutions on the stability and function of human proteins using structural and comparative evolutionary considerations. It performs functional annotation of single‐nucleotide polymorphisms (SNPs), maps coding SNPs to gene transcripts, extracts protein sequence annotations and structural attributes, and builds conservation profiles. It then estimates the probability of the missense mutation being damaging based on a combination of all these properties. PolyPhen‐2 features include a high‐quality multiple protein sequence alignment pipeline and a prediction method employing machine‐learning classification. The software also integrates the UCSC Genome Browser's human genome annotations and MultiZ multiple alignments of vertebrate genomes with the human genome. PolyPhen‐2 is capable of analyzing large volumes of data produced by next‐generation sequencing projects, thanks to built‐in support for high‐performance computing environments like Grid Engine and Platform LSF. Curr. Protoc. Hum. Genet. 76:7.20.1‐7.20.41. © 2013 by John Wiley & Sons, Inc.

Keywords: human genetic variation; single‐nucleotide polymorphism (SNP); mutation effect prediction; computational biology; PolyPhen‐2

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Predicting the Effect of a Single‐Residue Substitution on Protein Structure and Function Using the PolyPhen‐2 Web Server
  • Basic Protocol 2: Analyzing a Large Number of SNPs in a Batch Mode Using the PolyPhen‐2 Web Server
  • Basic Protocol 3: Quick Search in a Database of Precomputed Predictions
  • Support Protocol 1: Checking the Status of Your Query with the Grid Gateway Interface
  • Alternate Protocol 1: Automated Batch Submission
  • Alternate Protocol 2: Installing PolyPhen‐2 Standalone Software
  • Alternate Protocol 3: Using PolyPhen‐2 Standalone Software
  • Support Protocol 2: Updating Built‐In Databases
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Predicting the Effect of a Single‐Residue Substitution on Protein Structure and Function Using the PolyPhen‐2 Web Server

  Materials
  • An up‐to‐date Web browser, such as Firefox, Internet Explorer, or Safari. JavaScript support and cookies should be enabled in the browser configuration; the Java browser plug‐in is required for the protein 3‐D structure viewer to function.

Basic Protocol 2: Analyzing a Large Number of SNPs in a Batch Mode Using the PolyPhen‐2 Web Server

  Materials
  • An up‐to‐date Web browser, such as Firefox, Internet Explorer, or Safari. Cookies should be enabled in the browser configuration.

Basic Protocol 3: Quick Search in a Database of Precomputed Predictions

  Materials
  • An up‐to‐date Web browser, such as Firefox, Internet Explorer, or Safari. JavaScript support should be enabled in the browser configuration.

Support Protocol 1: Checking the Status of Your Query with the Grid Gateway Interface

  Materials
  • An up‐to‐date Web browser, such as Firefox, Internet Explorer, or Safari. Cookies should be enabled in the browser configuration.

Alternate Protocol 1: Automated Batch Submission

  Materials
  • A text editor and curl command‐line utility (http://curl.haxx.se/)

Alternate Protocol 2: Installing PolyPhen‐2 Standalone Software

  Materials
  • A Linux computer with the PolyPhen‐2 standalone software installed as described in protocol 6

Alternate Protocol 3: Using PolyPhen‐2 Standalone Software

  Materials
  • A Linux computer with the PolyPhen‐2 standalone software installed as described in protocol 6 and a sufficiently fast Internet connection. Steps 5 and 6 require Blat tools installed (see protocol 6, step 9) and involve substantial amounts of calculation. In order for these steps to complete within a reasonable time, it is recommended to use a powerful multi‐CPU workstation or a Linux cluster.
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Figures

Videos

Literature Cited

Literature Cited
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