Tools

PGC members have built tools with which to see PGC results in genomic context: Ricopili (thanks to Stephan Ripke and Brett Thomas) and LdOOKUP (thanks to Shaun Purcell).

Ricopili

Published PGC results can be viewed using ”ricopili," a web site that generates high-resolution images of PGC results. This web resource takes as input a gene name or genomic region, and produces a plot of PGC findings in genomic context. Thanks to Stephan Ripke and Brett Thomas of the Broad Institute. 

Stephan Ripke and Raymond Walters presented on the ricopili pipeline at the World Congress of Psychiatric Genetics (WCPG) 2015 Education Day. They have made their PowerPoint presentation available here for review.

Introduction

Preimputation: QC Module

Prinicipal Component Analysis

Imputation

Postimputation: Analysis

Example output from ricopili, MHC region in schizophrenia and CACNA1C in bipolar disorder.

schizophreniaThumb bipolarThumb
 

LdOOKUP

Published PGC results can also be viewed by "LdOOKUP," a web-based platform that allows users to view GWAS summary statistics as "LD (linkage disequilibrium) aware". Thanks to Shaun Purcell of the Icahn School of Medicine at Mount Sinai.