High Performance QTL Analysis Via The Grid

BBSRC

An Integrative Biology Project

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Project Overview

The mapping of Quantitative Trait Loci (QTL) is the first step towards the identification of genes and causal polymorphisms that affect traits of importance in human medicine and agriculture. Fast, efficient and robust methods to map QTL have been developed by groups at The Institute of Evolutionary Biology (IEB), Edinburgh University and The Roslin Institute (RI), Edinburgh and can be deployed in QTLExpress, the first publicly available Web-based application that can perform QTL mapping on a variety of population types.

GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models.

Towards a More Predictive Biology.

These developments will provide an essential core component of a future integrated biological system incorporating genetic, phenotypic, transcription and comparative information with the goal being to allow prediction from gene sequence to consequence.

Project Partners

University of Edinburgh Institute of Evolutionary Biology (IEB), Edinburgh University
     
     
NeSC National e-Science Centre (NeSC), Edinburgh
     
     
Roslin Institute Roslin Institute (RI), Edinburgh

Project Goals

GridQTL's goal is to develop, test, apply and implement a grid-based platform for robust and fast multiple trait mapping of multiple Quantitative Trait Loci in simple and complex pedigrees. A detailed list of these developments, with the responsible project partner highlighted, follows:

  • Evolution of QTLExpress from a Web Application to a Grid portal based system. (NeSC & IEB).
  • Development of QTL mapping methods to enable simultaneous analysis of multiple traits and pleiotropic models in simple and complex traits. (IEB).
  • Development of methods to analyse the vast numbers of traits and genetic data made available from expression-QTL (eQTL) data. (IEB).
  • Development of methods and algorithms to detect two-QTL and higher order epistatic interactions in both simple and complex pedigrees. (RI).
  • Investigatation of fine-mapping of QTLs by Linkage Disequilibrium (LD) analysis. (RI).
  • Implementation of the new QTL models into the GridQTL portal. (NeSC & IEB).
  • Make GridQTL accessible as an analysis component of an Integrative Biology workflow system. (NeSC & IEB).
  • Disseminatation of the GridQTL applications and algorithms and expansion of the QTL user-base. (IEB, NeSC & RI).

Current Status

GridQTL Portal

Delivery of the above services to the end users needs to be robust but simple since these users may be inexperienced in grid technology. GridQTL therefore uses a portal as its user interface with the choice of portal environment being that offered by GridSphere, largely on grounds of versatility and robustness. The portal allows users to configure their individual workspaces and their settings are stored between sessions. Delivery of the applications is through purpose-written portlets which allows for easy and centralised delivery of applications.

Citation

 Users may publish any text or graphics output from GridQTL in original or adapted form. It is expected only that such material be presented or attributed in such a way that it is reasonably apparent that GridQTL was the original source. The proper citations are:

LDLA

Hernández-Sánchez J., Grunchec J.-A. and Knott S. Bioinformatics 2009, 25(11):1377-1383; doi:10.1093/bioinformatics/btp171.

A web application to perform linkage disequilibrium and linkage analyses on a computational grid.

Haplotyping

Hernandez J. & Knott S. (2009) BMC Proceedings/2009, 3(Suppl 1):S7

Haplotyping via minimum recombinant paradigm.

GridQTL

Seaton G., Hernandez J., Grunchec J.A., White I., Allen J., De Koning D.J., Wei W., Berry D., Haley C., Knott S. (2006) GridQTL: A Grid Portal for QTL Mapping of Compute Intensive Datasets. Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, August 13-18, 2006. Belo Horizonte, Brazil.

GridQTL: A Grid Portal for QTL Mapping of Compute Intensive Datasets ISBN: 85-60088-01-6

Disclaimer

 Although every effort is made to ensure the correct functioning of the software at this site users use it at their own risk. GridQTL members and their respective institutions can not be held responsible for any problems resulting or consequential losses arising from the use of this software.

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