GridQTL : A Grid Portal for QTL Mapping of Compute Intensive Datasets - PowerPoint PPT Presentation

GridQTL : A Grid Portal for QTL Mapping of Compute Intensive Datasets. John Allen 1 , Jean-Alain Grunchec

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GridQTL: A Grid Portal for QTL Mapping of Compute Intensive Datasets

John Allen1, Jean-Alain Grunchec1, Jules Hernandez1, Wenhua Wei3, Ian M.S. White1, Burak Karacaören2, Suzanne Rowe2, Dirk-Jan de Koning2, Chris S. Haley3 and Sara A. Knott1

1Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland.

2The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, Midlothian EH25 9PS, Scotland.

3MRC Human Genetics Unit, Western General Hospital, Edinburgh, EH4 2XU Scotland

www.gridqtl.org.uk

  • Standard analyses
  • Based on QTL Express routines:
    • F2/BC crosses (inbred, outbred, large full-sib)
    • Half-sib populations
    • Sib pair analyses
    • Power calculations
  • All models can use HPC if required
  • Aims
  • Bring QTL analyses to the lab bench
  • Provide free web based QTL analyses for outbred species
  • Accommodate advanced genetic models
  • Exploit high performance computing (HPC) to facilitate increased complexity
  • Currently: > 600 users; > 30,000 analyses
  • LDLA
  • Linkage and linkage disequilibrium analyses in general pedigrees
  • Chromosomes analysed across UK HPC
  • 83 users since March, >10.000 analyses and 22,000 hours of analyses
  • Epistasis
  • Two way interactions between QTL in F2 populations.
  • Also useful for analyzing large numbers of traits for single QTL.

Figure 1. Example of LDLA results from GridQTL

Figure 2. Example of epistasis results from GridQTL

  • Ongoing and future work
  • Increased number of markers and traits
  • Integration into workflows
    • MIQAS, TargetQTL, eQTLexplorer etc.
  • NOIA model (with Carl Nettelblad and Jose Alvarez-Castro)

References

Hernández-Sánchez et al. 2009. Bioinformatics 25: 1377-1383.

Grunchec et al. ICCGS 2009, Oslo, Norway ; 600-607.

Grunchec et al. Submitted

Seaton et al. 2006 WCGALP, ISBN: 85-60088-01-6

Wei et al. 2010 Heredity 104:401-409

Wei et al. 2010 Anim. Genet. in press

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