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VISG RESEARCH

VISG develops and applies new analytical methods and accompanying software to address challenges associated with large genotypic and sequence databases. Methods and software are released in the public domain for use by geneticists across a wide range of sectors and species. These methods are applicable to analysis of datasets generated in New Zealand health and primary sector-based research and were selected to complement international research activities.

Research funding was provided by the Ministry of Business Innovation and Employment (MBIE) from 2008 to 2013. This page describes some of the key research conducted by the Virtual Institute of Statistical Genetics during that time and provides contacts for further information.

VISG research falls within four main areas:

  • Efficient methods for estimating gene copy number variation (CNV) in next generation sequence data sets – both on a gene-specific and genome-wide basis. A read-depth based approach has been developed and implemented in software. Methods have been developed for human datasets and are being applied to agronomically important plant species. Contact: Michael.Black@otago.ac.nz or Tony.Merriman@otago.ac.nz
  • Bayesian multi-locus detection methods for quantitative trait loci detection (QTL) in bi-parental pedigrees in allopolyploids, including methods for unbiased estimates of QTL effect. Contact: Gail.Timmerman-Vaughan@plantandfood.co.nz
  • Developing a Galaxy-based analytical pipeline to detect signatures of selection in next generation (re)sequence data sets, and applying these to New Zealand-relevant datasets to identify candidate genes. Contact: Phillip.Wilcox@scionresearch.com
  • Bayesian methods for designing candidate gene and genome-wide association genetics experiments in human medical genetics and agricultural contexts.

Other VISG-funded research and related activities:

  • Development of Bayesian methods for predicting phenotype from large genotypic datasets. Contact: Phillip.Wilcox@scionresearch.com
  • Improvements in a Galaxy-based analytical pipeline to design high resolution melting (HRM) assays using next generation (re)sequence data to automate polymorphism discovery in silico and design HRM assays. This pipeline was initially developed by Plant and Food Research Ltd. researchers and has been successfully applied to design high resolution melting assays for a number of New Zealand-relevant species. Contact: John.McCallum@plantandfood.co.nz
  • Reviews of relevant areas to inform research priorities and to communicate important research to the wider New Zealand gene mapping research community. Reviews have included international progress and statistical issues regarding genomic selection and application of ‘omics’ technologies. Contact: Phillip.Wilcox@scionresearch.co.nz
  • Surveys of New Zealand-based end-user geneticists regarding analytical development needs. We have conducted surveys regarding future use of association genetics and skill needs in regard to applying methods to analyse large data sets typical of modern genetical genomics. Contact Phillip.Wilcox@scionresearch.co.nz
  • Training. VISG holds end user training courses. A course was held at Otago University in 2012 to update skills of geneticists in large data set manipulation and also to train end users in VISG-funded methods. Contact Phillip.Wilcox@scionresearch.co.nz
  • Communicating methods to end users via presentations at various conferences and workshops – for example, regular progress updates at the annual MapNet workshop to the New Zealand gene mapping research community and via New Zealand Genomics Ltd-provided training courses.

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