Genetics and Bioinformatics

2004-2005

Left to right: Simon Foote (joint Division Head), Terry Speed (joint Division Head), Melanie Bahlo, Tom Brodnicki, Hamish Scott & Gordon Smyth.

• Research Focus
• Overview
• Laboratories
  • Bioinformatics Group
  • Scott Lab
• Email the Genetics & Bioinformatics Division

Research Focus

• Genetics of human diseases
• Mapping disease genes
• Bioinformatics for gene discovery

Overview

This year could be described as the “Year of the SNP” for the Genetics and Bioinformatics Division. Single Nucleotide Polymorphisms, (abbreviated SNPs) are nucleotide variants, usually biallelic, at well-defined positions in the genome. It has been estimated that there is about one SNP every 100-300 base pairs in humans, and the situation is expected to be similar between inbred strains of mice. To date over 2 million human SNPs have been characterised, with more being found every day. They are now the marker of choice for genetic and association mapping of disease genes, both primary aims of this Division, and they are becoming increasingly widely used for other tasks, such as chromosomal copy number determination. We have used a number of techniques for our SNP genotyping, including a novel one developed by Genera Pty Ltd, a WEHI start-up company, and the Affymetrix SNP chip, which permits the genotyping of over 50,000 SNPs in one assay. Perhaps the most significant use of SNPs in the Division has been the genotyping done by our collaborators at GlaxoSmithKline of most of our original Tasmanian Multiple Sclerosis (MS) study participants and a further 888 Victorians, at over 850 SNPs concentrated in the two regions which showed most promise of harboring MS susceptibility genes. Other members of the Division have been developing techniques for the in silico mapping of disease-related genes using soon to be available genome-wide SNP data on 50 inbred strains of mice, while yet others have used SNPs for the homozygosity mapping of rare diseases in small numbers of inbred families. More details on these projects can be found in the following pages.

The other theme which comes out strongly in this year’s report is the close collaborations that exist between geneticists and the bioinformaticians in our Division. Most of our major genetics research projects have substantial bioinformatic components, which is in line with experience elsewhere in the world.