Presenter Powerpoint Presentations
Dr Paul Spellman - Lawrence Berkeley National Laboratory
Molecular Subtype Specific Responses to Anti-cancer Compounds in Breast Cancer
Prof Andrew Biankin - Garvan Institute of Medical Research
The Australian Pancreatic Cancer Genome Initiative
Assoc Prof Ian Campbell - Peter MacCallum Cancer Centre
Identification of breast cancer susceptibility genes using whole exome sequencing
Dr Logan Walker - Queensland Institute of Medical Research
The role of germ-line DNA copy number variation in familial breast cancer risk
Mr Aaron Stratham - Garvan Institute of Medical Research
High resolution DNA methylation epigenome sequencing of formalin-fixed paraffin embedded tissue
(FFPET) DNA identifies novel epigenetic markers in breast cancer
Dr Mark Corbett - SA Pathology
Discovery of mutations that cause epilepsy and intellectual disability using sequence enrichment and
next-generation sequencing
Mr Lam Son Nguyen - The University of Adelaide
Genome-wide identification of nonsense-mediated mRNA surveillance targets by RNA-SEQ and exon
array
Dr Leming Shi - National Centre for Toxicological Research
Genomics, Bioinformatics, and Personalized Medicine: The MicroArray Quality Control (MAQC) Project
Dr Mark Robinson - Walter & Eliza Hall Institute of Medical Research
Joint analysis of copy number and enrichment-based epigenomics sequencing data
Dr David Fung - University of New South Wales
Systems modelling of myocardial infarction in Mus musculus using microarray expression data
Assoc Prof Xiaole Shirley Liu - Dana-Farber Cancer Institute
Inferring transcription regulatory mechanism from nucleosome dynamics
Mr Matthew Young - Walter & Eliza Hall Institute of Medical Research
Using ChIP-seq to identify distinct and functionally correlated classes of PRC2 binding across genes in
mouse
Program at a glance
DOWNLOAD A COPY OF THE FINAL PROGRAM HERE
The 2010 AMATA Conference reserves the right to amend or alter any advertised details relating to dates, program and speakers if necessary and without notice, as a result of circumstances beyond their control. All attempts will be made to keep any changes to an absolute minimum.
Sponsored Workshops
The Friday workshops are now free of charge - if you have already paid to attend then you will receive a refund shortly. Please contact natalie@leishman-assocaites.com.au for more information.
Hotel Grand Chancellor
Friday 17 September 2010
2.00pm – 5.00pm
Workshops are limited to 30 participants each
Workshop 1
Sponsored by Australian Genome Research Facility (AGRF)
AGRF Bioinformatics . . . A key tool in enhancing your NGS output
- NGS Technologies, Project Design and Sample Preparation
- Bioinformatics applications for NG sequencing including different types of secondary analysis
- Special focus on data analysis for RNA-Seq and Transcriptomics
- Custom bioinformatics including:
- Trouble shooting
- Custom de-multiplexing for GS FLX
- Using file manipulation tools and BioPerl
- Real data examples from AGRF experiences
Workshop 2
Sponsored by Partek
Partek(R) Genomics Suite Next-Generation Sequencing (NGS) data analysis Workshop
In this workshop, we will present a brief overview of Partek(R) Genomics Suite capabilities for analyzing high-throughput sequencing data. Specific example applications will include RNA-seq analysis for whole transcriptome and ChIP-seq analysis for transcription factor binding. By following the step-by-step RNA-seq workflow, all known and novel RNAs can be visualized together with transcript information from public databases such as RefSeq or AceView. Estimation of differential expression, alternative splicing, and isoform abundances are calculated on known mRNAs. Coding SNPs can be discovered for allele specific expression identification. For ChIP-seq studies, we will detect enriched regions to discover de novo motif as well as search for known motifs. Partek can also overlap detected regions with genes to identify genes that are possible candidates for transcription factor regulation. Finally, sequence comparison across multiple samples will also be shown.
Workshop 3
Sponsored by
Illumina
Next Generation GWAS – Illumina’s Omni Roadmap for Rare Variant Discovery and Imputation
Presenters Name: Arjuna Kumarasuriyar – Illumina Product Marketing Manager South Asia Pacific
Derek Campbell – Illumina Senior Field Application Scientist, Australia and New Zealand
Building upon the HapMap Project, massive re-sequencing efforts, such as the 1000 Genomes Project, are delivering a catalogue of human variation at an unprecedented scale. These data are already offering a much richer understanding of the true spectrum of genetic variation across human populations. The 2010 Omni Roadmap leverages proven intelligent tagSNP selection and the ability to type up to 5 million markers per sample, delivering the power needed to fuel new genetic discoveries and enable an expanded understanding of how genetic variation contributes to human health and disease.In this workshop we will provide an overview of our next generation microarrays which contain rare variant content down to 1% MAF. In addition we will outline the process and applications available for imputation enabling you to leverage existing studies.
Optional Genepattern Workshop
Menzies Building: Medical Science 1, Medical Science Precinct
17 Liverpool Street, Hobart, TAS, 7001
Saturday 18 September 2010
9.00am - 4.00pm
Workshop is limited to 20 participants
Michael Reich, Director of Cancer Informatics Development Broad Institute of MIT and Harvard
Helga Thorvaldsdottir, Senior Project Manager
Broad Institute Tools for Integrative Genomics Analysis
Integrative genomics provides unprecedented power to increase our understanding of basic biological processes and determine the mechanisms of disease. This approach - the combining of evidence from multiple data modalities such as gene expression, copy number, epigenetic, and mutation data to find the genomic causes of a disease state has resulted in the identification of novel mutations, the discovery of causal relationships between genomic aberrations and clinical pathologies, and other important insights in the short time it has been in practice. To take advantage of this wealth of data, new tools are needed that can span data modalities and support the very large datasets characteristic of integrative efforts. The Broad Institute has produced a number of software tools to facilitate integrative genomics investigations, including GenePattern, a suite of over 120 tools for the analysis of gene expression, copy number, proteomics, flow cytometry, and other data, along with extensive capabilities for combining these tools to create complex, reproducible methodologies; and the Integrative Genomics Viewer (IGV), a flexible, scalable, high-performance tool for the concurrent visualization of multiple large scale datasets. These freely available tools are used by tens of thousands of researchers worldwide to improve our understanding of cancer, immunology, microbial genomics, stem cell biology, and other fields.
Participants will learn the major features and benefits of GenePattern and IGV and will understand how these tools may be applied in their own research.
The Friday workshops are now free of charge - if you have already paid to attend then you will receive a refund shortly. Please contact natalie@leishman-assocaites.com.au for more information.
