DNA micro arrays: from profiles to biology

Welwyn Garden City , Hertfordshire
Tuesday, 01 May 2007

DNA micro arrays: from profiles to biology
Tuesday, 01 May 2007 09:00 - 16:30

BioPark Hertfordshire
Broadwater Road
Welwyn Garden City
Hertfordshire
AL7 3AX
United Kingdom

"In Follow-up to the very successful Euroscicon 2005 meeting "DNA micro arrays: from target collections to profiles", our 2007 meeting will focus more on downstream applications and will run by the title "DNA micro arrays: from profiles to biology"

 
Focus of this meeting will not as much be on the in-house preparation of micro-arrays, but rather on the subsequent data processing steps, validation strategies, and the translation of validated findings into biological / clinical context.

Chair:  Eric F.P.M. Schoenmakers, The Netherlands



09:00 – 09:45 Registration - Tea/Coffee

09:45 – 10:00 Introduction by the Chair
Professor Eric F.P.M. Schoenmakers, The Netherlands

10:00 – 10:30 The next generation of biological microarray experiments
Dr Rainer Breitling, University of Groningen, The Netherlands
Gene expression microarrays have revolutionized the way we study biological systems. Beyond studying differential expression in response to a specific experimental intervention, they are also suitable for large “genetical genomics” experiments. In these studies, genetic variation is used as a comprehensive multifactorial perturbation. This approach enables the study of complex cellular networks and the elucidation of mechanisms underlying gene expression regulation. In this talk, I will present some recent applications of “genetical genomics” in microarray research.

10:30 – 11:00
Ingenuity Pathways Analysis: resolving the array conundrum
Dr Adam Corner, Ingenuity Systems, UK
Microarray analysis of clinical samples in many disease areas is becoming the major route forward with regards to understanding disease mechanisms. Ingenuity Pathways Analysis is a simple, biologist oriented, web-based tool that allows researchers to analyse and compare array data from multiple disease populations, multiple disease tissues or even to proteomic data, all within the application. It is becoming increasingly apparent that genes do not function alone but through complex biological pathways. IPA can be used in unravelling these intricate pathways with a view to understanding biological mechanisms, disease states, and the relationships that these have to drugs. IPA provides, through the Ingenuity Pathways Knowledge Base, access to the world’s largest manually curated resource for biological interpretation of DNA microarray data.  Case studies illustrating the application of IPA to published data will be presented.
11:00 – 11:20
Morning Tea/Coffee and Poster Viewing

11:20 – 11:50 Tissue Microarrays in Cancer Research
Professor Colin Cooper, Institute of Cancer Research,London
This talk will outline the history of tissue microarray (TMA) development, from the original development of 'sausage' tissue bundles to the use of modern tissue microarrays and the recent development of tissue microarrays from needle biopsy specimens. Examples from the prostate cancer field will be provided. Specifically data will be presented showing the analysis of ERG gene alterations in a cohort of 446 prostate cancers, and this example will cancer to highlight the potential advantages and limitations of the TMA approach.

11:50 – 12:20 DNA microarrays: An Industry Perspective
Dr Rose McCormack, AstraZeneca, UK
DNA microarrays are one of many technologies used in genetics support for drug discovery. Using the cancer research area as an example, the presentation will provide an account of our experiences to date, a view of how this technology fits together with other tools available, and what impact this may have on the future of drug development.

12:20 – 12:50 Data mining of array CGH for constitutional disorders: from diagnosis to disease gene discoveryProfessor Yves Moreau, University of Leuven, Belgium The Netherlands
Array Comparative Genomic Hybridization for the diagnosis of constitutional disorders is the microarray application that is fastest entering clinical application. We discuss bioinformatics methods for the analysis of array CGH for this application.

Furthermore, array CGH can be used as a forward genetics screen for the discovery of disease genes. For the prioritization of candidate genes, we present Endeavour, a method for genomic data fusion that ranks candidate genes based on their similarity to genes already known for the disorder under investigation through profiling across multiple data sources (functional annotation, sequence similarity, microarray data, cis-regulatory sequence analysis, or MEDLINE abstracts).

12:50 – 13:10 Tour of the BioPark

13:10 – 14:00 Lunch and Poster Viewing

14:00 – 14:30 Beyond microarrays,
Professor Colin Campbell, Engineering Mathematics, Bristol, UK

14:30 – 15:00 High Throughput Microarrays for Analysis of Multiple Samples
Dr John Anson, R&D Director at Oxford Gene Technology
High density microarrays are useful for identifying a subset of probes or “signatures” which can differentiate between one biological state and another. Further validation of these sub-sets of probes on appropriate samples is critical to derive statistical confirmation that the signature is informative. To do this more efficiently, microarrays can be subdivided to allow testing of the same set of probes at multiple locations on the array. To advance this concept further we are developing the use of microfluidic channels to couple the physical subdivision of the array with enhanced hybridization performance. The design and performance of these Multiple Sample Arrays (MSAs) will be outlined, along with applications which are being developed.

15:00 – 15:30
DNA microarrays in the clinic: how soon, how extensively?
Dr. Bertrand Jordan, Marseille-Nice Genopole, France
DNA microarrays, widely used in research settings, are slow to penetrate clinical practice. This is due to very different requirements for a clinical test versus a research tool, and to the necessity for demonstrated clinical utility. “Genomic” tests aim to ascertain the presence of mutations, deletions or duplications, whose clinical importance is known; tests using expression profiling for prognosis or predictive purposes require proof of the clinical correlate. Future improvements in tailored technology, as well as a logical trend towards  measuring an ever increasing number of parameters, will increase the role of diagnostic DNA arrays.

15:30 – 16:30
Afternoon Tea/Coffee and Last Poster Viewing

16:00 – 16:30 Dissecting the pathways of transcriptional responses to hypoxia
Dr. Ioannis (Jiannis) Ragoussis, Head of Genomics, Wellcome Trust Centre for Human Genetics Oxford University, UK
The presented work aims to study the effects of low hypoxia and hypoxia mimicing drugs on gene transcription in cell culture. Expression analysis was undertaken using Affymetrix and Illumina expression arrays leading to the detection of novel transcripts that have not been previously reported to show induction by hypoxia. Furthermore the microRNA response was profiled using arrays of specially designed probes (Ambion). We have used a series of RNA interference experiments conducted using siRNA targeted to the hypoxia inducible factors HIF1a and HIF2a, which enabled us to further dissect the control mechanisms involved in the hypoxia response pathway.

16:30 – 16:45
The feature selection problem and micro array data analysis
Dr Albrecht, University of Hertfordshire, UKWe discuss complexity issues of the Feature Selection Problem (FSP) in the context of micro array data analysis. The FSP is known to be NP-complete, and within the sub-classification of NP-problems by fixed parameter complexity classes it has been shown to be W[2]-complete, i.e. two classes above the set of Fixed Parameter Tractable (FPT) problems, if proper inclusions are assumed. We present a stochastic local search procedure with a proven time bound that comes close to an FPT-bound. The approach has been applied to Golub’s ALL/AML micro array dataset, and we identified three significant
genes out of 7129 initial genes.


16:45 – 17:15
Microarrays and the biology of Mycobacterium tuberculosis
Professor Neil Stoker, Department of Pathology and Infectious Diseases, Royal Veterinary College, UK
Mycobacterium tuberculosis is a global pathogen that kills almost 2 million people per year. Though antibiotics and a vaccine are available, both aspects have major problems. It has become clear that we need to understand the biology of the organism better in order to make serious advances. Microarrays are being used with mycobacteria to look at both gene expression and gene essentiality on a genome-wide scale. This talk will review the current status, and assess the impact of microarray technology on our understanding of the biology of this important bacterium.

17:15 Chairman’s summing up & close

*Please note that a tour for exhibitors is scheduled for 2:15- 2:45

Fees

  • Standard - £485.00
  • Academic - £298
  • Student - £198

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