Genetics Education

Agenda

Dates and Location

Contact

Cost

Faculty

Links and Files

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Click here to see an interview with workshop organizer, Dr. Simon Gregory.

The 2007 DBW was featured on NPR by WUNC's Rose Hoban. Click here to listen to the report.

Workshop Description

Background

The finished sequence of the human genome represents an invaluable resource that will greatly accelerate scientific research. However, the bewildering array of genomic information, analysis tools, and ancillary databases are difficult to navigate without being properly equipped with skills necessary to make optimal use of these data. The purpose of the Duke Bioinformatics Workshop (DBW) is to provide its participants, graduate students and experienced scientific researchers alike, with the expertise to efficiently explore this myriad of information. The DBW is directed at individuals with previous genomics experience and has been designed to give a broad overview of topics relevant to innovative research with examples chosen by six experienced instructors who use these data on a daily basis. The 2008 DBW builds upon the success of the 2004, 2005, 2006 and 2007 workshops that have trained over 160 researchers in the use of publicly available bioinformatic data, and will include new topics that reflect advances in technological and scientific fields of research. The DBW, whose class size is limited to approximately 40 students, provides intensive 3-days of training in an environment that fosters close interaction between student and instructors.

Significance

The major factors that will influence the use of the vast amount of data arising from the Human Genome Project will be an awareness of the diversity of data that is publicly available and the development of skills that can make full use of it. The significance of the DBW lays not only in its content,( i.e. utilization of evolving biological databases and the innovative tools with which they are queried) but also the Instructors who present the class. The DBW instructors understand the inherent strengths and weaknesses of the analyses they perform. The DBW will provide scientific researchers with a workshop at which the participants are exposed to, and have use of, biological databases that they will utilize in their respective fields or research.

Content

Web based tools are used in each of the workshop modules (see agenda link) to help interrogate biological data. The aims of each of the modules is outlined below

De novo analysis of sequence

• View manually annotated genes in the Vega browser.

• Sequence similarity searching using Blastn and PSI-blast to identify similar proteins.

• de novo analysis of cDNAs, including ORF finder to highlight putative protein products of a cDNA, blastp link from within this to investigate the potential protein products, Spidey to align cDNA to genomic DNA.

• Clustalw to align similar sequences, view in Jalview and use GeneDoc to produce a graphics file.

• InterPro to investigate protein domain structures.

Browsing the human genome

• Appreciate ability to now work with the whole genome

• Introduce primary human genome browsers

• Discuss how genome annotations are displayed and relevant information is made accessible

• Using the UCSC Genome Browser, demonstrate some general features and applications of genome browsers.

• Introduce the Table Browser at UCSC

• Explore ability to view your own annotations in the browser

• Provide examples to facilitate becoming more comfortable using browser resources.

Sequence Variation

• Introduction to SNPs

• Introduction to various SNP resources on the web, including Ensembl, dbSNP and JSNP

• Integration of information from various databases to identify SNPs in target gene or chromosomal regions

• Export SNP information from databases

• Introduction to genotypes and haplotypes, including the HapMap database

• Introduction to genotyping low, medium and high throughput genotyping platforms and information about study design and QC

Comparative sequence analysis

• Review the sequence available from different organisms

• Identify putative homologous genes and generate a phylogenetic tree

• Compare genome sequences from different organisms and identify conserved sequences

• Analyze conserved sequences for potential regulatory function

Exploring function and disease

• Identify information available to determine the possible function of a gene product

• Highlight various inter-linked information resources that are available for this purpose

• Identify published information on the gene

• Identify known mendelian inherited disorder(s) associated with the gene

• Summarize predicted function from several linked databases

• Identify domains found within the protein

• View structural information if available.

DNA/RNA microarrays

• Review common array-based technologies to measure DNA and RNA

• Review common approaches to analysis

• Identify a region of chromosomal gain using Array CGH data

• Determine Genes with differential expression in region of chromosomal gain

Instructors

All instructors participating in the 2008 DBW are from Duke University or the Wellcome Trust Sanger Institute (UK) and are acknowledged experts in their field. Each instructor's module is based upon publicly available resources that they use on a daily basis as part of their own specialized fields of research.

Total number of attendees

This year the DBW has been extended to 3-days, therefore we will only be hosting one workshop that will accommodate approximately 40 participants. A class of this size promotes close interaction between the instructors and students in the didactic and exercise components of each module and the free research time at the end of the workshop.

Format

Each topic module contains a short didactic component, together with worked examples and exercises to reinforce the lessons of the module. The workshop is accompanied by a 250 page color manual that contains all the worked examples, exercises and additional information pertaining to each module. In addition to the manual, the cost of the workshop includes lunch, as well as morning and afternoon coffee.