PSB'2004 - Human Genome Variation

Call For Papers & Participation

A large project to define the fine structure of haplotype blocks of a number of populations has been funded recently with the aim of generating a genome-wide SNP map useful for association studies. The outcome of this "HapMap" project would provide large amounts of empirical data on the patterns of linkage disequilibrium across the human genome in a set of reference samples. Although the funding that the project has received will ensure the data will be generated, its use in designing and analyzing data from association studies has received comparatively less attention. On the other hand, some researchers are not waiting for the outcome of the HapMap project, but instead a number of large projects to test the feasibility of whole-genome association studies are starting, and include whole-chromosome studies as an intermediary step.

Surveys of haplotype diversity in a limited number of genomic segments, and up to a chromosome, support the notion of haplotype "blocks" of limited diversity. It is not clear how these finding will translate to other regions or populations and a heated debate on this subject is still ongoing. New empirical evidence and theoretical work suggests that not all the genome could be described in terms of haplotype blocks, and that in some regions of the genome the block boundaries may not be well defined. In such case the development of genome-wide SNP panels and the use of reference LD data would need different tools to those envisioned today. Finally, while the best case scenario for association studies assumes the prevalence of the common-disease/common variant hypothesis, mounting evidence suggests that at least a number of complex-traits are influenced by low frequency variants, with possibly more than a few variants per loci, and located in many interacting genes. This complex genetics poses a major challenge to currently available analytical tools.

Call for Full Papers and Poster Contributions

This session of PSB 2004 will be focused in the novel computational and statistical strategies required for planning, executing, and analyzing the data of large association studies aimed to elucidate the basis of complex-traits, either common disease, response to environmental impact, or adverse drug response. The goal of the session is the presentation and discussion of new research, methods, algorithms, and tools, that promises to facilitate the elucidation of the connections between genotypes and complex-traits using the data generated by high-throughput SNP genotyping technologies.

We encourage academic, industrial and government scientists to submit manuscripts to the session. In addition to a session for oral presentation of novel peer-reviewed contributions, a panel discussion devised to encourage exchange between industry and academic scientists will be held. Participants are invited to discuss their issues with other peers in this panel session. Posters and computer demonstrations are also requested to complement the the panel and the peer-reviewed papers.

Submission Topics

The contributions should pose novel approaches and discuss problems that need to be addressed by the scientific community. The accepted contributions are expected to describe models, propose specific solutions, identify major problems, or address computational or theoretical aspects of topics related to the challenges posed above.

Among the anticipated topics are:

Construction of linkage disequilibrium and haplotype maps
Computational strategies for exploiting haplotype data for gene mapping
Tools for the analysis of whole genome scans for association
Computational and statistical approaches to deal with allelic heterogeneity
Analysis of gene epistasis and multigene traits
Tools for planning genetic studies using empirical reference data
Algorithms and metrics to select minimum subsets of SNP markers
Benchmarks for comparison of tools and algorithms

Other related topics are also possible. Please contact the session co-chairs if in doubt.

Full Paper Submissions

PSB will publish accepted full papers in an archival proceedings indexed in MEDLINE. All contributed papers will be rigorously peer-reviewed by at least three referees. A limited number of papers will be selected for a oral presentation to the full assembled conference. Accepted poster abstracts will be distributed at the conference separately from the archival Proceedings. To be eligible for Proceedings publication, each full paper must be accompanied by a cover letter stating that it contains original unpublished results not currently under consideration elsewhere.

All papers must be submitted to russ.altman@smi.stanford.edu in electronic format. The file formats we accept are: postscript (*.ps), adobe acrobat (*.pdf) and Microsoft Word documents (*.doc). Attached files should be named with the last name of the first author (e.g. altman.ps, altman.pdf, or altman.doc). Hardcopy submissions or unprocessed TEX or LATEX files will be rejected without review.

Each paper must be accompanied by a cover letter. The cover letter must state the following:

The email address of the corresponding author
The specific PSB session that should review the paper or abstract
The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.
All co-authors concur with the contents of the paper.

Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at:

http://www.smi.stanford.edu/projects/helix/psb-online/psb-submit/

If figures can not be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit. Color pictures can be printed at the expense of the authors. The fee is $500 per page of color pictures, payable at the time of camera ready submission.

Posters and Computer Demonstrations

The poster session at PSB is another possibility to present results or to share ideas in the Conference. Posters are exhibited several days during the conference and include topics from all PSB sessions.

Computer stations for live software or Web site demonstrations are also available during the conference and are encouraged as a complement to a poster or presentation.

In order to be included in the Abstracts booklet to be distributed at the conference, one-page posters abstracts should be submitted by November 1 to russ.altman@smi.stanford.edu. Posters are not peer-reviewed nor indexed in MEDLINE.

Dates and Deadlines

Full manuscript submissions due: July 14, 2003
Notification of paper acceptance: August 18, 2003
Camera ready of accepted papers copy due: September 8, 2003
Poster/demo abstract deadline: November 1, 2003
Meeting: January 6-10, 2004

FAQ

Q1. How can my paper be included in PSB's hardbound proceedings?

PSB publishes peer-reviewed full papers in an archival proceedings. Each accepted paper will be allocated 12 pages in the proceedings volume. Paper authors are required to register (and pay) for the conference by the time they submit their camera-ready copy, or the paper will not be published.

Q2. How does a PSB publication compare to a journal publication?

PSB papers are strenuously peer reviewed, and must report significant original material. PSB proceedings are indexed in Medline and other indexing services. All accepted full papers will be indexed just as if they had appeared in a journal. It is too early to assess the impact of a PSB paper quantitatively, but we will take every action we can to improve the visibility and significance of PSB publication.

Q3. If I do not want to submit a full paper to PSB, but wish to participate?

Authors who do not wish to submit a full paper are welcome to submit one page abstracts, which will be distributed at the meeting separately from the archival proceedings, and are also welcome to display standard or computer-interactive posters.

Q4. How can I obtain travel support to come to PSB?

We have been able to offer partial travel support to many PSB attendees in the past, including most authors of accepted full papers who request support. However, due to our sponsoring agencies' schedules, we are unable to offer travel awards before the registration (and payment) deadlines for authors. NO ONE IS GUARANTEED TRAVEL SUPPORT. Travel support applications will be available on our web site (http://psb.stanford.edu).

Conference Information

The Pacific Symposium on Biocomputing (PSB 2004) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. The symposium is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to the data-rich areas of molecular biology. PSB 2004 will be held January 6-10, 2004, on The Fairmont Orchid, Big Island of Hawaii.

For more information see the official PSB 2004 Web page: http://psb.stanford.edu

Session Chairs
Andrew Collins University of Southampton, School of Medicine Southampton, UK E-mail: arc @ soton.ac.uk
Francisco M. De La Vega Applied Biosystems Foster City, CA, USA E-mail:delavefm @ appliedbiosystems.com (Main Contact)
Kenneth K. Kidd Yale University Medical School, New Haven, CT, USA. E-mail: Kenneth.Kidd @ yale.edu