PSB'2006 - Design & Analysis of Genetic Studies after the HapMap Project

Call For Papers & Participation

A large international effort to define the fine patterns of sequence variation along the human genome has been carried out using samples of four human populations. The aim was to generate a genome-wide validated SNP resource and survey of the patterns of allelic association and common haplotypes useful for designing association studies. The outcome of this “HapMap” project is the genotypes of over three million SNPs in DNA samples of individuals from Africa, China, Utah, and Japan. This project is providing an unprecedented amount of empirical data on the patterns of linkage disequilibrium across the human genome that is fueling a large number of population genetic analyses. A goal of the HapMap project is the selection of a subset of the common SNPs to serve as a representative set of the entire common variation. Methods for the selection of subsets of SNPs have proliferated, and their effectiveness in different disease architectures and populations still needs to be evaluated. However, the use of the HapMap data in other aspects of study design and for the analysis of association studies has received comparatively less attention. For example, methods which estimate power and sample size for genetic studies using the empirically observed patterns of LD are yet to be fully developed. Also, what is the power of whole-genome direct association studies with putative causal variants (i.e. non-synonymous cSNPs)? Questions about power are critically important, as it is evident that the failures of replication that have plagued the literature of disease association studies are likely to be the result of underpowered studies. There are many other questions, for example: What are the criteria to reject a gene or region for causality on a disease? What are the necessary tools to better present the data from the HapMap with other relevant annotations in a seamless way to allow the selection of SNPs for particular candidate gene/region studies? What additional information about selection, population history, recombination and related phenomena can be gleaned from the HapMap data and future studies?

Call for Full Papers and Poster Contributions

The goal of this session of the PSB conference is the presentation and discussion of new research, methods, algorithms, and tools that facilitate the planning, executing, and analysis of studies of human genomic variation leveraging the reference survey of variation performed by the HapMap project as well as other genome-wide datasets becoming available on the public domain.

We encourage academic, government, and industrial scientists to submit manuscripts with original work in the subject area. 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 oral presentation to the full assembled conference. Posters and computer demonstrations are also requested to complement the session, and require the submission of a one-page abstract. Accepted poster abstracts will be distributed at the conference separately from the archival Proceedings. In addition of the oral presentation of the full papers, and the poster session, an invited panel discussion devised to encourage exchange between industry and academic scientists will be also held.

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:

Selection of SNPs for genetic studies
Power calculations and study design
Methods for analysis of association mapping studies
Methods for inference of natural selection
Tools for presentation and use of the HapMap & other data

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://psb.stanford.edu/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 18, 2005
Notification of paper acceptance: September 6, 2005
Camera ready of accepted papers copy due: September 23, 2005
Poster/demo abstract deadline: November 1, 2005 at noon PST
Meeting: January 3-7, 2006

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 2006) 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 2006 will be held January 3-7, 2006, on The Grand Wailea Resort, Wailea, Maui, Hawaii.

For more information see the official PSB 2006 Web page: http://psb.stanford.edu

Session Chairs
Andrew G. Clark Department of Molecular Biology and Genetics Cornell University, Ithaca, NY, USA
Andrew Collins University of Southampton, School of Medicine Southampton, 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.