PSB'2003 - Human Genome Variation

Call For Papers & Participation

The post-genomic research in human and population genetics is centering around the study of the patterns of genetic variation across the genome and among populations with the aim of understanding the origin of complex disease and the evolutionary history of our species. Recently, a major initiative to develop the so-called Haplotype Map of the Human Genome has been enacted. The rationale of such major enterprise is that this information will make it possible to conduct disease gene association studies more quickly and efficiently than ever before, resulting in the more rapid elucidation of the variants that predispose to disease and influence drug response. Recent surveys of haplotype diversity in a number of genomic segments, and up to a chromosome, support the notion of haplotype "blocks" of limited diversity. While it is not clear how these finding will translate to other regions or populations, it seems imminent that large studies to elucidate the patterns of genomic variation will be carried out.

With the imminent flood of data from the Haplotype Map project, there is an urgent need to extend haplotype-related computational methods to the whole-genome scale. There are many fundamental computational and statistical problems to solve: how to calculate genome-wide haplotypes and determine haplotype block boundaries on sequence, how to find the optimal number of SNPs per haplotype block, how to account for the variation in LD across different populations, how to find the most informative SNPs for each haplotype block, how to deal with uncertainty in annotations and map locations, development of controls for spurious statistical association, the effects of population substructure, estimation of statistical significance, effects of genotyping error, how to manage and represent the large amount of data, methods for modeling the genotyping process in silico to avoid artifacts and failures in the massive genotyping projects, etc. Finally, methodologies to use the haplotype information for more efficient design and analysis of whole-genome association studies are in their infancy and deserve attention.

An Invitation to Participate

The session of the Pacific Symposium on Biocomputing 2003 "Human Genomic Variation: Haplotypes, Linkage Disequlibrium, and Populations" will be devoted to the computational and statistical challenges of the studies of human genome variation. This year's session is preceded by three succesful sessions on the topic carried out in PSB editions 2000-2002. Please visit the PSB Electronic Proceedings to explore the contributions accepted in previous years.

As in the previous instances of the Human Genomic Variation session, its goal is to foster the discussion of new research, methods, algorithms, and tools, that promise to facilitate the elucidation of the connections between genotypes and phenotypes using the data generated by high-throughput 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 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:

Strategies for SNP selection as markers for whole-genome association studies across different populations.
Theoretical and statistical frameworks for the construction of haplotype maps, and their variability across populations.
Algorithms for haplotype inference, construction of linkage disequilibrium maps, haplotype tagging, and optimization of SNP marker sets.
Methods for analyzing association, linkage disequilibrium, and QTL using SNPs in candidate gene sets and whole genome scans.
Ontologies, control vocabularies, and data models for genotypic, haplotype, and phenotypic databases.
Visualization and analysis of large-scale genotypic-haplotypic data.
Evolutionary models of genome variability and linkage disequilibrium vs. empirical data findings.
Data management and quality control methods for the high-throughput genotyping laboratory

Other related topics are also possible.Please visit the PSB Electronic Proceedings to explore the contributions accepted in previous years.

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 altman@smi.stanford.edu in electronic format. The file formats we accept are: Adobe Acrobat (*.pdf) and Microsoft Word documents (*.doc). Attached files should be named with the last name of the first author (e.g. 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 altman@smi.stanford.edu. Posters are not peer-reviewed nor indexed in MEDLINE.

Dates and Deadlines

Full manuscript submissions due: July 15, 2002
Notification of paper acceptance: September 6, 2002
Camera ready of accepted papers copy due: September 23, 2002
Poster/demo abstract deadline: November 1, 2002
Meeting: January 3-7, 2003

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 2003) 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 2003 will be held January 3-7, 2003, on Lihue, Kauai at the Kauai Marriott Resort and Beach Club.

For more information see the official PSB 2003 Web page: http://psb.stanford.edu

Session Chairs
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
Isaac S. Kohane Children's Hospital of Boston and Harvard Medical School, Cambridge, MA, USA. E-mail: isaac_kohane @ harvard.edu