Genome-wide association mapping and rare alleles: from population genomics to personalized medicine. Session at PSB 2011

PSB 2011 - Full paper submission deadline: July 12 2010 (let the co-chair know if you need a few days extension)

Genome-wide associations studies (GWAS) have been very 
successful in identifying common genetic variation associated to 
numerous complex diseases.

However, most of the identified 
common genetic variants appear to confer modest risk and few 
causal alleles have been identified. Furthermore, these 
associations account for a small portion of the total 
heritability of inherited disease variation.

This has led to the 
reexamination of the contribution of environment, gene-gene and 
gene-environment interactions, and rare genetic variants in 
complex diseases.

There is strong evidence that rare variants 
play an important role in complex disease etiology and may have 
larger genetic effects than common variants.

Currently, much of 
what we know regarding the contribution of rare genetic variants 
to disease risk is based on a limited number of phenotypes and 
candidate genes.

However, rapid advancement of second 
generation sequencing technologies will invariably lead to 
widespread association studies comparing whole exome and 
eventually whole genome sequencing of cases and controls.

A 
tremendous challenge for enabling these "next generation" 
medical genomic studies is developing statistical approaches for 
correlating rare genetic variants with disease outcome. 



The analysis of rare variants is challenging since methods used 
for common variants are woefully underpowered (e.g., accurately 
estimating allele frequencies in cases vs. controls requires ~10 
observations of the minor allele; however, many of the 
functional rare alleles may be present only once in the 
resequence data).

Therefore, methods that can deal with genetic 
heterogeneity at the trait-associated locus and that can be 
applied to both in cases vs. controls and quantitative trait 
studies are needed.

Currently, these approaches are in their 
infancy and very basic criteria (such as functional annotation, 
sequence conservation, or biological pathway classification) are 
used.

There is tremendous opportunity to apply data mining 
methods outside of the standard statistical toolkit to this 
problem.

Additionally, deep sequencing will reveal many variants 
that are not causal, and in order to reduce the problems of 
misclassification, i.e. inclusion of non-causal variants and 
exclusion of causal variants in the analysis, it is beneficial 
to predict their potential functionality.

Thus, methods to 
classify and annotate rare variants for subsequent analysis are 
necessary. 



The session of PSB 2011 would focus on distilling current 
knowledge in assessing rare variant functionality and their 
correlation with complex traits, and more importantly bring 
forth methodological questions that need to be addressed for 
successful analysis of rare variants.

"GWAS by sequencing" 
presents many new challenges and proposed solutions for 
interpreting sequencing data from clinical case/control cohorts 
will be of particular interest to a diverse audience.

The 
session will similarly consider application-specific algorithms, 
analysis methods, or study planning and design tools with 
emphasis in the leveraging rare genetic variation in complex 
trait/disease correlation. 



Deadline for full paper submission: July 12, 2010. Deadline for poster abstracts: November 1, 2010. 



CONFERENCE INFORMATION 


The Pacific Symposium on Biocomputing (PSB 2011) 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. 


PSB 2011 will be held at the Big Island of 
Hawaii on January 4-7, 2011. 

For more information see the official PSB 2011 Web page: 

http://psb.stanford.edu

See also

- How to read a genome-wide association study, genomes unzipped, July 18th 2010