DIMACS/RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotype Inference

November 21 - 22, 2002
DIMACS Center, Rutgers University, Piscataway, NJ

Organizers:

Andrew G. Clark, Cornell University and Celera, Andy.Clark@celera.com

Sorin Istrail, Celera, Sorin.Istrail@celera.com

Michael Waterman, University of Southern California and Celera, msw@hto.usc.edu

Workshop Program:

NOVEMBER 21, 2002

Session I:  Statistical inferences to be drawn from haplotypes

 7:45 -  8:25  Breakfast and registration

 8:25 -  8:30  Opening remarks
               Fred Roberts, Director of DIMACS

 8:30 -  9:00  Peter Donnelly, Oxford University
	       Bayesian methods for statistical reconstruction of haplotypes

 9:00 -  9:20  Kathryn Roeder, Carnegie Mellon University
	       Evolutionary-based association analysis using haplotype data

 9:20 -  9:40  Jonathan Pritchard, University of Chicago
	       "Use of a local approximation to the ancestral recombination
               graph for fine mapping disease genes"

 9:40 - 10:00  Molly Przeworski, Max-Planck Institute
	       "Insights into recombination from patterns of linkage disequilibrium"

10:00 - 10:20  Maoxia Zheng, University of Chicago
	       "Assessment of goodness of fit of models for block haplotype structure"
 
10:20 - 10:40  BREAK

10:40 - 11:00  Elizabeth Thompson, University of Washington
	       "Genome sharing in small populations"

11:00 - 11:20  Monty Slatkin, University of California, Berkeley
	       "Testing for differences in haplotype frequencies in case-control studies"
 
11:20 - 11:40  Dahlia Nielsen, North Carolina State University
	       "Multi-locus linkage disequilibrium and haplotype-based tests of association"

11:40 - 12:00  Matthew Stephens, University of Washington
	       "Haplotypes, hotspots, and a multilocus model for linkage disequilibrium"

12:00 - 12:30  DISCUSSION - led by Andrew Clark

12:30 -  1:30  LUNCH


Session II:  Haplotypes and the ancestral recombination graph

 1:30 -  2:00  Andrew Clark, Cornell University and Celera/Applied Biosystems
	       "Exhaustive enumeration and Bayesian phase inference"

 2:00 -  2:20  Sorin Istrail, Celera/Applied Biosystems
	       "Haplotypes and block-free SNP selection algorithms"

 2:20 -  2:40  David Cutler, Johns Hopkins University
	       "Haplotype inference in random population samples"

 2:40 -  3:00  Magnus Nordborg, University of Southern California
	       "The pattern of polymorphism on human chromosome 21"

 3:00 -  3:20  Bruce Rannala, University of Alberta
	       "Joint Bayesian estimation of mutation location and age
	       using linkage disequilibrium"

 3:20 -  3:40  BREAK 

 3:40 -  4:00  Russell Schwartz, Carnegie Mellon University
	       "Inferring piecewise ancestral history from haploidsequences"

 4:00 -  4:20  Fengzhu Sun, University of Southern California
	       "Dynamic programming algorithms for haplotype block partition
	       and applications to association studies 

 4:20 -  5:00  Discussion


NOVEMBER 22, 2002

SESSION III:  Inference of Haplotype phase

 8:00 -  8:30  Breakfast and registration

 8:30 -  9:00  Jun Liu, Stanford University
	       "Haplotype inference and haplotype information"

 9:00 -  9:20  Jinghui Zhang, National Cancer Institute, NIH
               "A software system for automated and visual analysis of
               functionally annotated haplotypes"

 9:20 -  9:50  Dan Gusfield, University of California, Davis
	       "Combinatorial approaches to haplotype inference"

 9:50 - 10:10  Eran Halperin, University of California, Berkeley
	       "Large scale recovery of haplotypes from genotype data 
               using imperfect phylogeny"

10:10 - 10:30  Vineet Bafna, The Center for the Advancement of Genomics
               "Haplotyping as perfect phlogeny"

10:30 - 11:00  DISCUSSION

11:00 - 12:00  LUNCH


Session IV:  Empirical approaches

12:00 - 12:30  David Altschuler, Harvard Medical School
	       "Empirical studies of human population variation"

12:30 - 12:50  Nancy Cox, University of Chicago
	       "How does choice of polymorphism influence estimation 
               of LD and mapping?"

12:50 - 1:10   Francisco de la Vega, Applied Biosystems
	       "Patterns of linkage disequilibrium across human 
	       chromosomes 6, 21, and 22"

1:10 - 1:30    Li Jin, University of Cincinnati
	       TBA

1:30 - 1:50    Steve Sherry, National Center for Biotechnology Information, NIH
	       "dbSNP resources to assist haplotype reconstruction"

1:50 - 2:30    DISCUSSION

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