MONDAY
July 7, 2008 |
Morning |
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Lecture |
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Basic terminology,
introduction to population genetics, calculating LOD scores |
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Afternoon |
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Lecture |
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Getting started using
UNIX, introduction to linkage analysis, file system used by the LINKAGE programs, locus
types, data entry for a dominant disease |
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Exercises
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LINKAGE programs (MLINK,
ILINK) |
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TUESDAY
July 8, 2008 |
Morning |
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Lecture |
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Incomplete penetrance, penetrances for autosomal recessive and x-linked inheritence,
allele frequency estimation, loops and detecting genotyping errors.
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Exercises
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MERLIN, UNKNOWN,
PEDMANAGER and PEDCHECK |
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Afternoon |
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Lecture |
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Parametric multipoint
linkage analysis, genetic maps and overview of programs for analyzing family data |
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Exercises
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LINKAGE(LINKMAP),
GENEHUNTER, MEGA2 and SIMWALK2 |
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WEDNESDAY
July 9, 2008 |
Morning |
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Lecture |
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Allele-sharing (nonparametric) methods for quantitative and qualitative traits for sib-pairs and extended families |
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Exercises
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ALLEGRO |
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Afternoon |
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Time for
sightseeing |
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THURSDAY
July 10, 2008 |
Morning |
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Lecture |
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Linkage disequilibrium, tag SNPs selection, Haplotype reconstruction, Association studies-case control and family based (trios)
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Exercises
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SNPHAP, UNPHASED, TAGGER |
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Afternoon |
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Lecture |
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scan data for
Analysis of Case-Control data continued, population substructure and admixture. |
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Exercises
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R |
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FRIDAY
July 11, 2008 |
Morning |
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Lecture |
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Linkage Admixture, problems of intermarker linkage disequilibrium, designing a genetic study, who should be ascertained for a linkage study |
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Exercises
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HOMOG, and
GENEHUNTER |
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Afternoon |
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Lecture |
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Sample size estimation
and calculating empirical p-values for linkage and association studies; False discovery rate (FDR) and Family wise error rate (FWER) |
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Exercises
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SLINK, MSIM,
SIMPED, R and Cochran-Armitage test for trend, |
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