Each session will start with a theoretical introduction followed by
practical exercises. The instructors for the course are Andrew DeWan (The Rockefeller University)
and Suzanne Leal (Baylor College of Medicine). Please feel free to bring your
own data sets for discussion and/or analysis.
The course will be held daily from 9:00 AM - 5:00 PM, except on Wednesday when the course will end at
12:30 PM for sightseeing.
MONDAY
July 5, 2004 |
| Morning |
|
Lecture |
| |
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Basic terminology, introduction to population genetics, calculating lod scores |
| |
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| Afternoon |
|
Lecture |
| |
|
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 |
| |
|
LINKAGE programs (MLINK, ILINK) |
|
| |
|
TUESDAY
July 6, 2004 |
| Morning |
|
Lecture |
| |
|
Incomplete penetrance, penetrances for autosomal recessive and x-linked inheritence,
allele frequency estimation, loops and detecting genotyping errors
|
| |
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Exercises |
| |
|
MEGA2, UNKNOWN, PEDMANAGER and PEDCHECK |
| |
|
|
| Afternoon |
|
Lecture |
| |
|
Designing a gene mapping study. Association studies - case
control and family based (trios)
|
| |
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Exercises |
| |
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TBA |
|
| |
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WEDNESDAY
July 7, 2004
|
| Morning |
|
Lecture |
| |
|
Parametric multipoint gene mapping and genetic maps
|
| |
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Exercises |
| |
|
LINKAGE (LINKMAP), GENEHUNTER and SIMWALK2 |
| |
|
|
| Afternoon |
|
Time for sightseeing |
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|
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|
| |
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THURSDAY
July 8, 2004
|
| Morning |
|
Lecture |
| |
|
Allele-sharing (nonparametric) methods for both sib-pairs
and extended families
|
| |
|
Exercises |
| |
|
GENEHUNTER and SIMWALK2 |
| |
|
|
| Afternoon |
|
Lecture |
| |
|
Computer tools for fine mapping and gene identification |
| |
|
Exercises |
| |
|
Continued from morning session |
|
| |
|
FRIDAY
July 9, 2004 |
| Morning | |
Lecture |
| |
|
Linkage Admixture |
| | |
Exercises
|
| | |
HOMOG, ANALYZE and GENEHUNTER
|
| | | |
| Afternoon |
|
Lecture |
| | |
Sample size estimation and calculating empirical p-values
|
| |
|
Exercises |
| |
|
SIMULATE, SLINK, MSIM and EpiInfo |
|