Introductory course in linkage and association analysis

Day 1

• Approaches to gene mapping (Talk)
• Explanation of computer systems, course set-up (Talk)
• Notes on running the exercises, file types used in exercises
• Setting up a simple two-point analysis using LINKAGE datafiles
• Explanation of mlink output (Talk)
• Using utility programs to carry out a two-point analysis
• Carrying out a three-point analysis
• Explanation of output from multipoint analysis (Talk)

• Lunch

• Discussion of data management issues (Talk)
• Using the qdb database to manage pedigree data
• Adding an additional locus to the qdb database
• Using quiklink with an additional locus
• Effect of transmission model specification on lod score analysis (Talk)
• Exercises in the analysis of diseases with complex inheritance

Day 2

• Model-free linkage analysis using likelihoods (Talk)
• Statistical significance of lod scores (Talk)
• Non-parametric methods of analysis (Talk)
• Using MFLINK to carry out linkage analysis
• Using SPLINK to carry out linkage analysis
• Using Genehunter to carry out linkage analysis
• Lunch

• Use of simulation (Talk)
• Using association to map disease genes (Talk)
• Using CLUMP to carry out case-control analysis
• Using ETDT to carry TDT analysis
• Haplotype-based association analysis (Talk)
• Using genecounting to carry out multimarker association analysis
• Discussion and analysis of participants' datasets