DemonstrationofLinkageAnalysis.ppt

Jan, 2003 YMGC Genotyping Core VGH Linkage Analysis Workshop 2001 Demonstration of Linkage Analysis 林明薇 Ming-Wei Lin, PhD 陽明大學醫學系家庭醫學科 台北榮民總醫院教學研究部 Linkage Data Files Pedigree file Parameter file ABO Genotype and Phenotype Incomplete Penetrance- Dominant Disease - Incomplete Penetrance- Recessive Disease - Chromosome 1 Map Preplink Use the Preplink to make the parameter file Makeped The pedigree file *.pre has to run the Makeped program first before applying to the LINKAGE program. Makeped makeped n no loop Ex: makeped demo.pre demo.ped n Linkage Control Program LCP Linkage Control Program LCP - MLINK - Linkage Control Program LCP - LINKMAP - GENEHUNTER Reference Kruglyak L, Daly MJ, Reeve-Daly MR, Lander ES 1996 Parametric and non-parametric analysis: a unified multipoint approach. American Journal of Human Genetics 58: 1347-1363. LINKAGE I. Analysis Program of LINKAGE: 1. ILINK: estimation of recombination rates and calculation of the maximum lod score. 2. MLINK: lod score tables and risk analysis. 3. LINKMAP: location scores. 4. LODSCORE: estimation of recombination rate and the maximum lod score from two-locus data. It is almost identical to ILINK. II. Steps for running the LINKAGE program: 1. Input pedigree and genotypic data pedigree file . 2. Description of loci parameter file . Program code: 1 CILINK 2 CMAP 3 ILINK 4 LINKMAP 5 MLINK 6 LODSCORE 7 CLODSCORE Locus description: 0 Quantitative trait 1 Affected status 2 Binary factors 3 Numbered alleles Recombination information: Sex difference: 0 no sex-difference 1 constant sex-difference 2 variable sex-difference Interference: 0 no interference 1 interference without a mapping function 2 user-specific mapping function Analysis: use LINKAGE CONTROL PROGRAM LCP to generate command files to control the analysis programs. Window Control Characters Key Ctrl Chr Action F10 ^U Delete the line. ^ ^I Move to t