阳明大学医学系家庭医学科.ppt

GGAW - Oct, 2001 M-W LIN VGH Linkage Analysis Workshop 2001 Demonstration of Statistical Analysis and Discussion 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 Data Files Pedigree file Parameter file Chromosome 22q Map ABO Genotype and Phenotype Incomplete Penetrance- Dominant Disease - Incomplete Penetrance- Recessive Disease - Preplink, Makeped Preplink Preplink Use the Preplink to make the parameter file. Makeped Makeped The pedigree file (*.pre) has to run the Makeped program first before applying to the LINKAGE program. Makeped makeped input pedigree filename output pedigree filename n (no loop) Ex: makeped demo.pre demo.ped n Linkage LCP Linkage Control Program (LCP) Linkage Control Program (LCP) - MLINK - Linkage Control Program (LCP) - LINKMAP - GENEHUNTER Thresholds for Mapping Complex Traits 1. 開啟 Makeped，得到下列的畫面。 2. 鍵入Pedigree file、Output file名稱，及選擇 家族是否含有Loop，Proband 是否自動設定。 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 3. Analysis: use LINKAGE CONTROL PROGRAM (LCP) to generate command fi