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Education

Published on January 15, 2008

Author: Maurizio

Source: authorstream.com

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Demonstration of Linkage Analysis:  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:  Linkage Data Files Pedigree file Parameter file Slide3:  Pedigree file format (demo.pre) 1 1 0 0 1 1 5 5 5 5 2 2 2 3 4 7 3 4 5 7 2 7 4 6 3 3 1 5 1 10 13 2 2 1 4 5 3 4 2 4 3 4 4 8 1 1 6 6 2 6 4 7 3 3 1 1 1 12 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 13 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 12 2 2 4 5 4 5 2 2 2 3 4 7 1 3 5 6 2 6 6 7 3 3 1 1 1 3 1 12 1 1 3 5 4 5 2 2 3 3 4 4 1 4 6 7 6 7 4 7 3 3 1 5 1 4 1 12 2 2 4 5 4 5 2 2 2 3 4 4 1 3 5 6 2 6 6 7 3 3 1 1 1 9 13 2 1 1 4 5 3 5 2 4 2 4 7 8 1 3 5 6 1 2 4 6 3 3 1 1 2 1 0 0 2 2 4 5 4 5 2 4 3 3 4 7 1 3 1 6 1 6 5 5 3 3 3 5 2 10 22 6 2 1 4 5 5 6 2 2 2 3 4 7 1 2 6 6 1 6 7 9 3 4 3 5 A B C D E F G H I J K L M N O P Q A: pedigree name B: individual Id C: father's ID D: mother's ID E: sex (1= male, 2= female) F: affection status (1 = unaffected, 2 = affected; 0 = unknown) G-Q: marker genotypes Slide4:  Parameter file format (demo.par) 12 0 0 5 << no loci, risk locus, sexlinked(if 1) 0 0.0 0.0 0 << mut locus, mut rate, haplotype freq(if 1) 1 2 3 4 5 6 7 8 9 10 11 12 << order of loci 1 2 << affection, #alleles [amyloidosis] 0.9999 0.0001 << gene freqs 1 << number of liability classes 0.00002 0.9 0.9 << penetrence 3 7 << numbered alleles, #alleles [d1s498] 0.02 0.29 0.07 0.36 0.21 0.04 0.01 3 7 << numbered alleles, #alleles [d1s2635] 0.02 0.05 0.1 0.38 0.38 0.05 0.02 3 4 << numbered alleles, #alleles [d1s2771] 0.02 0.79 0.07 0.12 ABO Genotype and Phenotype:  ABO Genotype and Phenotype Penetrances = Prob(phenotype given genotype) Incomplete Penetrance - Dominant Disease -:  Incomplete Penetrance - Dominant Disease - Incomplete Penetrance - Recessive Disease -:  Incomplete Penetrance - Recessive Disease - Slide8:  Parameter file format (demo.par) cont.1 3 4 << numbered alleles, #alleles [d1s484] 0.33 0.12 0.5 0.05 3 9 << numbered alleles, #alleles [d1s2675] 0.02 0.05 0.31 0.15 0.02 0.4 0.03 0.01 0.01 3 4 << numbered alleles, #alleles [d1s2768] 0.5 0.12 0.33 0.05 3 9 << numbered alleles, #alleles [d1s2844] 0.02 0.12 0.17 0.05 0.07 0.21 0.1 0.14 0.12 3 7 << numbered alleles, #alleles [d1s2878] 0.29 0.21 0.17 0.02 0.29 0.01 0.01 3 11 << numbered alleles, #alleles [d1s2681] 0.02 0.02 0.05 0.14 0.19 0.4 0.02 0.03 0.05 0.05 0.03 3 4 << numbered alleles, #alleles [d1s194] 0.14 0.02 0.72 0.12 Slide9:  Parameter file format (demo.par) cont.2 3 5 << numbered alleles, #alleles [d1s196] 0.64 0.02 0.05 0.05 0.24 0 0 << sex difference, interference (if 1 or 2) 0 0.09 0.028 0.011 0.01 0.017 0.025 0.025 0.011 0.005 0.03 << recombination values 1 0.05 0.45 << rec varied, increment, finishing value Chromosome 1 Map:  Chromosome 1 Map Markers cM D1S498 D1S2635 D1S2771 D1S484 D1S2675 D1s2768 9.0 2.8 1.7 2.5 1.1 qter 3.0 1.1 1.0 cen 2.5 0.4 D1S2844 D1S2878 D1S2681 D1S194 D1S196 Preplink:  Preplink Use the Preplink to make the parameter file Slide12:  1. 鍵入 Preplink。 Slide13:  2. 開啟 Preplink ,得到下列的畫面。 Slide14:  3. 鍵入Enter ,及選擇選項 (k) see or modify loci description。 Slide15:  4. 選取(e) change locus type ,鍵入locus to change 及選取 new locus type後,按 Enter。 Slide16:  5. 選取(a) see or modify a locus ,並鍵入locus number to see or modify。 Slide17:  6. 選取(d) gene frequencies 並鍵入新 gene frequencies 值。 Slide18:  7. 選取(c) penetrances , 並鍵入三組新penetrance值。 Slide19:  8. 選取(e) EXIT。 Slide20:  9. 選取(a) See or modify a locus及鍵入 Locus number。 Slide21:  10. 選取(a) number of alleles 及鍵入正確之 number of alleles。 Slide22:  11. 選取(b) gene frequencies 及鍵入新的 gene frequencies。 Slide23:  12. 選取(c) EXIT。 Slide24:  13. 選取(f) RETURN TO MAIN MENU。 Slide25:  14. 選取(n) Write datafile。 Slide26:  15. 鍵入 Output file name。 Slide27:  16. 選取(o) Exit。 Makeped:  Makeped The pedigree file (*.pre) has to run the Makeped program first before applying to the LINKAGE program. Slide29:  1. 開啟 Makeped,得到下列的畫面。 Slide30:  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。 Makeped:  Makeped makeped <input pedigree filename> <output pedigree filename> n (no loop) Ex: makeped demo.pre demo.ped n Slide32:  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. Slide33:  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 Slide34:  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 Slide35:  Analysis: use LINKAGE CONTROL PROGRAM (LCP) to generate command files to control the analysis programs. Linkage Control Program (LCP):  Linkage Control Program (LCP) Slide37:  Window Control Characters Key Ctrl Chr Action F10 ^U Delete the line. ^ ^I Move <up> to the previous entry. V ^K Move <down> to the next entry. Return ^M Move <down> to the next entry. (on entry screens) Prev Scr ^P Move <up> to the previous screen. Next Scr ^N Move <down> to the next screen. F8 ^Z Exit the current session. F9 ^A Abort the current session.. Linkage Control Program (LCP) - MLINK -:  Linkage Control Program (LCP) - MLINK - Slide39:  1. 開啟LCP,出現下列畫面: Slide40:  2. 輸入COMMAND file name, LOG file name, PEDIGREE file name, PARAMETER file name的名稱。 Slide41:  3. 按Ctrl-N,出現下列畫面,選取General pedigrees。 Slide42:  4. 按Ctrl-N,出現下列畫面,選取MLINK。 Slide43:  5. 按Ctrl-N,出現下列畫面,選取Lod score table。 Slide44:  6. 按Ctrl-N,出現下列畫面,選取 No sex difference。 Slide45:  7. 按Ctrl-N,出現下列畫面,輸入Locus order, Other recomb,再按Ctrl-N及Ctrl-Z,即完成LCP之設定。 Slide46:  8. 在Unix 命令列鍵入 demo,即可執行MLINK的分析。 Slide47:  9. MLINK的分析畫面。 Linkage Control Program (LCP) - LINKMAP -:  Linkage Control Program (LCP) - LINKMAP - Slide49:  1. 開啟LCP,得到下列畫面: Slide50:  2. 輸入COMMAND file name, LOG file name, PEDIGREE file name, PARAMETER file name的名稱。 Slide51:  3. 按Ctrl-N,出現下列畫面,選取General pedigrees。 Slide52:  4. 按Ctrl-N,出現下列畫面,選取LINKMAP。 Slide53:  5. 按Ctrl-N,出現下列畫面,選取All intervals。 Slide54:  6. 按Ctrl-N,出現下列畫面,選取No sex difference。 Slide55:  7. 按Ctrl-N,出現下列畫面,輸入Test loci、Order of fixed loci、Recombination fractions,再按 Ctrl-N Ctrl-Z,即完成LCP之設定。 Slide56:  8. 在Unix 命令列鍵入 demo1,即可執行LINKMAP的 分析。 Slide57:  9. LINKMAP的分析畫面。 Slide58:  10. 在DOS下,執行 Table.exe 的功能。 Microsoft(R) Windows 98 (C)Copyright Microsoft Corp 1981-1998. C:\WINDOWS>cd\ C:\>cd ming-wei C:\Ming-Wei>cd vghworkshop C:\Ming-Wei\vghworkshop>cd 2002 C:\Ming-Wei\vghworkshop\2002>cd demo C:\Ming-Wei\vghworkshop\2002\demo>table demo.res /a C:\Ming-Wei\vghworkshop\2002\demo>table demo1.res /a C:\Ming-Wei\vghworkshop\2002\demo> Slide59:  11. 用 WORD 開啟 demo.tab,得到MLINK的結果。 Slide60:  12. 用 WORD 開啟 demo1.tab,得到LINKMAP的結果。 Slide61:  13. 解讀LINKMAP的結果。 GENEHUNTER:  GENEHUNTER Reference:  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. Slide64:  Running GENEHUNTER 1. type gh.sun 2. photo demo.out 3. skip large off 4. load demo.par 5. scan demo.pre 6. total stat het 7. quit Slide65:  1. 鍵入gh.sun ,在npl下鍵入 photo demo.out 、skip large off 、load demo.par 、 scan demo.pre等指令。 Slide66:  2. 所有家族分析完成後 ,鍵入total stat het指令。 Slide67:  3. 所有家族分析完成後,鍵入total stat het指令, 得到 total lod score 、 NPL score 、 information score。 Slide68:  4. 鍵入 quit 離開 genehunter。

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