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1、Haplotype analysis using HaploviewI. The Java Runtime Environment (JRE)v1.4 or later was requiredto work with the haploviewprogram.1. Downloaded Java Runtime Environment (JRE) and installed the program at; http:/II.Haploview Downloads1. Search Haploview using Google search.2. The Haploview s webpage
2、3.Choose to download the Haploview Windows installer (hapinstall.exe) fromHapInstall.exe4. Install Haploview by double-clicking the installer file. The installer will create a Haploview folder in Start Menu. -To run the program, click on “Haploview.jar” file in that folder.5. Haploviews welcoming pa
3、geQuestion 1. What is the name of haploview format to use in this analysis?The name of assigned haploview format used in the haplotype analysis is “HapMap Projectdata dumps format”. This file format has several header lines beginning with “#”.6. To input the file from the assignment to Haploview for
4、 ana lysis.6.1 CopySNP datafrom the asssigment. 6.2Paste it to MS word. 6.3 Save file as plain text file. (file name; SNP data.txt) 6.4 Plain text file.7. Open the Haploview program.8. Choose HapMap format tobrowse saved file SNP data.txt. Then click OK.9. Set the HW p-value at 0.05. Then click at R
5、escore Markers. -The screenshot will appear;Question2. Please show us the marker and individual quality control of the genotype data use in the analysis. From the screenshot above, after loading a file, Haploview shows basic data quality checks for the markers.The description of terms use as follow;
6、 # is the marker number. Name is the marker ID specified (only if an info file is loaded). Position is the marker position specified (only if an info file is loaded). ObsHET is the markers observed heterozygosity. PredHET is the markers predicted heterozygosity (i.e. 2*MAF*(1-MAF). HWpval is the Har
7、dy-Weinberg equilibrium p value, which is the probability that its deviation from H-W equilibrium could be explained by chance. %Geno is the percentage of non-missing genotypes for this marker. FamTrio is the number of fully genotyped family trios for this marker (0 for datasets with unrelated indiv
8、iduals). MendErr is the number of observed Mendelian inheritance errors (0 for datasets with unrelated individuals). MAF is the minor allele frequency (using founders only) for this marker. Alleles are the major and minor alleles for this marker. Rating is checked if the marker passes all the tests
9、and unchecked if it fails one or more tests (highlighted in red). 10. Click at LD Plot on the Menu bar to show LD map.Question 3. Please show us the LD map then explain what do you get from the LD map? Haploview calculates several pairwise measures of LD, which it uses to create a graphical represen
10、tation as shows in above screenshot. Halpoview allows a number of different color schemes to represent The LD relationship. It generates haplotypes and their population frequencies. The LD display shows lines to indicate transition from one block to the next with frequencies corresponding to the thi
11、ckness of the lines. The LD display presents Hedridges multialleic D, which represent the degree of LD between 2 blocks, treating each haplotype within ablock as an allele of that region.This LD maps above show color scheme in themode of Standard D/LOD.When; D is the value of D prime between the two
12、 loci. LOD is the log of the likelihood odds ratio, a measure of confidence in the value of D. Question 4. How many haplotype blocks in this region of Chromosome X, then explain how to interprete them?There are 3 haplotype blocks in this region of Chromosome X and the values to present the relations
13、hip between each locus or markerof each blocks was shown in the white box. The two most common pairwise measures of LD is D and r2. D is defined to be 1 in the absence of obligate recombination, declining only due to recombination or recurrent mutation. r2 is the squared correlation coefficient betw
14、een the two SNPs. Thus, r2 is 1 when two SNPs arose on the same branch of the genealogy and remain undisrupted by recombination, but has a value less than 1 when SNPs arose on different branches, or if an initially strong correlation has been disrupted by crossing over. Block 1 comprises marker numb
15、er 8, rs908005 and marker no. 9, rs979484. Block 2 comprises marker number 13-17.For instance, this figure in the white boxonly shows the correlation between marker 13 and 17 of haplotype block. Block 3 comprises marker number 24-29.For instance, this figure in the white boxonly shows the correlatio
16、n between marker 24 and 27 of the haplotype block.When; D is the value of D prime between the two loci. LOD is the log of the likelihood odds ratio, a measure of confidence in the value of D. r2 is the correlation coefficient between the two loci. Question 5. Could you find out the tagging SNP in ea
17、ch haplotype block, then explain what the tagging SNPs?A tag SNP is a representative single nucleotide polymorphism (SNP) in a region of the genome with high linkage disequilibrium (LD). To find out the tagging SNP in each haplotype block-At the Display Menu,choose Show tags in blocks.There are 3 ha
18、plotype blocks and each block consisting 2 tagging SNP; Block 1 comprises 2 tagging SNP i.e., marker number 8 and 9. -The frequency of GA was 33.3%. -The frequency of AT was 64.4%. -The frequency of GTwas 2.2%. Block 2 comprises 2 tagging SNP i.e., marker number 13 and 15. -The frequency ofTT was 48.9%. -The frequency of GT was 27.8%. -The frequency of TGwas 22.3%. Block 3 comprises 2 tagging SNP i.e., marker number 24 and 27. -The frequency of CA was 73.3%. -The frequency of GG was 25.6%. -The frequency of CGwas 1.1%.