HaploView
1 Download HaploView program from http://www.broad.mit.edu/haploview/haploview-downloads
2 Prepare data for Hapmap format
( Save the SNP genotyping data in notepad files (.txt) to prepare for loading on the HapMap.)
3 Open the Haploview and choose HapMap format
Load file (.txt) which can be created from step 2
Click OK4 click on check marker
The alleles of this data will be seen
5 Click on Haplotypes you can see haplotype blocks containing in this data.
In this here there are 3 haplotype blocks in this region of chromosome X will be seen
Block 1 compose of 08 , 09
Block 2 compose of 13 , 14, 15, 16, 17
Block 3 compose of 24 , 25, 26, 27, 28, 29
6 Click LD Plot you can see the result of whole SNPs, and including the position of
all SNPs in each haplotype block.
Three block of haplotype will be seen and each block are composed of SNPs which can be shown in below
Block 1 Haplotype block 1 has 2 SNPs (rs908005 and rs979848).
Block 2
Haplotype block 2 has 5 SNPs (rs1548474, rs1356037, rs1877924, rs997294 and rs1877923).
Block 3
Haplotype block 3 has 6 SNPs (rs1795683, rs1229073, rs1229076, rs1795686, rs1634652 and rs1634656).
7 find the tagging SNPs in each haplotype block
For tagging SNP click Display> show tagging block
in this here Tagging SNPs are include
Block 1 08, 09
Block 2 13, 15
Block 2 24, 27
Answer the question
1. What is the name of haploview format to use in this analysis?
Block 1 Haplotype block 1 has 2 SNPs (rs908005 and rs979848).
Block 2
Haplotype block 2 has 5 SNPs (rs1548474, rs1356037, rs1877924, rs997294 and rs1877923).
Block 3
Haplotype block 3 has 6 SNPs (rs1795683, rs1229073, rs1229076, rs1795686, rs1634652 and rs1634656).
7 find the tagging SNPs in each haplotype block
For tagging SNP click Display> show tagging block
in this here Tagging SNPs are include
Block 1 08, 09
Block 2 13, 15
Block 2 24, 27
Answer the question
1. What is the name of haploview format to use in this analysis?
HapMap Format
2. Please show us the marker and individual quality control of the genotype data use in the analysis?
The marker details are shown in below
# 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 marker’s observed heterozygosity.
PredHET is the marker’s predicted heterozygosity (i.e. 2*MAF*(1-MAF)).
HWpval is the Hardy-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 individuals).
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 and unchecked if it fails one or more tests.
The individual quality controls’ details are:
Hardy-Weinberg p-value cutoff: >0.0010 (per population)
Minimum genotype %: < style="TEXT-ALIGN: center; MARGIN: 0px auto 10px; WIDTH: 515px; DISPLAY: block; HEIGHT: 482px; CURSOR: hand" id="BLOGGER_PHOTO_ID_5409762832125646898" border="0" alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAYQZU7UMbEtqDoL8YjQNDzyXo28cvAwzIrhNniORJech1RmDRsdV4y1IK3mlmg00HnrEoQyASArkFS66JOWnrqNzDm8dSHiAdQ4ILIrRrVZNg_259_2jUXrGt0kDD6pZk29Mr6RlzclKP/s320/2009-11-29_235850.gif">
2. Please show us the marker and individual quality control of the genotype data use in the analysis?
The marker details are shown in below
# 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 marker’s observed heterozygosity.
PredHET is the marker’s predicted heterozygosity (i.e. 2*MAF*(1-MAF)).
HWpval is the Hardy-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 individuals).
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 and unchecked if it fails one or more tests.
The individual quality controls’ details are:
Hardy-Weinberg p-value cutoff: >0.0010 (per population)
Minimum genotype %: < style="TEXT-ALIGN: center; MARGIN: 0px auto 10px; WIDTH: 515px; DISPLAY: block; HEIGHT: 482px; CURSOR: hand" id="BLOGGER_PHOTO_ID_5409762832125646898" border="0" alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAYQZU7UMbEtqDoL8YjQNDzyXo28cvAwzIrhNniORJech1RmDRsdV4y1IK3mlmg00HnrEoQyASArkFS66JOWnrqNzDm8dSHiAdQ4ILIrRrVZNg_259_2jUXrGt0kDD6pZk29Mr6RlzclKP/s320/2009-11-29_235850.gif">
3. Please show us the LD map then explain what do you get from the LD map?
The linkage disequilibrium (LD) map shows the strength of linkage disequilibrium between each SNPs. The more intensity of red color, the higher linkage disequilibrium value it is. This LD map obtained from the question has 30 markers. By using “Confidence Intervals” algorithm, there are 3 haplotype blocks in the map. The first block, 18 kb in size, consists of marker number 8 and 9. The second block, 80 kb in size, consists of marker number 13 – 17. Finally, the third block, 48 kb in size, consists of marker number 24-29. (See answer of the 4th question for the detailed on Haplotype block)
4. How many haplotype blocks in this region of Chromosome X, then explain how to interpret them
The haplotype display shows each haplotype in a block with its population frequency and connections from one block to the next. This represents the level of recombination between the two blocks .
there are 3 haplotype blocks in the map.
The first block consists of marker number 8 and 9.
The second block consists of marker number 13,14,15,16 and 17.
The third block consists of marker number 24, 25, 26, 27, 28 and 29
The linkage disequilibrium (LD) map shows the strength of linkage disequilibrium between each SNPs. The more intensity of red color, the higher linkage disequilibrium value it is. This LD map obtained from the question has 30 markers. By using “Confidence Intervals” algorithm, there are 3 haplotype blocks in the map. The first block, 18 kb in size, consists of marker number 8 and 9. The second block, 80 kb in size, consists of marker number 13 – 17. Finally, the third block, 48 kb in size, consists of marker number 24-29. (See answer of the 4th question for the detailed on Haplotype block)
4. How many haplotype blocks in this region of Chromosome X, then explain how to interpret them
The haplotype display shows each haplotype in a block with its population frequency and connections from one block to the next. This represents the level of recombination between the two blocks .
there are 3 haplotype blocks in the map.
The first block consists of marker number 8 and 9.
The second block consists of marker number 13,14,15,16 and 17.
The third block consists of marker number 24, 25, 26, 27, 28 and 29
5 Could you find out the tagging SNP in each haplotype block, then explain what the tagging SNPs?
For tagging SNP click Display> show tagging block
the grey triangles which will appear at the location of tagging SNPs in each haplotype block
in this here Tagging SNPs are include
Block 1 08, 09
Block 2 13, 15
Block 2 24, 27
For tagging SNP click Display> show tagging block
the grey triangles which will appear at the location of tagging SNPs in each haplotype block
in this here Tagging SNPs are include
Block 1 08, 09
Block 2 13, 15
Block 2 24, 27
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