This Assignment gave us the part of chromosome X, SNP genotyping result from Hapmap project (http://www.hapmap.org) and asked 2 questions
1. How many haplotype blocks in this region of Chromosome X?
2. Could you find out the tagging SNP in each haplotype block
Introduction about Hapmap project, SNP,and Haplotype
Hapmap project
The International HapMap Project is a multi-country effort to identify and
catalog genetic similarities and differences in human beings.
Goals to compare the genetic sequences of different individuals to identify
chromosomal regions where genetic variants are shared.
SNP
SNP is DNA sequence variations that occur when a single nucleotide (A, T, C, or G)
in the genome sequence is altered. Each individual has many single nucleotide
polymorphisms that together create a unique DNA pattern for that person.
SNPs promise to significantly advance our ability to understand and treat human disease.
Haplotype
haplotype is the genetic constitution of an individual chromosome and it may refer to only one locus or to an entire genome.
Answer the questions
We can answer the above questions by using "Haploview" which is bioinformatics software tool designed to analyze and visualize patterns of linkage disequilibrium in genetic data. Haploview also provides functionality for performing association studies, choosing tagSNPs and estimating haplotype frequencies. Haploview is developed and maintained by Dr. Mark Daly's lab at the MIT/Harvard Broad Institute.
This software available to download at http://www.broad.mit.edu/mpg/haploview/download.php
First download and Install haploview into thecomputer,this software need java for open that can download from the same site.
Second prepare data by copy & paste SNPs data and save in form of Text document.
Open haploview and doing follow the below pictures step by step
The result will show in " Check Markers " display and can select the other displays.
Select LD plot display .This picture is the result from "LD plot" display show the pattern calculated lingkage disequilibium
LD display can show in varies color scheme that user can select but for the first time this program set for standard and have the mening for each color
Select Haplotype display . It shows haplotype in each box.
From all of the result can conclud that this part of chromosome X has 3 haplotype blocks.
