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Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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HapMap SNP Scanner: an online program to mine SNPs responsible for cell phenotype.

T Yamamura¹, J Hikita, M Bleakley

¹Division of Immunology, Aichi Cancer Center Research Center, Nagoya, Aichi, Japan.

Tissue Antigens

|May 10, 2012

Summary

This study introduces HapMap SNP Scanner, an online tool to identify single-nucleotide polymorphisms (SNPs) linked to minor histocompatibility antigens. This aids in understanding transplant rejection and developing personalized therapies.

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Published on: April 4, 2018

Area of Science:

Immunogenetics
Computational Biology
Genomics

Background:

Minor histocompatibility (H) antigens are crucial in allogeneic hematopoietic stem cell transplantation (HSCT), driving graft-vs-host and graft-vs-tumor responses.
Identifying these antigens is key to improving HSCT outcomes and developing targeted therapies.

Purpose of the Study:

To develop and present an interactive online program, 'HapMap SNP Scanner', for identifying single-nucleotide polymorphisms (SNPs) associated with minor H antigen generation.
To demonstrate the utility of this tool in conjunction with existing datasets and immunologic assays.

Main Methods:

Utilized the International HapMap Project dataset, focusing on linkage disequilibrium blocks.
Integrated immunologic assays assessing T-cell recognition of minor H antigen-specific T cells against HapMap B-lymphoid cell lines.
Developed an interactive website incorporating genotyping data (CEU, JPT, CHB, YRI) and phenotype data to identify candidate SNPs.

Main Results:

The 'HapMap SNP Scanner' successfully identifies candidate SNPs correlated with observed phenotypes related to minor H antigens.
The tool facilitates the discovery of novel SNPs responsible for minor H antigen generation.

Conclusions:

The HapMap SNP Scanner substantially accelerates the discovery of minor H antigens.
This approach is adaptable for identifying SNPs related to other cell phenotypes, such as drug sensitivity, enabling personalized medicine strategies.