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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.
GWAS does not require the identification of the target gene involved in...

Single Nucleotide Polymorphisms-SNPs

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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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Comparing Copy Number Variations and SNPs

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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Related Experiment Video

Updated: Jun 2, 2026

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array.

Thomas J Hoffmann¹, Mark N Kvale, Stephanie E Hesselson

¹Institute for Human Genetics, University of California, San Francisco 94143-0794, CA, USA. tjhoffm@gmail.com

|May 14, 2011

Summary

A new Affymetrix Axiom microarray enables efficient genotyping for large-scale genome-wide association studies. This technology provides high-quality genetic data for European ancestry individuals, advancing genetic research.

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Published on: June 21, 2018

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Infinium Assay for Large-scale SNP Genotyping Applications

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Area of Science:

Genetics
Genomics
Bioinformatics

Background:

Genome-wide association studies (GWAS) rely on efficient genotyping technologies.
Advancements in genotyping are crucial for large-scale genetic research.

Purpose of the Study:

To develop and evaluate a next-generation microarray for genotyping individuals of European ancestry.
To assess the performance of the Affymetrix Axiom genotyping technology for GWAS.

Main Methods:

Development of a microarray with 674,517 single nucleotide polymorphisms (SNPs).
Genotyping of 80,301 saliva-derived DNA samples from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH).
Coverage assessment using imputation and cross-validation.

Main Results:

High-quality genotypes with sample success rates above 94%.
SNP call rates exceeding 98% for successful samples.
Production of 462 million genotypes per week per Axiom system.

Conclusions:

The new Axiom microarray offers excellent genome-wide, gene-based, and candidate-SNP coverage.
This technology is a valuable tool for large-scale GWAS.
The platform demonstrates high efficiency and data quality for genetic studies.