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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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

Single Nucleotide Polymorphisms-SNPs

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,...

Pharmacogenomics: Identification of New Drug Targets

Pharmacogenomics: Identification of New Drug Targets

Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...

Comparing Copy Number Variations and SNPs

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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Microarray-based approach for genome-wide survey of nucleotide polymorphisms.

Brian W Brunelle, Tracy L Nicholson

Methods in Molecular Biology (Clifton, N.J.)

|November 21, 2007

Summary

DNA microarrays reveal genetic differences in Chlamydia trachomatis strains. This comparative genomics approach identifies variable DNA regions, aiding in understanding strain diversity and unique biological traits.

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Area of Science:

Genomics
Molecular Biology
Microbiology

Background:

DNA microarrays are versatile tools for genomic analysis.
Comparative genomics aids in understanding species diversification.
Identifying genetic variations is crucial for linking genotype to phenotype.

Purpose of the Study:

To employ DNA microarrays as a comparative genomics tool.
To identify nucleotide polymorphisms in closely related Chlamydia trachomatis strains.

Main Methods:

Utilizing a competitive hybridization assay.
Employing DNA microarrays for comparative analysis.

Main Results:

Successfully identified polymorphic loci within Chlamydia trachomatis strains.
Demonstrated the utility of DNA microarrays for detecting genomic variations.

Conclusions:

DNA microarrays are effective for comparative genomics in identifying strain-specific genetic differences.
This method facilitates the characterization of genes associated with distinct biological attributes in Chlamydia trachomatis.