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Updated: May 12, 2026
10:27
Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria
Published on: November 10, 2015
Single-nucleotide polymorphism masking
Nicole A R Walter1, Shannon K McWeeney, Sandra T Peters
1Department of Behavioral Science, Oregon Health & Science University, Portland, Oregon.
Summary
Single nucleotide polymorphisms (SNPs) can impact genome-wide gene expression analysis. This study introduces SNP masking to remove SNP-affected probes, improving data accuracy for genetically diverse samples.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Microarrays are essential for genome-scale gene expression evaluation.
- Analysis at the individual probe level is often neglected, especially in studies involving genetic variations.
- Naturally occurring single nucleotide polymorphisms (SNPs) differentiate individuals and can interfere with gene expression data.
Purpose of the Study:
- To highlight the impact of SNPs on gene expression analysis using microarrays.
- To introduce and validate a method called SNP masking for improving data accuracy.
- To address challenges in comparing gene expression across genetically diverse populations.
Main Methods:
- Describing the potential effects of SNPs on microarray probe hybridization.
- Implementing a computational approach termed SNP masking.
- Removing probes affected by single nucleotide polymorphisms (SNPs) from the dataset.
Main Results:
- SNP masking effectively identifies and removes probes influenced by genetic variations.
- This method ameliorates hybridization issues caused by SNPs.
- Improved accuracy in detecting gene expression differences among genetically unique or modified animals.
Conclusions:
- SNP masking is a valuable and feasible strategy for enhancing the reliability of microarray gene expression data.
- Addressing probe-level variations, particularly SNPs, is crucial for accurate genomic comparisons.
- This approach facilitates more precise gene expression studies in diverse animal models.
Related Concept Videos
01:05Single 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,...
02:26Comparing 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%...
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%...