Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

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,...
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu01:29

Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu

Genetic variations significantly influence drug response through pharmacokinetics, receptor interactions, and biologic milieu modifications. Pharmacokinetic alterations impact drug metabolism and clearance, affecting efficacy and toxicity. Variants in drug-metabolizing enzymes, such as CYP2C9 and CYP2C19, alter drug activation and elimination. For example, CYP2C9 loss-of-function variants require lower warfarin doses to prevent excessive bleeding, while CYP2C19 variants reduce clopidogrel...
Genome Copying Errors02:46

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
Mutations01:39

Mutations

Overview
Mutations01:35

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Genetic architecture of the murine serum metabolome reveals carboxyl esterases as master regulators of circulating fatty acid metabolism.

bioRxiv : the preprint server for biology·2026
Same author

Integrated analysis of blood donor metabolic phenotypes and genetic traits on red blood cell transfusion effectiveness.

Blood. Red cells & iron·2026
Same author

The red blood cell proteome and interactome identify a Band 3-BLVRB axis regulating hypoxic metabolic adaptation.

Blood·2026
Same author

GPX4 regulates lipid peroxidation and ferroptosis of stored red blood cells.

Blood. Red cells & iron·2026
Same author

A single-nucleus multiome analysis of transcriptome and chromatin accessibility reveals cell-type-specific immune modulation for chronic cannabis use among people with HIV infection.

bioRxiv : the preprint server for biology·2026
Same author

Improved red blood cell storage quality of blood from donors carrying the hypermorphic PIMT I120 variant.

HemaSphere·2026
Same journal

Integrating transcriptomics and metabolomics reveals the molecular landscape of sperm maturation driven by regional differentiation in the epididymis of Guizhou-Guiqian semi-fine wool sheep.

Genomics·2026
Same journal

Impact of genotype on histopathology and clinical characters in a Chinese cohort with obstructive hypertrophic cardiomyopathy.

Genomics·2026
Same journal

A novel reusable transcriptome-wide association study workflow used to map key genes linked to important cattle traits.

Genomics·2026
Same journal

The large mitochondrial genome of Syndiclis anlungensis (Lauraceae): Genome structure, comparative analysis, and phylogenetic relationships with other Syndiclis species.

Genomics·2026
Same journal

DeepGEP: Deep learning for gene expression prediction from multi-omics in mammals.

Genomics·2026
Same journal

Molecular features of external Auditory Canal cholesteatoma by microbial metagenomic sequencing.

Genomics·2026
See all related articles

Related Experiment Video

Updated: Jun 25, 2026

Frequency and Distribution of Crossovers in Caenorhabditis elegans Meiosis by SNP Genotyping using Real-time PCR
06:18

Frequency and Distribution of Crossovers in Caenorhabditis elegans Meiosis by SNP Genotyping using Real-time PCR

Published on: July 11, 2025

Single nucleotide polymorphisms affect both cis- and trans-eQTLs.

Lang Chen1, Grier P Page, Tapan Mehta

  • 1Department of Biostatistics, Section on Statistical Genetics, School of Public Health, University of Alabama at Birmingham, AL 35209, USA.

Genomics
|March 3, 2009
PubMed
Summary
This summary is machine-generated.

Single nucleotide polymorphisms (SNPs) can impact gene expression array performance. Filtering out SNP-containing probes improves expression quantitative trait loci (eQTL) mapping accuracy by enhancing probe set summaries.

More Related Videos

A Method to Study the C924T Polymorphism of the Thromboxane A2 Receptor Gene
07:00

A Method to Study the C924T Polymorphism of the Thromboxane A2 Receptor Gene

Published on: April 1, 2019

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Related Experiment Videos

Last Updated: Jun 25, 2026

Frequency and Distribution of Crossovers in Caenorhabditis elegans Meiosis by SNP Genotyping using Real-time PCR
06:18

Frequency and Distribution of Crossovers in Caenorhabditis elegans Meiosis by SNP Genotyping using Real-time PCR

Published on: July 11, 2025

A Method to Study the C924T Polymorphism of the Thromboxane A2 Receptor Gene
07:00

A Method to Study the C924T Polymorphism of the Thromboxane A2 Receptor Gene

Published on: April 1, 2019

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Single nucleotide polymorphisms (SNPs) located between microarray probes and RNA targets can compromise expression array performance by reducing hybridization efficiency.
  • This phenomenon can introduce noise and bias into gene expression measurements, potentially affecting downstream analyses such as expression quantitative trait loci (eQTL) mapping.

Purpose of the Study:

  • To investigate the impact of SNPs on Affymetrix GeneChip probe set summaries.
  • To evaluate the effect of SNPs on expression quantitative trait loci (eQTL) mapping results using both mouse and human datasets.

Main Methods:

  • Analysis of two eQTL datasets (one mouse, one human) examining Affymetrix GeneChip data.
  • Systematic removal of probes containing SNPs to assess changes in probe set summaries.
  • Comparison of eQTL mapping results with and without SNP-containing probes across varying significance thresholds.

Main Results:

  • Removing SNP-containing probes significantly altered probe set summaries, with greater changes observed as more SNP probes were excluded.
  • Less than 70% of significant eQTL peaks remained concordant when comparing analyses with and without SNP-containing probes, irrespective of the significance threshold.
  • SNPs were found to influence both cis- and trans-acting eQTLs.

Conclusions:

  • SNPs demonstrably affect both probe set summaries and eQTL mapping outcomes.
  • Filtering out SNP-containing probes is a crucial step to enhance the accuracy and reliability of eQTL mapping.
  • This study underscores the importance of accounting for genetic variation at the probe level for robust genomic analyses.