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

Epistasis Analysis01:09

Epistasis Analysis

Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Epistasis01:39

Epistasis

In addition to multiple alleles at the same locus influencing traits, numerous genes or alleles at different locations may interact and influence phenotypes in a phenomenon called epistasis. For example, rabbit fur can be black or brown depending on whether the animal is homozygous dominant or heterozygous at a TYRP1 locus. However, if the rabbit is also homozygous recessive at a locus on the tyrosinase gene (TYR), it will have an unshaded coat that appears white, regardless of its TYRP1...
Human Genetics01:28

Human Genetics

Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
Incomplete Dominance01:43

Incomplete Dominance

Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
Genome-wide Association Studies-GWAS01:11

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...

You might also read

Related Articles

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

Sort by
Same author

The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors.

Cell genomics·2026
Same author

Beyond Identifier Matching: An Empirical Characterization of Failure Modes in Biomedical Knowledge Graph Integration.

medRxiv : the preprint server for health sciences·2026
Same author

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026
Same author

Advances in Protein Function Prediction from the Fifth CAFA Challenge.

bioRxiv : the preprint server for biology·2026
Same author

Transcriptomic subtypes in high-grade serous ovarian cancer are driven by tumor cellular composition.

bioRxiv : the preprint server for biology·2026
Same author

The Common Fund Data Ecosystem (CFDE).

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jun 21, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Accelerating epistasis analysis in human genetics with consumer graphics hardware.

Nicholas A Sinnott-Armstrong1, Casey S Greene, Fabio Cancare

  • 1Computational Genetics Lab, Department of Genetics, Norris-Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA. Nicholas.A.Sinnott-Armstrong@dartmouth.edu

BMC Research Notes
|July 28, 2009
PubMed
Summary
This summary is machine-generated.

Harnessing graphics processing units (GPUs) for Multifactor Dimensionality Reduction (MDR) significantly accelerates the analysis of gene interactions (epistasis) for common diseases. This cost-effective approach offers a powerful alternative to traditional computing clusters for genetic research.

More Related Videos

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

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

Published on: June 21, 2018

Related Experiment Videos

Last Updated: Jun 21, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

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

Published on: June 21, 2018

Area of Science:

  • Genetics
  • Computational Biology
  • Bioinformatics

Background:

  • Analyzing large-scale human genetic data for disease associations is computationally challenging.
  • Epistasis, or gene-gene interactions, is crucial for understanding complex diseases but computationally intensive to detect.
  • Multifactor Dimensionality Reduction (MDR) is an algorithm for detecting epistasis, but exhaustive analysis is often too slow.

Purpose of the Study:

  • To implement and evaluate the performance of the MDR algorithm on Graphics Processing Units (GPUs).
  • To assess the time efficiency and cost-effectiveness of GPU-based MDR for epistasis analysis.
  • To explore the use of commodity graphics hardware for large-scale genetic analyses.

Main Methods:

  • Implementation of the Multifactor Dimensionality Reduction (MDR) algorithm on Graphics Processing Units (GPUs).
  • Performance comparison against a Java software package running on CPUs and a C++ cluster implementation.
  • Evaluation of computation time and price-to-performance ratio.

Main Results:

  • GPU-based MDR significantly increased performance per machine compared to CPU-based and cluster implementations.
  • A GPU workstation reduced computation time by a factor of 160 compared to an 8-core CPU workstation.
  • GPU solutions offered substantial cost savings, with a three-GPU workstation costing $2000 versus an estimated $82,500 for a comparable cluster.

Conclusions:

  • GPU computing provides a cost-effective method for performing genetic epistasis analysis using MDR on large datasets.
  • This approach eliminates the need for extensive computing cluster infrastructure.
  • Commodity graphics hardware offers a powerful and accessible solution for complex genetic analyses.