Related Experiment Video
Updated: Jun 1, 2026
09:10
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU
Satish Chikkagoudar1, Kai Wang, Mingyao Li
1Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA. satishc@mail.med.upenn.edu.
BMC Research Notes
|May 28, 2011
Summary
GENIE software accelerates gene-gene interaction analysis for binary traits by leveraging parallel processing on Graphics Processing Units (GPUs) and Central Processing Units (CPUs). This novel approach significantly speeds up computationally intensive genetic association studies.
Area of Science:
- Genetics
- Computational Biology
- Bioinformatics
Background:
- Gene-gene interaction analysis in genetic association studies is computationally demanding, especially with numerous single nucleotide polymorphisms (SNPs).
- Modern multi-core Central Processing Units (CPUs) and Graphics Processing Units (GPUs) offer significant parallel processing capabilities.
- Existing genetic analysis software often fails to fully exploit these multi-core architectures for interaction analysis in binary traits.
Purpose of the Study:
- To introduce GENIE, a novel software package designed to parallelize gene-gene interaction analysis.
- To enable efficient utilization of multi-core CPU and GPU processors for genetic association studies.
- To address the computational intensity of analyzing interactions involving a large number of SNPs.
Main Methods:
- GENIE parallelizes interaction analysis by partitioning genetic association study datasets into fragments.
- It analyzes interactions within fragments and between fragments concurrently using multiple CPU or GPU cores.
- The software reads the entire dataset into memory for efficient processing.
Main Results:
- GENIE was tested on a large-scale candidate gene study for high-density lipoprotein cholesterol.
- The GPU mode of GENIE demonstrated a 27-fold speedup compared to its single-core CPU mode.
- This highlights the substantial performance gains achievable with GPU acceleration.
Conclusions:
- GENIE is an open-source, economical, user-friendly, and scalable software solution.
- Future advancements in GPU technology are expected to yield even greater speedups.
- The software is available for download, including documentation and source code.
Related Concept Videos
01:11Genome-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...
GWAS does not require the identification of the target gene involved in...
02:02Genomics
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
02:46Genetic 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...
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...
01:29Pharmacogenomics: 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...
02:33Combinatorial Gene Control
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
00:49What is Genetic Engineering?
Overview