Related Experiment Video
Updated: May 21, 2026
11:35
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
Published on: August 21, 2016
FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to
Simon G Coetzee1, Suhn K Rhie, Benjamin P Berman
1Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
Nucleic Acids Research
|June 12, 2012
Summary
Identifying functional single nucleotide polymorphisms (SNPs) is challenging. This study introduces a software package to prioritize candidate functional SNPs using epigenomic data, aiding complex disease research.
Area of Science:
- Genetics
- Bioinformatics
Background:
- Genome-wide association studies (GWAS) identify tagSNPs for complex disease risk.
- Distinguishing functional SNPs from linked ones, especially in non-coding regions, is difficult.
Purpose of the Study:
- To introduce a novel R/Bioconductor software package for identifying candidate functional SNPs.
- To integrate diverse genomic datasets for improved SNP prioritization.
Main Methods:
- Utilized tagSNP locations and linkage disequilibrium data from the 1000 Genomes Project.
- Integrated non-coding chromatin and epigenomic mapping data.
- Developed an R/Bioconductor package named FunciSNP.
Main Results:
- The software enables the identification of candidate functional SNPs.
- It prioritizes SNPs based on epigenomic features, aiding functional interpretation.
- Facilitates distinguishing potentially functional SNPs from mere genetic associations.
Conclusions:
- The developed software provides a powerful tool for functional SNP discovery.
- This approach enhances the interpretation of GWAS results by prioritizing candidate functional variants.
- Aids in understanding the genetic basis of complex diseases.
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...
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%...
02:02Genomics
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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...
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