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Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
Evaluation of probabilistic and logical inference for a SNP annotation system
Terry H Shen1, Peter Tarczy-Hornoch, Landon T Detwiler
1Department of Biomedical and Health Informatics, University of Washington, Seattle, WA 98195-7240, USA. hyshen@u.washington.edu
Journal of Biomedical Informatics
|December 18, 2009
Summary
This study introduces a new system to identify functional single nucleotide polymorphisms (SNPs) that may cause disease. The system uses logical and probabilistic inference for accurate SNP annotation, improving genetic studies.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Genome-Wide Association Studies (GWAS) are crucial for understanding genetic disease mechanisms.
- Single Nucleotide Polymorphisms (SNPs) are key markers in GWAS, and predicting their functionality is vital for analysis.
Purpose of the Study:
- To design and evaluate a system for identifying potentially functional SNPs.
- To assess the feasibility of combining logical and probabilistic inference with federated data for SNP annotation.
Main Methods:
- Development of a system integrating logical and probabilistic inference.
- Application of federated data integration for SNP annotation.
- Evaluation of predictive accuracy for SNP function prediction.
Main Results:
- The developed system demonstrates strong predictive value for SNP annotation.
- Combinations of logical and probabilistic inference show high accuracy in identifying functional SNPs.
- Federated data integration supports both point and regional SNP analysis.
Conclusions:
- Logical and probabilistic inference methods are effective for SNP annotation in GWAS.
- The system provides a valuable tool for a priori and a posteriori analysis of GWA studies.
- Accurate identification of functional SNPs enhances understanding of genetic disease underpinnings.
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,...
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...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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%...
01:09Epistasis 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...