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Updated: Jul 9, 2026
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and
Joke Reumers1, Lucia Conde, Ignacio Medina
1Switch Laboratory, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Switch Laboratory, VIB, Pleinlaan 2, 1050 Brussel, Belgium.
Nucleic Acids Research
|December 19, 2007
Summary
The SNPeffect and PupaSuite databases now offer synchronized annotations for human genetic variations, including coding and non-coding single nucleotide polymorphisms (SNPs). This integration aids in interpreting disease associations and guiding genetic research.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Single nucleotide polymorphisms (SNPs) are a primary source of human genome variation, influencing drug response, disease susceptibility, and phenotypic traits.
- Distinguishing disease-causing mutations from polymorphisms is challenging in genetic studies.
- Functional annotation of single nucleotide changes is crucial for experimental interpretation.
Purpose of the Study:
- To synchronize the SNPeffect and PupaSuite databases for comprehensive SNP annotation.
- To provide enhanced functional and structural implications for both coding and non-coding SNPs.
- To integrate human disease mutation data and protein information for broader research utility.
Main Methods:
- Synchronized annotation of coding and non-coding SNPs across SNPeffect and PupaSuite databases.
- Incorporated new prediction tools for protein aggregation (Tango2), amyloid formation (Waltz), and chaperone interactions (Hsp70).
- Added predictions for SNPs in regulatory elements (silencers, miRNAs, TFBSs, splice sites) and expanded to mouse and rat genomes.
- Developed a PupaSuite web service for programmatic data access.
Main Results:
- The combined database contains annotations for over 4.9 million regulatory and 133,000 coding human SNPs.
- Includes data for 14,935 human disease mutations and phenotypic descriptions for 43,797 human proteins.
- Provides predictions for SNPs in silencers, miRNAs, TFBSs, and splice sites, enhancing regulatory SNP analysis.
Conclusions:
- The synchronized SNPeffect and PupaSuite databases offer a valuable, integrated resource for annotating human genetic variations.
- Enhanced annotation capabilities facilitate the interpretation of SNP effects on protein function, disease association, and gene regulation.
- The expanded scope, including cross-species data and web services, supports diverse genomic research applications.
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