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SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip.
Hironori Fujisawa1, Youko Horiuchi, Yoshiaki Harushima
1The Institute of Statistical Mathematics, Tokyo, Japan. fujisawa@ism.ac.jp
BMC Bioinformatics
|May 8, 2009
Summary
We developed SNEP, a novel method for simultaneously detecting nucleotide and expression polymorphisms using oligonucleotide microarrays. This approach improves accuracy in biodiversity studies by distinguishing between genetic variations and gene activity levels.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- High-density oligonucleotide microarrays enable biodiversity studies by analyzing nucleotide and expression polymorphisms.
- Distinguishing between nucleotide and expression polymorphisms is challenging due to variable signal intensities.
- Current methods analyze nucleotide and expression polymorphisms separately.
Purpose of the Study:
- To develop a method for simultaneous detection of nucleotide and expression polymorphisms.
- To overcome the limitations of separate analyses in microarray studies.
- To improve the accuracy of polymorphism detection in biodiversity research.
Main Methods:
- Developed SNEP (Simultaneous Nucleotide and Expression Polymorphism detection), a robust statistical procedure.
- SNEP treats nucleotide polymorphisms as outliers reducing hybridization signal intensity.
- Validated SNEP using barley, rice, and mouse data, including strains with available genome sequences.
Main Results:
- SNEP successfully detected both nucleotide and expression polymorphisms simultaneously.
- Sensitivity and false positive rates for nucleotide polymorphism detection were accurately estimated.
- Expression polymorphism detection demonstrated robustness against nucleotide polymorphisms.
Conclusions:
- SNEP performs well across different genome sizes and outperforms previous methods for nucleotide polymorphism detection.
- The R-software 'SNEP' is publicly available for use.
- This method enhances the ability to study biodiversity by providing integrated polymorphism analysis.
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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%...
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