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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression
Youko Horiuchi1, Yoshiaki Harushima, Hironori Fujisawa
1Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan.
BMC Genomics
|May 21, 2010
Summary
This study demonstrates that oligonucleotide arrays can effectively genotype rice (Oryza sativa) using both whole-genome and transcript hybridization. Optimized methods significantly improved single feature polymorphism (SFP) detection, enabling robust genotyping for applications like mutant mapping.
Area of Science:
- Genomics
- Plant Science
- Molecular Biology
Background:
- High-density oligonucleotide arrays are established tools for high-throughput genotyping.
- Whole-genome and transcript hybridization methods have been applied in small and large genome species, respectively.
- Rice (Oryza sativa), a medium-sized genome model plant, has limited examples of oligonucleotide array utilization for genotyping.
Purpose of the Study:
- To evaluate and optimize single feature polymorphism (SFP) detection using whole-genome and transcript hybridization on rice oligonucleotide arrays.
- To compare the performance of these hybridization methods in rice (Oryza sativa) cultivars Nipponbare and 93-11.
Main Methods:
- Utilized Affymetrix GeneChip Rice Genome Array for both whole-genome and transcript hybridizations.
- Predicted SFPs by comparing Nipponbare and 93-11 sequences using single-copy probes.
- Investigated optimal conditions for SFP detection by analyzing probe intensity differences and comparing statistical methods.
Main Results:
- Optimized whole-genome hybridization increased true SFP detection by over 20%, identifying 22,936 SFPs with 23.58% false positives.
- Transcript hybridization achieved stable SFP detection for highly expressed genes, detecting approximately 3,500 SFPs with high sensitivity (>50%) in shoot and young panicle tissues.
- Significance analysis of microarrays (SAM) proved most effective for whole-genome hybridization SFP detection.
Conclusions:
- Optimized oligonucleotide array hybridization methods significantly enhance SFP detection in rice.
- Both whole-genome and transcript hybridization approaches are effective for rice genotyping.
- These findings support the use of rice microarrays for whole-genome genotyping, mutant mapping, and quantitative trait analysis.
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