A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays

Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masanori Kawakita, Takayuki Sakaguchi, Nori Kurata

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Background: High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: < ~300 Mb), whole-genome DNA hybridization to expression arrays has been used for various applications. In large genome species, transcript hybridization to expression arrays has been used for genotyping. Although rice is a fully sequenced model plant of medium genome size (~400 Mb), there are a few examples of the use of rice oligonucleotide array as a genotyping tool.Results: We compared the single feature polymorphism (SFP) detection performance of whole-genome and transcript hybridizations using the Affymetrix GeneChip® Rice Genome Array, using the rice cultivars with full genome sequence, japonica cultivar Nipponbare and indica cultivar 93-11. Both genomes were surveyed for all probe target sequences. Only completely matched 25-mer single copy probes of the Nipponbare genome were extracted, and SFPs between them and 93-11 sequences were predicted. We investigated optimum conditions for SFP detection in both whole genome and transcript hybridization using differences between perfect match and mismatch probe intensities of non-polymorphic targets, assuming that these differences are representative of those between mismatch and perfect targets. Several statistical methods of SFP detection by whole-genome hybridization were compared under the optimized conditions. Causes of false positives and negatives in SFP detection in both types of hybridization were investigated.Conclusions: The optimizations allowed a more than 20% increase in true SFP detection in whole-genome hybridization and a large improvement of SFP detection performance in transcript hybridization. Significance analysis of the microarray for log-transformed raw intensities of PM probes gave the best performance in whole genome hybridization, and 22,936 true SFPs were detected with 23.58% false positives by whole genome hybridization. For transcript hybridization, stable SFP detection was achieved for highly expressed genes, and about 3,500 SFPs were detected at a high sensitivity (> 50%) in both shoot and young panicle transcripts. High SFP detection performances of both genome and transcript hybridizations indicated that microarrays of a complex genome (e.g., of Oryza sativa) can be effectively utilized for whole genome genotyping to conduct mutant mapping and analysis of quantitative traits such as gene expression levels.

Original languageEnglish
Article number315
JournalBMC Genomics
Volume11
Issue number1
DOIs
Publication statusPublished - May 20 2010

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Genome
Genome Size
Oligonucleotide Array Sequence Analysis
Gene Expression
Oryza
spleen fibrinolytic proteinase (human)

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Cite this

Horiuchi, Y., Harushima, Y., Fujisawa, H., Mochizuki, T., Kawakita, M., Sakaguchi, T., & Kurata, N. (2010). A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays. BMC Genomics, 11(1), [315]. https://doi.org/10.1186/1471-2164-11-315

A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays. / Horiuchi, Youko; Harushima, Yoshiaki; Fujisawa, Hironori; Mochizuki, Takako; Kawakita, Masanori; Sakaguchi, Takayuki; Kurata, Nori.

In: BMC Genomics, Vol. 11, No. 1, 315, 20.05.2010.

Research output: Contribution to journalArticle

Horiuchi, Y, Harushima, Y, Fujisawa, H, Mochizuki, T, Kawakita, M, Sakaguchi, T & Kurata, N 2010, 'A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays', BMC Genomics, vol. 11, no. 1, 315. https://doi.org/10.1186/1471-2164-11-315
Horiuchi, Youko ; Harushima, Yoshiaki ; Fujisawa, Hironori ; Mochizuki, Takako ; Kawakita, Masanori ; Sakaguchi, Takayuki ; Kurata, Nori. / A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays. In: BMC Genomics. 2010 ; Vol. 11, No. 1.
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abstract = "Background: High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: < ~300 Mb), whole-genome DNA hybridization to expression arrays has been used for various applications. In large genome species, transcript hybridization to expression arrays has been used for genotyping. Although rice is a fully sequenced model plant of medium genome size (~400 Mb), there are a few examples of the use of rice oligonucleotide array as a genotyping tool.Results: We compared the single feature polymorphism (SFP) detection performance of whole-genome and transcript hybridizations using the Affymetrix GeneChip{\circledR} Rice Genome Array, using the rice cultivars with full genome sequence, japonica cultivar Nipponbare and indica cultivar 93-11. Both genomes were surveyed for all probe target sequences. Only completely matched 25-mer single copy probes of the Nipponbare genome were extracted, and SFPs between them and 93-11 sequences were predicted. We investigated optimum conditions for SFP detection in both whole genome and transcript hybridization using differences between perfect match and mismatch probe intensities of non-polymorphic targets, assuming that these differences are representative of those between mismatch and perfect targets. Several statistical methods of SFP detection by whole-genome hybridization were compared under the optimized conditions. Causes of false positives and negatives in SFP detection in both types of hybridization were investigated.Conclusions: The optimizations allowed a more than 20{\%} increase in true SFP detection in whole-genome hybridization and a large improvement of SFP detection performance in transcript hybridization. Significance analysis of the microarray for log-transformed raw intensities of PM probes gave the best performance in whole genome hybridization, and 22,936 true SFPs were detected with 23.58{\%} false positives by whole genome hybridization. For transcript hybridization, stable SFP detection was achieved for highly expressed genes, and about 3,500 SFPs were detected at a high sensitivity (> 50{\%}) in both shoot and young panicle transcripts. High SFP detection performances of both genome and transcript hybridizations indicated that microarrays of a complex genome (e.g., of Oryza sativa) can be effectively utilized for whole genome genotyping to conduct mutant mapping and analysis of quantitative traits such as gene expression levels.",
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