Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.

High-density DNA microarrays are useful tools for analyzing sequence changes in DNA samples. Although microarray analysis provides informative signals from a large number of probes, the analysis and interpretation of these signals have certain inherent limitations, namely, complex dependency of sign...

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Autores principales:	Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Hiroshi Shimizu, Tetsuya Yomo
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c4056a9e5ed84dd088b4bd288eeb8da1
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spelling	oai:doaj.org-article:c4056a9e5ed84dd088b4bd288eeb8da12021-11-18T07:59:48ZDevelopment of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.1932-620310.1371/journal.pone.0054571https://doaj.org/article/c4056a9e5ed84dd088b4bd288eeb8da12013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23382915/?tool=EBIhttps://doaj.org/toc/1932-6203High-density DNA microarrays are useful tools for analyzing sequence changes in DNA samples. Although microarray analysis provides informative signals from a large number of probes, the analysis and interpretation of these signals have certain inherent limitations, namely, complex dependency of signals on the probe sequences and the existence of false signals arising from non-specific binding between probe and target. In this study, we have developed a novel algorithm to detect the single-base substitutions by using microarray data based on a thermodynamic model of hybridization. We modified the thermodynamic model by introducing a penalty for mismatches that represent the effects of substitutions on hybridization affinity. This penalty results in significantly higher detection accuracy than other methods, indicating that the incorporation of hybridization free energy can improve the analysis of sequence variants by using microarray data.Naoaki OnoShingo SuzukiChikara FurusawaHiroshi ShimizuTetsuya YomoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 1, p e54571 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Naoaki Ono Shingo Suzuki Chikara Furusawa Hiroshi Shimizu Tetsuya Yomo Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.
description	High-density DNA microarrays are useful tools for analyzing sequence changes in DNA samples. Although microarray analysis provides informative signals from a large number of probes, the analysis and interpretation of these signals have certain inherent limitations, namely, complex dependency of signals on the probe sequences and the existence of false signals arising from non-specific binding between probe and target. In this study, we have developed a novel algorithm to detect the single-base substitutions by using microarray data based on a thermodynamic model of hybridization. We modified the thermodynamic model by introducing a penalty for mismatches that represent the effects of substitutions on hybridization affinity. This penalty results in significantly higher detection accuracy than other methods, indicating that the incorporation of hybridization free energy can improve the analysis of sequence variants by using microarray data.
format	article
author	Naoaki Ono Shingo Suzuki Chikara Furusawa Hiroshi Shimizu Tetsuya Yomo
author_facet	Naoaki Ono Shingo Suzuki Chikara Furusawa Hiroshi Shimizu Tetsuya Yomo
author_sort	Naoaki Ono
title	Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.
title_short	Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.
title_full	Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.
title_fullStr	Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.
title_full_unstemmed	Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.
title_sort	development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/c4056a9e5ed84dd088b4bd288eeb8da1
work_keys_str_mv	AT naoakiono developmentofaphysicalmodelbasedalgorithmforthedetectionofsinglenucleotidesubstitutionsbyusingtilingmicroarrays AT shingosuzuki developmentofaphysicalmodelbasedalgorithmforthedetectionofsinglenucleotidesubstitutionsbyusingtilingmicroarrays AT chikarafurusawa developmentofaphysicalmodelbasedalgorithmforthedetectionofsinglenucleotidesubstitutionsbyusingtilingmicroarrays AT hiroshishimizu developmentofaphysicalmodelbasedalgorithmforthedetectionofsinglenucleotidesubstitutionsbyusingtilingmicroarrays AT tetsuyayomo developmentofaphysicalmodelbasedalgorithmforthedetectionofsinglenucleotidesubstitutionsbyusingtilingmicroarrays
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Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.

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