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Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations

BACKGROUND: Restriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this...

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Autores principales: Smiraglia, Dominic J, Kazhiyur-Mannar, Ramakrishnan, Oakes, Christopher C, Wu, Yue-Zhong, Liang, Ping, Ansari, Tahmina, Su, Jian, Rush, Laura J, Smith, Laura T, Yu, Li, Liu, Chunhui, Dai, Zunyan, Chen, Shih-Shih, Wang, Shu-Huei, Costello, Joseph, Ioshikhes, Ilya, Dawson, David W, Hong, Jason S, Teitell, Michael A, Szafranek, Angela, Camoriano, Marta, Song, Fei, Elliott, Rosemary, Held, William, Trasler, Jacquetta M, Plass, Christoph, Wenger, Rephael
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2235865/
https://www.ncbi.nlm.nih.gov/pubmed/18053125
http://dx.doi.org/10.1186/1471-2164-8-446
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author Smiraglia, Dominic J
Kazhiyur-Mannar, Ramakrishnan
Oakes, Christopher C
Wu, Yue-Zhong
Liang, Ping
Ansari, Tahmina
Su, Jian
Rush, Laura J
Smith, Laura T
Yu, Li
Liu, Chunhui
Dai, Zunyan
Chen, Shih-Shih
Wang, Shu-Huei
Costello, Joseph
Ioshikhes, Ilya
Dawson, David W
Hong, Jason S
Teitell, Michael A
Szafranek, Angela
Camoriano, Marta
Song, Fei
Elliott, Rosemary
Held, William
Trasler, Jacquetta M
Plass, Christoph
Wenger, Rephael
author_facet Smiraglia, Dominic J
Kazhiyur-Mannar, Ramakrishnan
Oakes, Christopher C
Wu, Yue-Zhong
Liang, Ping
Ansari, Tahmina
Su, Jian
Rush, Laura J
Smith, Laura T
Yu, Li
Liu, Chunhui
Dai, Zunyan
Chen, Shih-Shih
Wang, Shu-Huei
Costello, Joseph
Ioshikhes, Ilya
Dawson, David W
Hong, Jason S
Teitell, Michael A
Szafranek, Angela
Camoriano, Marta
Song, Fei
Elliott, Rosemary
Held, William
Trasler, Jacquetta M
Plass, Christoph
Wenger, Rephael
author_sort Smiraglia, Dominic J
collection PubMed
description BACKGROUND: Restriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning." RESULTS: We report the development of a virtual RLGS method (vRLGS) that allows for RLGS spot identification in any sequenced genome and with any enzyme combination. We report significant improvements in predicting DNA fragment migration patterns by incorporating sequence information into the migration models, and demonstrate a median Euclidian distance between actual and predicted spot migration of 0.18 centimeters for the most complex human RLGS pattern. We report the confirmed identification of 795 human and 530 mouse RLGS spots for the most commonly used enzyme combinations. We also developed a method to filter the virtual spots to reduce the number of extra spots seen on a virtual profile for both the mouse and human genomes. We demonstrate use of this filter to simplify spot cloning and to assist in the identification of spots exhibiting tissue-specific methylation. CONCLUSION: The new vRLGS system reported here is highly robust for the identification of novel RLGS spots. The migration models developed are not specific to the genome being studied or the enzyme combination being used, making this tool broadly applicable. The identification of hundreds of mouse and human RLGS spot loci confirms the strong bias of RLGS studies to focus on CpG islands and provides a valuable resource to rapidly study their methylation.
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spelling pubmed-22358652008-02-11 Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations Smiraglia, Dominic J Kazhiyur-Mannar, Ramakrishnan Oakes, Christopher C Wu, Yue-Zhong Liang, Ping Ansari, Tahmina Su, Jian Rush, Laura J Smith, Laura T Yu, Li Liu, Chunhui Dai, Zunyan Chen, Shih-Shih Wang, Shu-Huei Costello, Joseph Ioshikhes, Ilya Dawson, David W Hong, Jason S Teitell, Michael A Szafranek, Angela Camoriano, Marta Song, Fei Elliott, Rosemary Held, William Trasler, Jacquetta M Plass, Christoph Wenger, Rephael BMC Genomics Methodology Article BACKGROUND: Restriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning." RESULTS: We report the development of a virtual RLGS method (vRLGS) that allows for RLGS spot identification in any sequenced genome and with any enzyme combination. We report significant improvements in predicting DNA fragment migration patterns by incorporating sequence information into the migration models, and demonstrate a median Euclidian distance between actual and predicted spot migration of 0.18 centimeters for the most complex human RLGS pattern. We report the confirmed identification of 795 human and 530 mouse RLGS spots for the most commonly used enzyme combinations. We also developed a method to filter the virtual spots to reduce the number of extra spots seen on a virtual profile for both the mouse and human genomes. We demonstrate use of this filter to simplify spot cloning and to assist in the identification of spots exhibiting tissue-specific methylation. CONCLUSION: The new vRLGS system reported here is highly robust for the identification of novel RLGS spots. The migration models developed are not specific to the genome being studied or the enzyme combination being used, making this tool broadly applicable. The identification of hundreds of mouse and human RLGS spot loci confirms the strong bias of RLGS studies to focus on CpG islands and provides a valuable resource to rapidly study their methylation. BioMed Central 2007-11-30 /pmc/articles/PMC2235865/ /pubmed/18053125 http://dx.doi.org/10.1186/1471-2164-8-446 Text en Copyright © 2007 Smiraglia et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Smiraglia, Dominic J
Kazhiyur-Mannar, Ramakrishnan
Oakes, Christopher C
Wu, Yue-Zhong
Liang, Ping
Ansari, Tahmina
Su, Jian
Rush, Laura J
Smith, Laura T
Yu, Li
Liu, Chunhui
Dai, Zunyan
Chen, Shih-Shih
Wang, Shu-Huei
Costello, Joseph
Ioshikhes, Ilya
Dawson, David W
Hong, Jason S
Teitell, Michael A
Szafranek, Angela
Camoriano, Marta
Song, Fei
Elliott, Rosemary
Held, William
Trasler, Jacquetta M
Plass, Christoph
Wenger, Rephael
Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations
title Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations
title_full Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations
title_fullStr Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations
title_full_unstemmed Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations
title_short Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations
title_sort restriction landmark genomic scanning (rlgs) spot identification by second generation virtual rlgs in multiple genomes with multiple enzyme combinations
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2235865/
https://www.ncbi.nlm.nih.gov/pubmed/18053125
http://dx.doi.org/10.1186/1471-2164-8-446
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