Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.

DNA-methylation is an important epigenetic feature in health and disease. Methylated sequence capturing by Methyl Binding Domain (MBD) based enrichment followed by second-generation sequencing provides the best combination of sensitivity and cost-efficiency for genome-wide DNA-methylation profiling....

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Autores principales:	Tim De Meyer, Evi Mampaey, Michaël Vlemmix, Simon Denil, Geert Trooskens, Jean-Pierre Renard, Sarah De Keulenaer, Pierre Dehan, Gerben Menschaert, Wim Van Criekinge
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f607c926905745418aa1e8efdb96cc89
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spelling	oai:doaj.org-article:f607c926905745418aa1e8efdb96cc892021-11-18T07:53:15ZQuality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.1932-620310.1371/journal.pone.0059068https://doaj.org/article/f607c926905745418aa1e8efdb96cc892013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23554971/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203DNA-methylation is an important epigenetic feature in health and disease. Methylated sequence capturing by Methyl Binding Domain (MBD) based enrichment followed by second-generation sequencing provides the best combination of sensitivity and cost-efficiency for genome-wide DNA-methylation profiling. However, existing implementations are numerous, and quality control and optimization require expensive external validation. Therefore, this study has two aims: 1) to identify a best performing kit for MBD-based enrichment using independent validation data, and 2) to evaluate whether quality evaluation can also be performed solely based on the characteristics of the generated sequences. Five commercially available kits for MBD enrichment were combined with Illumina GAIIx sequencing for three cell lines (HCT15, DU145, PC3). Reduced representation bisulfite sequencing data (all three cell lines) and publicly available Illumina Infinium BeadChip data (DU145 and PC3) were used for benchmarking. Consistent large-scale differences in yield, sensitivity and specificity between the different kits could be identified, with Diagenode's MethylCap kit as overall best performing kit under the tested conditions. This kit could also be identified with the Fragment CpG-plot, which summarizes the CpG content of the captured fragments, implying that the latter can be used as a tool to monitor data quality. In conclusion, there are major quality differences between kits for MBD-based capturing of methylated DNA, with the MethylCap kit performing best under the used settings. The Fragment CpG-plot is able to monitor data quality based on inherent sequence data characteristics, and is therefore a cost-efficient tool for experimental optimization, but also to monitor quality throughout routine applications.Tim De MeyerEvi MampaeyMichaël VlemmixSimon DenilGeert TrooskensJean-Pierre RenardSarah De KeulenaerPierre DehanGerben MenschaertWim Van CriekingePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 3, p e59068 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tim De Meyer Evi Mampaey Michaël Vlemmix Simon Denil Geert Trooskens Jean-Pierre Renard Sarah De Keulenaer Pierre Dehan Gerben Menschaert Wim Van Criekinge Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
description	DNA-methylation is an important epigenetic feature in health and disease. Methylated sequence capturing by Methyl Binding Domain (MBD) based enrichment followed by second-generation sequencing provides the best combination of sensitivity and cost-efficiency for genome-wide DNA-methylation profiling. However, existing implementations are numerous, and quality control and optimization require expensive external validation. Therefore, this study has two aims: 1) to identify a best performing kit for MBD-based enrichment using independent validation data, and 2) to evaluate whether quality evaluation can also be performed solely based on the characteristics of the generated sequences. Five commercially available kits for MBD enrichment were combined with Illumina GAIIx sequencing for three cell lines (HCT15, DU145, PC3). Reduced representation bisulfite sequencing data (all three cell lines) and publicly available Illumina Infinium BeadChip data (DU145 and PC3) were used for benchmarking. Consistent large-scale differences in yield, sensitivity and specificity between the different kits could be identified, with Diagenode's MethylCap kit as overall best performing kit under the tested conditions. This kit could also be identified with the Fragment CpG-plot, which summarizes the CpG content of the captured fragments, implying that the latter can be used as a tool to monitor data quality. In conclusion, there are major quality differences between kits for MBD-based capturing of methylated DNA, with the MethylCap kit performing best under the used settings. The Fragment CpG-plot is able to monitor data quality based on inherent sequence data characteristics, and is therefore a cost-efficient tool for experimental optimization, but also to monitor quality throughout routine applications.
format	article
author	Tim De Meyer Evi Mampaey Michaël Vlemmix Simon Denil Geert Trooskens Jean-Pierre Renard Sarah De Keulenaer Pierre Dehan Gerben Menschaert Wim Van Criekinge
author_facet	Tim De Meyer Evi Mampaey Michaël Vlemmix Simon Denil Geert Trooskens Jean-Pierre Renard Sarah De Keulenaer Pierre Dehan Gerben Menschaert Wim Van Criekinge
author_sort	Tim De Meyer
title	Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
title_short	Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
title_full	Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
title_fullStr	Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
title_full_unstemmed	Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
title_sort	quality evaluation of methyl binding domain based kits for enrichment dna-methylation sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/f607c926905745418aa1e8efdb96cc89
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Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.

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