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Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples

BACKGROUND: DNA methylation plays crucial roles in epigenetic gene regulation in normal development and disease pathogenesis. Efficient and accurate quantification of DNA methylation at single base resolution can greatly advance the knowledge of disease mechanisms and be used to identify potential b...

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Autores principales: Lee, Yew Kok, Jin, Shengnan, Duan, Shiwei, Lim, Yen Ching, Ng, Desmond PY, Lin, Xueqin Michelle, Yeo, George SH, Ding, Chunming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895702/
https://www.ncbi.nlm.nih.gov/pubmed/24406024
http://dx.doi.org/10.1186/1480-9222-16-1
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author Lee, Yew Kok
Jin, Shengnan
Duan, Shiwei
Lim, Yen Ching
Ng, Desmond PY
Lin, Xueqin Michelle
Yeo, George SH
Ding, Chunming
author_facet Lee, Yew Kok
Jin, Shengnan
Duan, Shiwei
Lim, Yen Ching
Ng, Desmond PY
Lin, Xueqin Michelle
Yeo, George SH
Ding, Chunming
author_sort Lee, Yew Kok
collection PubMed
description BACKGROUND: DNA methylation plays crucial roles in epigenetic gene regulation in normal development and disease pathogenesis. Efficient and accurate quantification of DNA methylation at single base resolution can greatly advance the knowledge of disease mechanisms and be used to identify potential biomarkers. We developed an improved pipeline based on reduced representation bisulfite sequencing (RRBS) for cost-effective genome-wide quantification of DNA methylation at single base resolution. A selection of two restriction enzymes (Taq(α)I and MspI) enables a more unbiased coverage of genomic regions of different CpG densities. We further developed a highly automated software package to analyze bisulfite sequencing results from the Solexa GAIIx system. RESULTS: With two sequencing lanes, we were able to quantify ~1.8 million individual CpG sites at a minimum sequencing depth of 10. Overall, about 76.7% of CpG islands, 54.9% of CpG island shores and 52.2% of core promoters in the human genome were covered with at least 3 CpG sites per region. CONCLUSIONS: With this new pipeline, it is now possible to perform whole-genome DNA methylation analysis at single base resolution for a large number of samples for understanding how DNA methylation and its changes are involved in development, differentiation, and disease pathogenesis.
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spelling pubmed-38957022014-01-21 Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples Lee, Yew Kok Jin, Shengnan Duan, Shiwei Lim, Yen Ching Ng, Desmond PY Lin, Xueqin Michelle Yeo, George SH Ding, Chunming Biol Proced Online Methodology BACKGROUND: DNA methylation plays crucial roles in epigenetic gene regulation in normal development and disease pathogenesis. Efficient and accurate quantification of DNA methylation at single base resolution can greatly advance the knowledge of disease mechanisms and be used to identify potential biomarkers. We developed an improved pipeline based on reduced representation bisulfite sequencing (RRBS) for cost-effective genome-wide quantification of DNA methylation at single base resolution. A selection of two restriction enzymes (Taq(α)I and MspI) enables a more unbiased coverage of genomic regions of different CpG densities. We further developed a highly automated software package to analyze bisulfite sequencing results from the Solexa GAIIx system. RESULTS: With two sequencing lanes, we were able to quantify ~1.8 million individual CpG sites at a minimum sequencing depth of 10. Overall, about 76.7% of CpG islands, 54.9% of CpG island shores and 52.2% of core promoters in the human genome were covered with at least 3 CpG sites per region. CONCLUSIONS: With this new pipeline, it is now possible to perform whole-genome DNA methylation analysis at single base resolution for a large number of samples for understanding how DNA methylation and its changes are involved in development, differentiation, and disease pathogenesis. BioMed Central 2014-01-09 /pmc/articles/PMC3895702/ /pubmed/24406024 http://dx.doi.org/10.1186/1480-9222-16-1 Text en Copyright © 2014 Lee 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. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology
Lee, Yew Kok
Jin, Shengnan
Duan, Shiwei
Lim, Yen Ching
Ng, Desmond PY
Lin, Xueqin Michelle
Yeo, George SH
Ding, Chunming
Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples
title Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples
title_full Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples
title_fullStr Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples
title_full_unstemmed Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples
title_short Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples
title_sort improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples
topic Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895702/
https://www.ncbi.nlm.nih.gov/pubmed/24406024
http://dx.doi.org/10.1186/1480-9222-16-1
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