Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

Qing Li; Masako Suzuki; Jennifer Wendt; Nicole Patterson; Steven R. Eichten; Peter J. Hermanson; Dawn Green; Jeffrey Jeddeloh; Todd Richmond; Heidi Rosenbaum; Daniel Burgess; Nathan M. Springer; John M. Greally

doi:10.1093/nar/gkv244

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

Qing Li, Masako Suzuki, Jennifer Wendt, Nicole Patterson, Steven R. Eichten, Peter J. Hermanson, Dawn Green, Jeffrey Jeddeloh, Todd Richmond, Heidi Rosenbaum, Daniel Burgess, Nathan M. Springer, John M. Greally

Genetics

Research output: Contribution to journal › Article › peer-review

48 Scopus citations

Abstract

We present a capture-based approach for bisulfite-converted DNA that allows interrogation of predefined genomic locations, allowing quantitative and qualitative assessments of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at CG dinucleotides and in non-CG contexts (CHG, CHH) in mammalian and plant genomes. We show the technique works robustly and reproducibly using as little as 500 ng of starting DNA, with results correlating well with whole genome bisulfite sequencing data, and demonstrate that human DNA can be tested in samples contaminated with microbial DNA. This targeting approach will allow cell type-specific designs to maximize the value of 5mC and 5hmC sequencing.

Original language	English (US)
Article number	e81
Journal	Nucleic acids research
Volume	43
Issue number	12
DOIs	https://doi.org/10.1093/nar/gkv244
State	Published - Jul 13 2015

ASJC Scopus subject areas

Genetics

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abstract = "We present a capture-based approach for bisulfite-converted DNA that allows interrogation of predefined genomic locations, allowing quantitative and qualitative assessments of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at CG dinucleotides and in non-CG contexts (CHG, CHH) in mammalian and plant genomes. We show the technique works robustly and reproducibly using as little as 500 ng of starting DNA, with results correlating well with whole genome bisulfite sequencing data, and demonstrate that human DNA can be tested in samples contaminated with microbial DNA. This targeting approach will allow cell type-specific designs to maximize the value of 5mC and 5hmC sequencing.",

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doi = "10.1093/nar/gkv244",

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T1 - Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

AU - Li, Qing

AU - Suzuki, Masako

AU - Wendt, Jennifer

AU - Patterson, Nicole

AU - Eichten, Steven R.

AU - Hermanson, Peter J.

AU - Green, Dawn

AU - Jeddeloh, Jeffrey

AU - Richmond, Todd

AU - Rosenbaum, Heidi

AU - Burgess, Daniel

AU - Springer, Nathan M.

AU - Greally, John M.

PY - 2015/7/13

Y1 - 2015/7/13

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AB - We present a capture-based approach for bisulfite-converted DNA that allows interrogation of predefined genomic locations, allowing quantitative and qualitative assessments of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at CG dinucleotides and in non-CG contexts (CHG, CHH) in mammalian and plant genomes. We show the technique works robustly and reproducibly using as little as 500 ng of starting DNA, with results correlating well with whole genome bisulfite sequencing data, and demonstrate that human DNA can be tested in samples contaminated with microbial DNA. This targeting approach will allow cell type-specific designs to maximize the value of 5mC and 5hmC sequencing.

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Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

Abstract

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