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MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods

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Research in Computational Molecular Biology (RECOMB 2013)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7821))

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Abstract

We introduce MethylCRF, a novel Conditional Random Fields-based algorithm to integrate methylated DNA immunoprecipitation (MeDIP-seq) and methylationsensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single CpG resolution. MethylCRF was benchmarked for accuracy against Infinium arrays, RRBS, whole-genome shotgun-bisulfite (WGBS) sequencing and locus specific-bisufite sequencing on the same DNA. MethylCRF transformation of MeDIP/MRE was equivalent to a biological replicate of WGBS in quantification, coverage and resolution, providing a lower cost and widely accessible strategy to create full methylomes.

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Author information

Authors and Affiliations

  1. Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, MO, USA, 63108

    Michael Stevens, Mingchao Xie & Ting Wang

  2. Department of Computer Science and Engineering, Washington University, St. Louis, MO, 63130, USA

    Michael Stevens & Ting Wang

  3. Department of Dermatology, University of California San Francisco, CA, 94143, USA

    Jeffrey B. Cheng

  4. Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, CA, USA, 94143

    Joseph F. Costello

Authors
  1. Michael Stevens
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  2. Jeffrey B. Cheng
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  3. Mingchao Xie
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  4. Joseph F. Costello
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  5. Ting Wang
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Editor information

Editors and Affiliations

  1. School of Mathematics, Peking University, Beijing, P.R. China

    Minghua Deng

  2. Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, 100084, Beijing, P.R. China

    Rui Jiang

  3. Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA

    Fengzhu Sun

  4. Department of Automation, Tsinghua University, P.O. Box, 100084, Beijing, China

    Xuegong Zhang

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© 2013 Springer-Verlag Berlin Heidelberg

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Stevens, M., Cheng, J.B., Xie, M., Costello, J.F., Wang, T. (2013). MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods. In: Deng, M., Jiang, R., Sun, F., Zhang, X. (eds) Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science(), vol 7821. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37195-0_23

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  • DOI: https://doi.org/10.1007/978-3-642-37195-0_23

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-37194-3

  • Online ISBN: 978-3-642-37195-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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