title: QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments.
abstract: Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data. As the central part of the workflow we have developed a Bayesian statistical model that transforms the enrichment read counts to absolute levels of methylation and, thus, enhances interpretability and facilitates comparison with other methylation assays. We suggest several calibration strategies for the critical parameters of the model, either using additional data or fairly general assumptions. By comparing the results with bisulfite sequencing (BS) validation data, we show the improvement of QSEA over existing methods. Additionally, we generated a clinically relevant benchmark data set consisting of methylation enrichment experiments (MeDIP-seq), BS-based validation experiments (Methyl-seq) as well as gene expression experiments (RNA-seq) derived from non-small cell lung cancer patients, and show that the workflow retrieves well-known lung tumour methylation markers that are causative for gene expression changes, demonstrating the applicability of QSEA for clinical studies. QSEA is implemented in R and available from the Bioconductor repository 3.4 (www.bioconductor.org/packages/qsea).
authors.affiliation: Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Lienhard
authors.affiliation: Functional Epigenomics, University Hospital Cologne, Cologne 50937, Germany.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Grasse
authors.affiliation: Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin 13125, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Rolff
authors.affiliation: Department of Thoracic Surgery, ELK Berlin Chest Hospital, Berlin 13125, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Frese
authors.affiliation: Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Schirmer
authors.affiliation: Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin 13125, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Becker
authors.affiliation: Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Börno
authors.affiliation: Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Timmermann
authors.affiliation: Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
authors.forename: Lukas
authors.initials: L
authors.lastname: Chavez
authors.affiliation: Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Sültmann
authors.affiliation: Department of Thoracic Surgery, ELK Berlin Chest Hospital, Berlin 13125, Germany.
authors.forename: Gunda
authors.initials: G
authors.lastname: Leschber
authors.affiliation: Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin 13125, Germany.
authors.forename: Iduna
authors.initials: I
authors.lastname: Fichtner
authors.affiliation: Functional Epigenomics, University Hospital Cologne, Cologne 50937, Germany.|Department of Vertebrate Genomics, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany.
authors.forename: Michal R
authors.initials: MR
authors.lastname: Schweiger
authors.affiliation: Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Herwig
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D019175:DNA Methylation; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D051379:Mice; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites; D057188:Workflow
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite