The SEQC2 epigenomics quality control (EpiQC) study

Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W. Langhorst, V. K.Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M. Greally, Masako Suzuki, Mark Menor, Masaki Nasu, Alicia AlonsoCaroline Sheridan, Andreas Scherer, Stephen Bruinsma, Gosia Golda, Agata Muszynska, Paweł P. Łabaj, Matthew A. Campbell, Frank Wos, Amanda Raine, Ulrika Liljedahl, Tomas Axelsson, Charles Wang, Zhong Chen, Zhaowei Yang, Jing Li, Xiaopeng Yang, Hongwei Wang, Ari Melnick, Shang Guo, Alexander Blume, Vedran Franke, Inmaculada Ibanez de Caceres, Carlos Rodriguez-Antolin, Rocio Rosas, Justin Wade Davis, Jennifer Ishii, Dalila B. Megherbi, Wenming Xiao, Will Liao, Joshua Xu, Huixiao Hong, Baitang Ning, Weida Tong, Altuna Akalin, Yunliang Wang, Youping Deng, Christopher E. Mason

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Background: Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group. Results: Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. Conclusions: The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.

Original languageEnglish (US)
Article number332
JournalGenome biology
Volume22
Issue number1
DOIs
StatePublished - Dec 2021

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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