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Published on: August 3, 2018
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The SEQC2 epigenomics quality control (EpiQC) study.
Jonathan Foox1,2, Jessica Nordlund3,4, Claudia Lalancette5
1Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.
Genome Biology
|December 7, 2021
Summary
This study benchmarks multiple DNA methylation sequencing methods, finding high concordance but also platform-specific differences. The results offer guidance for epigenetics research and best practices for experimental design using reference materials.
Area of Science:
- Epigenetics
- Genomics
- Molecular Biology
Background:
- DNA methylation, including 5-methylcytosine (5mC), is crucial for development, cell lineage, and disease stratification.
- Diverse interrogation methods necessitate harmonization and benchmarking for reliable genome-wide methylome sequencing.
- The FDA's Epigenomics Quality Control Group provides a cross-validated resource for epigenetics research.
Purpose of the Study:
- To conduct a multi-platform assessment of DNA methylation analysis techniques.
- To establish harmonized materials and methods for epigenetics research.
- To provide a benchmark for improving genome-wide methylome sequencing applications.
Main Methods:
- Evaluation of multiple whole-genome bisulfite sequencing (WGBS) protocols, oxidative bisulfite sequencing, enzymatic deamination, targeted methylation sequencing, nanopore sequencing, and methylation arrays.
- Rigorous quality assessment, cross-validation against Illumina EPIC microarrays, and testing of various analysis algorithms.
- Utilizing seven human cell lines as publicly available reference materials.
Main Results:
- High overall concordance was observed between different DNA methylation assays.
- Differences were noted in read mapping efficiency, CpG capture, coverage, and platform performance.
- Variable performance was found across 26 microarray normalization algorithms.
Conclusions:
- The presented data guide the use of DNA reference materials in epigenomics.
- Best practices for experimental design in future epigenetics studies are provided.
- The findings establish a baseline for advancing epigenomics research using standardized reference materials.
