Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans
| Autor: | Xihong Lin, Joel Schwartz, Allan C. Just, Alexandra M. Binder, John N. Hutchinson, Sami S. Amr, Lorena Pantano, William P. Accomando, Karin B. Michels, Benedetta Izzi, Andrea A. Baccarelli, Pantel S. Vokonas, Juan Carmona |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Genetics Methylation Biology QH426-470 Human genetics Article 03 medical and health sciences 030104 developmental biology CpG site Reduced representation bisulfite sequencing DNA methylation Illumina Methylation Assay Medicine Epigenetics Molecular Biology Genetics (clinical) Illumina dye sequencing |
| Zdroj: | npj Genomic Medicine, Vol 2, Iss 1, Pp 1-10 (2017) NPJ Genomic Medicine NPJ genomic medicine, vol 2, iss 1 |
| ISSN: | 2056-7944 |
| Popis: | We empirically examined the strengths and weaknesses of two human genome-wide DNA methylation platforms: rapid multiplexed reduced representation bisulfite sequencing and Illumina’s Infinium BeadChip. Rapid multiplexed reduced representation bisulfite sequencing required less input DNA, offered more flexibility in coverage, and interrogated more CpG loci at a higher regional density. The Infinium covered slightly more protein coding, cancer-associated and mitochondrial-related genes, both platforms covered all known imprinting clusters, and rapid multiplexed reduced representation bisulfite sequencing covered more microRNA genes than the HumanMethylation450, but fewer than the MethylationEPIC. Rapid multiplexed reduced representation bisulfite sequencing did not always interrogate exactly the same CpG loci, but genomic tiling improved overlap between different libraries. Reproducibility of rapid multiplexed reduced representation bisulfite sequencing and concordance between the platforms increased with CpG density. Only rapid multiplexed reduced representation bisulfite sequencing could genotype samples and measure allele-specific methylation, and we confirmed that Infinium measurements are influenced by nearby single-nucleotide polymorphisms. The respective strengths and weaknesses of these two genome-wide DNA methylation platforms need to be considered when conducting human epigenetic studies. Epigenetics: choose your DNA methylation probing tool wisely! Researchers who study human epigenetics need to carefully consider the platform used to measure genome-wide patterns of DNA methylation. A team led by Karin Michels and Andrea Baccarelli from Harvard University in Boston, Massachusetts, USA, empirically examined the strengths and weaknesses of two methylation profiling tools: Illumina’s Infinium BeadChip, which uses a microarray system to interrogate hundreds of thousands of methylation sites across the genome at single-nucleotide resolution; and a high-throughput sequencing-based approach known as rapid multiplexed reduced representation bisulfite sequencing, or rmRRBS. The former did a better job at reading methylation in protein-coding and mitochondrial-related genes, while the latter required less input DNA and covered more methylation sites across the genome. The authors conclude that a scientist’s platform preference should depend on the nature of his or her investigation. |
| Databáze: | OpenAIRE |
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