Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

被引:22
|
作者
Carmona, Juan J. [1 ,2 ,3 ]
Accomando, William P., Jr. [4 ,5 ]
Binder, Alexandra M. [4 ,5 ]
Hutchinson, John N. [6 ]
Pantano, Lorena [6 ]
Izzi, Benedetta [7 ]
Just, Allan C. [1 ]
Lin, Xihong [6 ]
Schwartz, Joel [1 ]
Vokonas, Pantel S. [8 ]
Amr, Sami S. [9 ,10 ]
Baccarelli, Andrea A. [1 ,4 ]
Michels, Karin B. [4 ,5 ]
机构
[1] Harvard TH Chan Sch Publ Hlth, Dept Environm Hlth, Boston, MA 02115 USA
[2] Harvard TH Chan Sch Publ Hlth, Program Quantitat Genom, Boston, MA 02115 USA
[3] Harvard Med Sch, Ctr Bioeth, Boston, MA 02115 USA
[4] Harvard TH Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA
[5] Harvard Med Sch, Brigham & Womens Hosp, Dept Obstet Gynecol & Reprod Biol, Obstet & Gynecol Epidemiol Ctr, Boston, MA 02115 USA
[6] Harvard TH Chan Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA
[7] Univ Freiburg, Inst Prevent & Canc Epidemiol, Freiburg Med Ctr, Freiburg, Germany
[8] Boston Univ, Dept Med, Vet Affairs Boston Healthcare Syst, Vet Affairs Normat Aging Study,Sch Med, Boston, MA 02118 USA
[9] Harvard Med Sch, Brigham & Womens Hosp, Dept Pathol, Boston, MA 02115 USA
[10] Translat Genom Core, Partners Healthcare Personalized Med, Cambridge, MA 02139 USA
来源
NPJ GENOMIC MEDICINE | 2017年 / 2卷
基金
美国国家卫生研究院;
关键词
PLURIPOTENT STEM-CELLS; ARRAY; MECHANISMS;
D O I
10.1038/s41525-017-0012-9
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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 Human Methylation 450, but fewer than the Methylation EPIC. 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.
引用
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页数:10
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