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Watkins SH, Ho K, Testa C, Falk L, Soule P, Nguyen LV, FitzGibbon S, Slack C, Chen JT, Davey Smith G, De Vivo I, Simpkin AJ, Tilling K, Waterman PD, Krieger N, Suderman M, Relton C. The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip. Epigenetics 2022; 17:2366-2376. [PMID: 36239035 DOI: 10.1080/15592294.2022.2123898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation (DNAm) is commonly assayed using the Illumina Infinium MethylationEPIC BeadChip, but there is currently little published evidence to define the lower limits of the amount of DNA that can be used whilst preserving data quality. Such evidence is valuable for analyses utilizing precious or limited DNA sources. We used a single pooled sample of DNA in quadruplicate at three dilutions to define replicability and noise, and an independent population dataset of 328 individuals (from a community-based study including US-born non-Hispanic Black and white persons) to assess the impact of total DNA input on the quality of data generated using the Illumina Infinium MethylationEPIC BeadChip. We found that data are less reliable and more noisy as DNA input decreases to 40ng, with clear reductions in data quality; and that low DNA input is associated with a reduction in power to detect EWAS associations, requiring larger sample sizes. We conclude that DNA input as low as 40ng can be used with the Illumina Infinium MethylationEPIC BeadChip, provided quality checks and sensitivity analyses are undertaken.
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Affiliation(s)
- Sarah Holmes Watkins
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Karen Ho
- Bristol Bioresource Laboratories, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christian Testa
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Louise Falk
- Integrative Cancer Epidemiology Programme (ICEP), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Patrice Soule
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Linda V Nguyen
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sophie FitzGibbon
- Bristol Bioresource Laboratories, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Catherine Slack
- Bristol Bioresource Laboratories, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jarvis T Chen
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Immaculata De Vivo
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew J Simpkin
- School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Kate Tilling
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Pamela D Waterman
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Nancy Krieger
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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