DNA methylation levels are highly correlated between pooled samples and averaged values when analysed using the Infinium HumanMethylation450 BeadChip array
Gallego-Fabrega, Cristina (Universitat Autònoma de Barcelona. Departament de Medicina)
Carrera, Caty (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Muiño, Elena (Hospital Universitari MútuaTerrassa (Terrassa, Catalunya))
Montaner, Joan (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Krupinski, Jurek (School of Healthcare Science, Manchester Metropolitan University)
Fernandez-Cadenas, Israel (Hospital Universitari MútuaTerrassa (Terrassa, Catalunya))

Date:	2015
Abstract:	DNA methylation is a heritable and stable epigenetic mark implicated in complex human traits. Epigenome-wide association studies (EWAS) using array-based technology are becoming widely used to identify differentially methylated sites associated with complex diseases. EWAS studies require large sample sizes to detect small effects, which increases project costs. In the present study we propose to pool DNA samples in methylation array studies as an affordable and accurate alternative to individual samples studies, in order to reduce economic costs or when low amounts of DNA are available. For this study, 20 individual DNA samples and 4 pooled DNA samples were analysed using the Illumina Infinium HumanMethylation450 BeadChip array to evaluate the efficiency of the pooling approach in EWAS studies. Statistical power calculations were also performed to discover the minimum sample size needed for the pooling strategy in EWAS. A total of 485,577 CpG sites across the whole genome were assessed. Comparison of methylation levels of all CpG sites between individual samples and their related pooled samples revealed highly significant correlations (rho > 0. 99, p -val < 10 −16). These results remained similar when assessing the 101 most differentially methylated CpG sites (rho > 0. 98, p -val < 10 −16). Also, it was calculated that n = 43 is the minimum sample size required to achieve a 95 % statistical power and a 10 −06 significance level in EWAS, when using a DNA pool strategy. DNA pooling strategies seems to accurately provide estimations of averaged DNA methylation state using array based EWAS studies. This type of approach can be applied to the assessment of disease phenotypes, reducing the amount of DNA required and the cost of large-scale epigenetic analyses.
Grants:	European Commission 7FP/F2-08-202213 Instituto de Salud Carlos III MiguelServet/CP12-03298 Instituto de Salud Carlos III CP12-0329
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	Clinical Epigenetics, Vol. 7 (july 2015) , ISSN 1868-7083

DOI: 10.1186/s13148-015-0097-x
PMID: 26236407

8 p, 1.0 MB

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