Establishing an analytic pipeline for genome-wide DNA methylation

Michelle L. Wright, Mikhail G. Dozmorov, Aaron R. Wolen, Colleen Jackson-Cook, Angela R. Starkweather, Debra E. Lyon, Timothy P. York

Research output: Contribution to journalReview article

10 Citations (Scopus)

Abstract

The need for research investigating DNA methylation (DNAm) in clinical studies has increased, leading to the evolution of new analytic methods to improve accuracy and reproducibility of the interpretation of results from these studies. The purpose of this article is to provide clinical researchers with a summary of the major data processing steps routinely applied in clinical studies investigating genome-wide DNAm using the Illumina HumanMethylation 450K BeadChip. In most studies, the primary goal of employing DNAm analysis is to identify differential methylation at CpG sites among phenotypic groups. Experimental design considerations are crucial at the onset to minimize bias from factors related to sample processing and avoid confounding experimental variables with non-biological batch effects. Although there are currently no de facto standard methods for analyzing these data, we review the major steps in processing DNAm data recommended by several research studies. We describe several variations available for clinical researchers to process, analyze, and interpret DNAm data. These insights are applicable to most types of genome-wide DNAm array platforms and will be applicable for the next generation of DNAm array technologies (e.g., the 850K array). Selection of the DNAm analytic pipeline followed by investigators should be guided by the research question and supported by recently published methods.

Original languageEnglish (US)
Article number45
JournalClinical Epigenetics
Volume8
Issue number1
DOIs
StatePublished - Apr 27 2016

Fingerprint

DNA Methylation
Genome
Research Personnel
Oligonucleotide Array Sequence Analysis
Research
Confounding Factors (Epidemiology)
Reproducibility of Results
Methylation
Research Design
Technology

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics
  • Developmental Biology
  • Genetics(clinical)

Cite this

Wright, M. L., Dozmorov, M. G., Wolen, A. R., Jackson-Cook, C., Starkweather, A. R., Lyon, D. E., & York, T. P. (2016). Establishing an analytic pipeline for genome-wide DNA methylation. Clinical Epigenetics, 8(1), [45]. https://doi.org/10.1186/s13148-016-0212-7

Establishing an analytic pipeline for genome-wide DNA methylation. / Wright, Michelle L.; Dozmorov, Mikhail G.; Wolen, Aaron R.; Jackson-Cook, Colleen; Starkweather, Angela R.; Lyon, Debra E.; York, Timothy P.

In: Clinical Epigenetics, Vol. 8, No. 1, 45, 27.04.2016.

Research output: Contribution to journalReview article

Wright, ML, Dozmorov, MG, Wolen, AR, Jackson-Cook, C, Starkweather, AR, Lyon, DE & York, TP 2016, 'Establishing an analytic pipeline for genome-wide DNA methylation', Clinical Epigenetics, vol. 8, no. 1, 45. https://doi.org/10.1186/s13148-016-0212-7
Wright ML, Dozmorov MG, Wolen AR, Jackson-Cook C, Starkweather AR, Lyon DE et al. Establishing an analytic pipeline for genome-wide DNA methylation. Clinical Epigenetics. 2016 Apr 27;8(1). 45. https://doi.org/10.1186/s13148-016-0212-7
Wright, Michelle L. ; Dozmorov, Mikhail G. ; Wolen, Aaron R. ; Jackson-Cook, Colleen ; Starkweather, Angela R. ; Lyon, Debra E. ; York, Timothy P. / Establishing an analytic pipeline for genome-wide DNA methylation. In: Clinical Epigenetics. 2016 ; Vol. 8, No. 1.
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