CpG Islands pp 83-107 | Cite as

Infinium DNA Methylation Microarrays on Formalin-Fixed, Paraffin-Embedded Samples

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1766)

Abstract

Formalin-fixed, paraffin-embedded (FFPE) samples usually yield fragmented DNA, which is incompatible with traditional Infinium Methylation beadchips. In this chapter, we aim to explain in detail all the processes carried out in order to obtain high-quality methylation profiles from FFPE samples through an FFPE restoration procedure. High-throughput methylation profiling platforms such as the Infinium Methylation beadchips have been extensively used by the scientific community to elucidate many hypotheses in multiple scenarios, now with the incorporation of FFPE samples to these platforms, a myriad of new opportunities is being opened.

Key words

Epigenetics DNA methylation Formalin-fixed, paraffin-embedded FFPE Methylation Microarray Restoration Degraded DNA 

References

  1. 1.
    Bibikova M, Lin Z, Zhou L, Chudin E (2006) High-throughput DNA methylation profiling using universal bead arrays. Genome Res 2006:383–393CrossRefGoogle Scholar
  2. 2.
    Bibikova M, Le J, Barnes B, Saedinia-melnyk S, Zhou L, Shen R, Gunderson KL (2009) Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 1:177–200CrossRefPubMedGoogle Scholar
  3. 3.
    Sandoval J, Heyn HA, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M (2011) Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6:692–702CrossRefPubMedGoogle Scholar
  4. 4.
    Moran S, Arribas C, Esteller M (2016) Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics 8:389–399CrossRefPubMedGoogle Scholar
  5. 5.
    Thirlwell C, Eymard M, Feber A, Teschendorff A, Pearce K, Lechner M, Widschwendter M, Beck S (2010) Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip. Methods 52:248–254CrossRefPubMedGoogle Scholar
  6. 6.
    Moran S, Vizoso M, Martinez-Cardús A, Gomez A, Matías-Guiu X, Chiavenna SM, Fernandez AG, Esteller M (2014) Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray. Epigenetics 9:829–833CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL)BarcelonaSpain
  2. 2.Department of Physiological Sciences II, School of MedicineUniversity of BarcelonaBarcelonaSpain
  3. 3.Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain

Personalised recommendations