Format

Send to

Choose Destination
See comment in PubMed Commons below
Clin Epigenetics. 2016 Jul 26;8:81. doi: 10.1186/s13148-016-0242-1. eCollection 2016.

Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots.

Author information

  • 1Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; Translational Neuropsychiatric Unit, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark.
  • 2Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark.
  • 3Department of Public Health, University of Southern Denmark, Odense C, 5000 Denmark.
  • 4Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark.
  • 5Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; Research Department P, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark.
  • 6Translational Neuropsychiatric Unit, Aarhus University Hospital, Risskov, 8240 Denmark ; Research Department P, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark.

Abstract

BACKGROUND:

In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.

RESULTS:

Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.

CONCLUSIONS:

In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.

KEYWORDS:

Archival dried blood spots; DNA methylation; Genome-wide; Low input; MeDIP-seq

PMID:
27462375
PMCID:
PMC4960904
DOI:
10.1186/s13148-016-0242-1
[PubMed - indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for PubMed Central
    Loading ...
    Support Center