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Epigenomes 2017, 1(3), 14; https://doi.org/10.3390/epigenomes1030014

Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing

1
Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
2
Translational Neuropsychiatric Unit, Aarhus University Hospital, 8240 Risskov, Denmark
3
Psychosis Research Unit, Aarhus University Hospital, 8240 Risskov, Denmark
4
The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
5
Center for Integrative Sequencing, iSEQ, Aarhus University, 8000 Aarhus C, Denmark
*
Author to whom correspondence should be addressed.
Academic Editor: Muller Fabbri
Received: 31 July 2017 / Revised: 5 October 2017 / Accepted: 11 October 2017 / Published: 19 October 2017
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Abstract

Abstract: Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest in peripheral surrogate tissues. Whereas most work has been conducted on blood, saliva is now becoming recognized as an interesting alternative due to the simple and non-invasive manner of collection allowing for self-sampling. Results: In this study we have evaluated if saliva samples are suitable for DNA methylation studies using methylated DNA immunoprecipitation coupled to next-generation sequencing (MeDIP-seq). This was done by comparing the DNA methylation profile in saliva against the benchmark profile of peripheral blood from three individuals. We show that the output, quality, and depth of paired-end 50 bp sequencing reads are comparable between saliva and peripheral blood and, moreover, that the distribution of reads along genomic regions are similar and follow canonical methylation patterns. Conclusion: In summary, we show that high-quality MeDIP-seq data can be generated using saliva, thus supporting the future use of saliva in the generation of DNA methylation information at annotated genes, non-RefSeq genes, and repetitive elements relevant to human disease. View Full-Text
Keywords: epigenetics; DNA methylation; MeDIP-seq; genome-wide; saliva; blood epigenetics; DNA methylation; MeDIP-seq; genome-wide; saliva; blood
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Staunstrup, N.H.; Starnawska, A.; Nyegaard, M.; Nielsen, A.L.; Børglum, A.; Mors, O. Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing. Epigenomes 2017, 1, 14.

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