Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing
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...
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doaj-af371f70d8b743359e3aad263a03e1e12021-04-02T02:32:36ZengMDPI AGEpigenomes2075-46552017-10-01131410.3390/epigenomes1030014epigenomes1030014Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) SequencingNicklas Heine Staunstrup0Anna Starnawska1Mette Nyegaard2Anders Lade Nielsen3Anders Børglum4Ole Mors5Department of Biomedicine, Aarhus University, 8000 Aarhus C, DenmarkDepartment of Biomedicine, Aarhus University, 8000 Aarhus C, DenmarkDepartment of Biomedicine, Aarhus University, 8000 Aarhus C, DenmarkDepartment of Biomedicine, Aarhus University, 8000 Aarhus C, DenmarkDepartment of Biomedicine, Aarhus University, 8000 Aarhus C, DenmarkTranslational Neuropsychiatric Unit, Aarhus University Hospital, 8240 Risskov, DenmarkAbstract: 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.https://www.mdpi.com/2075-4655/1/3/14epigeneticsDNA methylationMeDIP-seqgenome-widesalivablood |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Nicklas Heine Staunstrup Anna Starnawska Mette Nyegaard Anders Lade Nielsen Anders Børglum Ole Mors |
spellingShingle |
Nicklas Heine Staunstrup Anna Starnawska Mette Nyegaard Anders Lade Nielsen Anders Børglum Ole Mors Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing Epigenomes epigenetics DNA methylation MeDIP-seq genome-wide saliva blood |
author_facet |
Nicklas Heine Staunstrup Anna Starnawska Mette Nyegaard Anders Lade Nielsen Anders Børglum Ole Mors |
author_sort |
Nicklas Heine Staunstrup |
title |
Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing |
title_short |
Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing |
title_full |
Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing |
title_fullStr |
Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing |
title_full_unstemmed |
Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing |
title_sort |
saliva as a blood alternative for genome-wide dna methylation profiling by methylated dna immunoprecipitation (medip) sequencing |
publisher |
MDPI AG |
series |
Epigenomes |
issn |
2075-4655 |
publishDate |
2017-10-01 |
description |
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. |
topic |
epigenetics DNA methylation MeDIP-seq genome-wide saliva blood |
url |
https://www.mdpi.com/2075-4655/1/3/14 |
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