MeD-Seq Technology

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MeD-seq is a novel method to detect genome wide DNA methylation.

MeD-seq is a novel method to detect genome wide DNA methylation. It uses a methylation dependent restriction enzyme which is able to recognize methylated CpG sites in the following sequences; CCG, CGG and GCGC, which makes up around half of all the CpG sites in the human genome. Digestion takes place 16 base pairs downstream of the recognized CpG site. This leads to the production of small DNA fragments of around 32 bp when a CpG site is fully methylated. Subsequently, the digestion is converted into a sequencing library that can be used on common sequencing platforms. Before sequencing, the library is run on an automated size selection device which is used to select the DNA library fragments that contain the digested DNA fragments. Sequencing depths are aimed at around 20-30 million reads per sample. Because the MeD-seq method does not involve a bisulfite conversion step, which detracts from the DNA quality, the minimal DNA input (5-10 ng) is very low compared to other genome wide methods. This makes MeD-seq compatible with sample types with low DNA concentrations, like liquid biopsy samples and Laser Capture Microdissection (LCM). After sequencing, only reads containing CpG sites are used for data analysis, which leads to a very low level of background “noise”. Despite the small fragment size of the reads, mapping efficiency remains high. Due to its unbiased approach regarding genomic locations that can be analyzed, MeD-seq manages to detect the DNA methylation status of the vast majority of gene promoters, CpG islands and many CpG sites in intergenic regions. MeD-seq has been validated by comparing it with whole genome bisulfite sequencing (WGBS), MeDIP-seq and the 450K array.

Publications about our techniques

Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI Genome Res. 2018 28(1):88-99

DOI: 10.1101/gr.222885.117

MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma

Methylation markers FAM19A4 and miR124-2 as triage strategy for primary human papillomavirus screen positive women: A large European multicenter study.

DOI: 10.1002/ijc.33320.

Expression of p16 and HPV E4 on biopsy samples and methylation of FAM19A4 and miR124-2 on cervical cytology samples in the classification of cervical squamous intraepithelial lesions.

DOI: 10.1002/cam4.2855.

Cancer risk stratification of anal intraepithelial neoplasia in HIV-positive men by validated methylation markers associated with progression to cancer.

DOI: 10.1093/cid/ciaa397.

CADM1 and MAL methylation status in cervical scrapes is representative of the most severe underlying lesion in women with multiple cervical biopsies.

DOI: 10.1002/ijc.29706

Host Cell Deoxyribonucleic Acid Methylation Markers for the Detection of High-grade Anal Intraepithelial Neoplasia and Anal Cancer.

DOI: 10.1093/cid/ciy601.

Reliable identification of women with CIN3+ using hrHPV genotyping and methylation markers in a cytology-screened referral population.

DOI: 10.1002/ijc.31787

Intra- and inter-laboratory agreement of the FAM19A4/mir124-2 methylation test: Results from an international study.

DOI: 10.1002/jcla.22854

FAM19A4/miR124-2 methylation in invasive cervical cancer: A retrospective cross-sectional worldwide study.

DOI: 10.1002/ijc.32614

Defining hrHPV genotypes in cervical intraepithelial neoplasia by laser capture microdissection supports reflex triage of self-samples using HPV16/18 and FAM19A4/miR124-2 methylation.

DOI: 10.1016/j.ygyno.2018.09.006.

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