Toward Single Cell MeD-seq

MeD-seq requires a relatively low amount of DNA as input, opening the possibility to work with sample types that give below average DNA yields. The emerging field of liquid biopsy, for example cell free DNA (cfDNA) from blood, shows promising results in oncology for diagnostic purposes or follow-up. In collaboration with academia MeD-seq is already used to detect DNA methylation profiles in cfDNA to setup a tool in the follow-up of surgical treatment of liver metastases in patients with colorectal cancer. Because in healthy individuals the cfDNA mainly originates from blood cell types, both cancer-specific and tissue-specific methylation can be informative in the follow-up of these colon carcinoma patients. These tissue-specific methylations patterns found in cfDNA are also the basis which led to the use of MeD-seq in current studies involved in elaborating on the pathogenesis of various neurodegenerative diseases. Here, cfDNA, DNA from cerebral spinal fluid (CSF) and various sorted populations of cell types from brain tissues are being used for MeD-seq analysis. Our aim for the future is to push MeD-seq towards the single cell level. In close collaboration with multiple academic centers steps are undertaken to optimize the MeD-seq wetlab protocol to look at circulating tumor cells in the blood of cancer patients using single cell MeD-seq.

Publications about our techniques

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

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.

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.

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

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

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

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

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

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

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.

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