• Med-Seq

    See how our technique works in this video.

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  • Laser Capture Microdissection

    Target DNA enrichment using Laser Capture Microdissection

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  • Market Discovery

    Methylation marker discovery for specific cancers and cancer subgroups

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  • Toward Single Cell MeD-seq

    MeD-seq: Pushing down the limit of DNA required

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About Methylomics

Methylomics is a company that applies state of the art molecular diagnostic technologies to develop novel assays for monitoring cancer progression and therapy response. We study the epigenome by genome wide DNA methylation profiles in healthy and diseased tissue to detect differences that can be used as methylation markers. We are experienced in reseach and product development of cancers of the colorectal region, skin and uro-genital zone including cervical, ovarian, vulva and endometrial cancers. Methylomics is a young company founded in 2018, located in Rijswijk the Netherlands

In this video is the MeD-Seq technology explained.

A novel method to detect DNA methylation genome wide

Methylated DNA sequencing (MeD-seq) is a novel method to detect DNA methylation profiles genome wide. The method was developed by the founding members of Methylomics and utilizes a methylation dependent restriction enzyme. Digestion by this enzyme generates small DNA fragments containing methylated CpG sites which are isolated and prepared for Next Generation Sequencing. MeD-seq is capable of investigating about half of all the CpG sites in the human genome. In contrast to other methods, like bisulfite sequencing and array platforms, it omits the need for bisulfite conversion and enables genome wide profiling of DNA methylation in an unbiased manner. Because the DNA damaging bisulfite conversion is not needed, MeD-seq requires low amounts of DNA input compared to other methods. This makes MeD-seq very suitable in combination with other applications such as Laser Capture Microdissection (LCM), liquid biopsy samples (e.g. cell free DNA) and small populations of FACS sorted cell types. Because MeD-seq only sequences methylated DNA, MeD-seq has proven to provide high coverage DNA methylation data at low costs compared to other methods.

Alliances

In the NWO sponsored (500K) Building Blocks of Life project ‘MeD-seq, a novel assay for genome wide DNA methylation profiling’, Methylomics and the Erasmus MC departments of Developmental Biology and Pathology aim to develop MeD-seq as a superior low cost high throughput pipeline for genome wide DNA methylation analysis of tissue and single cells. MeD-seq will be improved and applied to better understand colorectal and cervical cancer progression. This way, markers that can be used for cancer prognosis and therapy can be identified.

With a ZonMW Enabling Technlogy Hotels (30K) subsidy ‘From cancer epigenomes to DNA methylation assays for cancer detection and staging’ Methylomics, in collaboration with Erasmus MC department of Developmental Biology and the technology hotel DDL will develop early detection assays of cancer type and stage, crucial to predict disease outcome and treatment strategy.

With the TKI-Health subsidy (350K) ‘Establishment of a cell type specific DNA methylation atlas to study health and disease,’ we collaborate with the departments of Medical Oncology, Pathology and Developmental Biology of the Erasmus MC to develop single cell MeD-seq and apply this methodology to establish DNA methylation maps of different cell types in the human body. These maps will serve as a resource for future studies on health and disease.

Profiling DNA Methylation genome wide

Transformation of healthy cells into cancer cells coincides with massive changes in genome wide DNA methylation. MeD-seq is applied to detect DNA methylation profiles of healthy tissues and (pre-) cancerous lesions and has already been compared to other techniques.

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Target DNA enrichment using Laser Capture Microdissection

Laser Capture Microdissection (LCM) is an accurate method to select and isolate specific cell populations from heterogeneous archived paraffine embedded tissue (Figure 1) for further downstream genome-wide DNA methylation profiling.

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Methylation marker discovery for specific cancers and cancer subgroups

With the sequencing data from MeD-seq we construct genome-wide DNA methylation profiles for normal and diseased tissue types to develop cancer detection markers.

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MeD-seq: Pushing down the limit of DNA required

MeD-seq requires a relatively low amount of DNA, making it compatible with a range of applications like cell free DNA and Laser Capture Micro dissected DNA samples. Efforts are undertaken to push MeD-seq towards the single cell level.

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Latest Publications

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

Vos M, Boers R, Vriends ALM, et al. PLoS One. 2020;15(1):e0228014. Published 2020 Jan 23. doi:10.1371/journal.pone.0228014

Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI

Boers R, Boers J, de Hoon B, et al. Genome Res. 2018;28(1):88-99. doi:10.1101/gr.222885.117

Wim Quint – CEO


Wim is founder and CEO of Methylomics and runs Methylomics together with the Scientific Advisory board. He received a Ph.D. in biochemistry for the University of Nijmegen. He had specialized in molecular diagnostics of infectious diseases and is a key opinion leader on molecular studies of human papillomavirus. Wim had published more than 440 papers on various topics in international scientific journals.

Joost Gribnau – Senior Scientific Advisor


Prof. dr. Gribnau is head of the department of Developmental Biology at the Erasmus MC, and is an EMBO member and recipient of several prizes/awards, including VICI and ERC grants, and the Huygens Descartes prize. He and his laboratory founded and developed the MeD-seq technology.

    Wilfred van IJcken – Scientific Advisor


    Wilfred is founder, member of the Scientific Advisory Board at Methylomics and specialized in the development on scientific topics. Wilfred studied Molecular Sciences at the Wageningen University and Research center and received a Ph.D. in Virology at the same university. He is a genomics expert and published more than 220 scientific papers in peer reviewed international journals.

    Ruben Boers – Advisor Biotechnology & Development


    Ruben is founder and works as Advisor Biotechnology & development in the Scientific Advisory board. Ruben is responsible for analyzing the sequencing data and further development of MeD-seq.

    Joachim Boers – Advisor Bioinformatics & development


    Joachim is founder and works as advisor Bioinformatics & development in the Scientific Advisory Board and responsible for the development of the software used at Methylomics.

    Henk van den Munkhof – Proces Coordinator


    Henk is process coordinator at Methylomics. Henk leads all laboratory processes including set-up of new projects and data analysis.

      Laura van der Hoeven – General Support Officer / Technician


      Laura works at Methylomics as General Support Officer and Technician.

      Lotte Martens – Technician


      Lotte works at Methylomics as Technician.

      Bobby Driessen – Technician


      Bobby works at Methylomics as Technician.
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