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
Boers R, Boers J, de Hoon B, et al. Genome Res. 2018;28(1):88-99. doi:10.1101/gr.222885.117
Vos M, Boers R, Vriends ALM, et al. PLoS One. 2020;15(1):e0228014. Published 2020 Jan 23. doi:10.1371/journal.pone.0228014
Bonde J, Floore A, Ejegod D, Vink FJ, Hesselink A, van de Ven PM, Valenčak AO, Pedersen H, Doorn S, Quint WG, Petry KU, Poljak M, Stanczuk G, Cuschieri K, de Sanjosé S, Bleeker M, Berkhof J, Meijer CJLM, Heideman DAM. Int J Cancer. 2020 Sep 30. doi: 10.1002/ijc.33320.
Leeman A, Jenkins D, Del Pino M, Ordi J, Torné A, Doorbar J, Meijer CJLM, van Kemenade FJ, Quint WGV. Cancer Med. 2020 Apr;9(7):2454-2461. doi: 10.1002/cam4.2855. Epub 2020 Feb 5.
van der Zee RP, Richel O, van Noesel CJM, Ciocănea-Teodorescu I, van Splunter AP, Ter Braak TJ, Nathan M, Cuming T, Sheaff M, Kreuter A, Meijer CJLM, Quint WGV, de Vries HJC, Prins JM, Steenbergen RDM. Clin Infect Dis. 2020 Apr 8:ciaa397. doi: 10.1093/cid/ciaa397. Online ahead of print.
van Baars R, van der Marel J, Snijders PJ, Rodriquez-Manfredi A, ter Harmsel B, van den Munckhof HA, Ordi J, del Pino M, van de Sandt MM, Wentzensen N, Meijer CJ, Quint WG. Int J Cancer. 2016 Jan 15;138(2):463-71. doi: 10.1002/ijc.29706. Epub 2015 Aug 14.
van der Zee RP, Richel O, van Noesel CJM, Novianti PW, Ciocanea-Teodorescu I, van Splunter AP, Duin S, van den Berk GEL, Meijer CJLM, Quint WGV, de Vries HJC, Prins JM, Steenbergen RDM. Clin Infect Dis. 2019 Mar 19;68(7):1110-1117. doi: 10.1093/cid/ciy601.
Leeman A, Del Pino M, Marimon L, Torné A, Ordi J, Ter Harmsel B, Meijer CJLM, Jenkins D, Van Kemenade FJ, Quint WGV. Int J Cancer. 2019 Jan 1;144(1):160-168. doi: 10.1002/ijc.31787. Epub 2018 Nov 18.
Floore A, Hesselink A, Oštrbenk A, Alcaniz E, Rothe B, Pedersen H, Torres Hortal M, Doorn S, Quint W, Petry KU, Poljak M, Cuschieri K, Bonde J, de Sanjosé S, Bleeker M, Heideman D. J Clin Lab Anal. 2019 May;33(4):e22854. doi: 10.1002/jcla.22854. Epub 2019 Feb 13.
Vink FJ, Meijer CJLM, Clifford GM, Poljak M, Oštrbenk A, Petry KU, Rothe B, Bonde J, Pedersen H, de Sanjosé S, Torres M, Del Pino M, Quint WGV, Cuschieri K, Boada EA, van Trommel NE, Lissenberg-Witte BI, Floore AN, Hesselink AT, Steenbergen RDM, Bleeker MCG, Heideman DAM. Int J Cancer. 2020 Aug 15;147(4):1215-1221. doi: 10.1002/ijc.32614. Epub 2019 Sep 9.
Leeman A, Ebisch RMF, Kasius A, Bosgraaf RP, Jenkins D, van de Sandt MM, de Strooper LMA, Heideman DAM, Snijders PJF, Massuger LFAG, Bekkers RLM, Meijer CJLM, van Kemenade FJ, Quint WGV, Melchers WJG. Gynecol Oncol. 2018 Nov;151(2):311-318. doi: 10.1016/j.ygyno.2018.09.006. Epub 2018 Sep 13.