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
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.