With the MeD-seq sequencing data from (cell population enriched) laser capture micro–dissected (LCM) formalin-fixed and paraffin-embedded tissue samples we construct genome-wide DNA methylation profiles for normal and diseased tissue types (Figure 1).
Comparison of cancer and control methylation profiles by an in house developed bioinformatics pipeline Mimir facilitates the identification of specific or general Differentially Methylated Regions (DMR) in a genome wide fashion (Figure 2).
Mimir is capable of detecting the following types of DMR’s
- General, for example regions methylated in all cancer types of the female genital zone
- Regional, for example methylated in 2 or more cancer types (Cervix and Vulva carcinoma)
- Specific, for example methylated in one specific cancer type (Cx-AdC or Vul-SCC-)
Figure 1. female urogenital zone, methylations profiles are generated for both control and cancer tissue samples.
Figure 2. illustrative representation of IGV captions of the 5 DMR types: Two general markers where all cancers have methylation reads and all controls do not have methylation reads. One regional marker with high methylation for cervix and vulva cancers, low methylation for cervical and vulva controls, all other controls and all other cancers. Two specific regions; one region with only methylation for cervical adenocarcinoma samples and one region with only methylation for vulva squamous cell carcinoma HPV negative samples.
Assay design and primer and probe selection:
From the DMR regions Methylomics develops specific, regional and general markers. However, not all DMR’s are suitable to create powerful cancer detection markers. To determine whether a DMR is discriminating enough and suitable to create a powerful marker, quality scores, predictive scores and visualizations are applied to select candidate markers for assay development.
Visualization of these selected DMR’s in grouped DNA methylation profiles through an Integrative Genomics Viewer (IGV) facilitates the identification of promising target sequences for the development of quantitative Methylation-Specific PCR (qMSP) assays (Figure 2).
Methylomics develops multiplex assays detecting the methylation status of multiple regions at once. To assess the potential of the newly discovered markers the developed assays are tested on bisulfite-converted DNA of relevant samples.
Publications about our techniques
Fu S, Deger T, Boers RG, Boers JB, Doukas M, Gribnau J, Wilting SM, Debes JD, Boonstra A
Eikenboom EL, Wilting SM, Deger T, Srebniak MI, Van Veghel-Plandsoen M, Boers RG, Boers JB, van IJcken WFJ, Gribnau JH, Atmodimedjo P, Dubbink HJ, Martens JWM, Spaander MCW, Wagner A
Siamoglou S, Boers R, Koromina M, Boers J, Tsironi A, Chatzilygeroudi T, Lazaris V, Verigou E, Kourakli A, van IJcken WFJ, Gribnau J, Symeonidis A, Patrinos GP
Bos MK, Verhoeff SR, Oosting SF, Menke-van der Houven van Oordt WC, Boers RG, Boers JB, Gribnau J, Martens JWM, Sleijfer S, van Herpen CML, Wilting SM
Boers R, Boers J, Tan B, van Leeuwen ME, Wassenaar E, Sanchez EG, Sleddens E, Tenhagen Y, Mulugeta E, Laven J, Creyghton M, Baarends W, van IJcken WFJ, Gribnau J
Shankar AS, Du Z, Tejeda Mora H, Boers R, Cao W, van den Bosch TPP, Korevaar SS, Boers J, van IJcken WFJ, Bindels EMJ, Eussen B, de Klein A, Pan Q, Oudijk L, Clahsen-van Groningen MC, Hoorn EJ, Baan CC, Gribnau J, Hoogduijn MJ
Mira-Bontenbal H, Tan B, Gontan C, Goossens S, Boers RG, Boers JB, Dupont C, van Royen ME, IJcken WFJ, French P, Bedalov A, Gribnau J
Smit KN, Boers R, Vaarwater J, Boers J, Brands T, Mensink H, Verdijk RM, van IJcken WFJ, Gribnau J, de Klein A, Kilic E
Deger T, Boers RG, de Weerd V, Angus L, van der Put MMJ, Boers JB, Azmani Z, van IJcken WFJ, Grünhagen DJ, van Dessel LF, Lolkema MPJK, Verhoef C, Sleijfer S, Martens JWM, Gribnau J, Wilting SM
Soochit W, Sleutels F, Stik G, Bartkuhn M, Basu S, Hernandez SC, Merzouk S, Vidal E, Boers R, Boers J, van der Reijden M, Geverts B, van Cappellen WA, van den Hout M, Ozgur Z, van IJcken WFJ, Gribnau J, Renkawitz R, Graf T, Houtsmuller A, Grosveld F, Stadhouders R, Galjart N
Slot E, Boers R, Boers J, van IJcken WFJ, Tibboel D, Gribnau J, Rottier R, de Klein A
Timbergen MJM, Boers R, Vriends ALM, Boers J, van IJcken WFJ, Lavrijsen M, Grünhagen DJ, Verhoef C, Sleijfer S, Smits R, Gribnau J, Wiemer EAC
Zhao M, Kiernan CH, Stairiker CJ, Hope JL, Leon LG, van Meurs M, Brouwers-Haspels I, Boers R, Boers J, Gribnau J, van IJcken WFJ, Bindels EM, Hoogenboezem RM, Erkeland SJ, Mueller YM, Katsikis PD
Kenter AT, Rentmeester E, van Riet J, Boers R, Boers J, Ghazvini M, Xavier VJ, van Leenders GJLH, Verhagen PCMS, van Til ME, Eussen B, Losekoot M, de Klein A, Peters DJM, van IJcken WFJ, van de Werken HJG, Zietse R, Hoorn EJ, Jansen G, Gribnau JH
Vos M, Boers R, Vriends ALM, Boers J, van Kuijk PF, van Houdt WJ, van Leenders GJLH, Wagrodzki M, van IJcken WFJ, Gribnau J, Grünhagen DJ, Verhoef C, Sleijfer S, Wiemer EAC
Chaves I, van der Eerden B, Boers R, Boers J, Streng AA, Ridwan Y, Schreuders-Koedam M, Vermeulen M, van der Pluijm I, Essers J, Gribnau J, Reiss IKM, van der Horst GTJ
Adrianse RL, Smith K, Gatbonton-Schwager T, Sripathy SP, Lao U, Foss EJ, Boers RG, Boers JB, Gribnau J, Bedalov A
Boers R, Boers J, de Hoon B, Kockx C, Ozgur Z, Molijn A, van IJcken W, Laven J, Gribnau J
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
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
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
Leeman A, Jenkins D, Del Pino M, Ordi J, Torné A, Doorbar J, Meijer CJLM, van Kemenade FJ, Quint WGV
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
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
Leeman A, Del Pino M, Marimon L, Torné A, Ordi J, Ter Harmsel B, Meijer CJLM, Jenkins D, Van Kemenade FJ, Quint WGV
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
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