The following primers were used for RT-PCR: GAPDH forward (Fw) 5 -GAA GGT GAA GGT

Supplementary Material and Methods RT-PCR Primers The following primers were used for RT-PCR: GAPDH forward (Fw) 5 -GAA GGT GAA GGT CGG AGT C-3, GAPDH reverse (Rev) 5 -GAA GAT GGT GAT GGG ATT TC-3, GPX3 QuantiTect Hs_GPX3_1_SG (QT62279; QIAGEN), RBP1 Fw 3 - tgcacgatctctttgtctgg- 3,RBP1 Rev 5 -caactggctccagtcactcc-3, SPARC QuantiTect Hs_SPARC_1_SG (QT186; QIAGEN), TGFBI QuantiTect Hs_TGFBI_1_SG (QT19477;QIAGEN). PCR products were visualised as single, defined bands by gel electrophoresis with the following sizes according to primers used: GAPDH 226bp, GPX3 14 bp, RBP1 159 bp, SPARC 6 bp, TGFBI 135 bp. Bisulfite pyrosequencing primers and conditions Bisulfite PCR and sequencing primer sequences were as follows: RBP1 Fw 5 - GGA AAG AGG TTA TTT ATA GGT TTT TGT T-3, RBP1 Rev biotin-5 - CCA CAT ACA CTT CAA ATA ACA TCA AC-3, RBP1 sequencing (Seq) 5 - GAG AAA ATT GGG GTA TT-3, SPARC Fw biotin-5 - GAA TGT GGA GGG GTT TAG AGA TAG-3, SPARC Rev 5 - CCA AAC CTA TCC AAC CCT AAC A-3, SPARC Seq 5 - CAA ATA AAA CAA ACA AAA TT-3, TGFBI Fw 5 - GTA AGG GTT GGG AAA ATT GAG-3, TGFBI Rev biotin-5 - AAC CTA CTA TAC TAC AAC ACC AAC TAA T-3, TGFBI Seq 5 - TGG GTG TTT AGG GTA GTT A-3. A total of ng of bisulfite converted DNA were used per µl PCR reaction. Thermal cycling using the peqgold Hot Start Mix Y enzyme mastermix was performed for 5 cycles (5 min at 95 C; then 3 sec each for 5 cycles: 58 C, 72 C, 95 C; followed by a 5 min 72 C). Amplification of a single, defined PCR product was confirmed by gel electrophoresis. PCR products bound to biotin labelled primers were attached to sepharose beads and cleaned up as per manufacturer s recommendations. Purified products were subjected to pyrosequencing on a Pyromark Q96 MD (QIAGEN) sequencer. Percentages of methylated and unmethylated cytosines were calculated using the Pyro-QCpG software (QIAGEN). Only assays with

satisfactory quality control values as defined by the software (e.g. bisulfite conversion controls) were permitted for analysis. Results show the methylation values for the CpGs that match the exact location of the array methylation probes for the respective genes.

Supplementary Table S1: Complete list of p-dmrs (5% FDR) Methylation probe Log-rank p-value Log-rank q-value Gene symbol Chrom osome CpG Island Beta Value Cut-off cg449714 2.7E-8.2 SLC6A2 16 Y.28 cg13323752 1.92E-8.2 SLC2A14 12 Y.17 cg1449461 4.8E-8.221 GRID2 4 Y.18 cg19182 1.29E-7.525 BAALC 8 Y.28 cg2675683 2.55E-7.83 MMP16 8 Y.37 cg856146 7.46E-7.1349 SOX7 8 Y.31 cg155111 7.18E-7.1349 GRHL3 1 Y.26 cg173122 5.13E-7.1349 EIF4EBP3 5 Y.27 cg25764464 7.25E-7.1349 PLEKHA5 12 Y.22 cg1642767 9.18E-7.1493 ARHGEF7 13 Y.27 cg1231779 1.3E-6.1517 NID2 14 Y.31 cg65537 1.37E-6.1854 INHA 2 Y.25 cg9229912 1.72E-6.2146 CUTL2 12 Y.29 cg2341285 1.9E-6.23 SOCS2 12 Y.29 cg25874 2.39E-6.2589 ITGA9 3 Y.28 cg25913233 2.87E-6.2743 SPARC 5 N.23 cg2664637 2.78E-6.2743 SHD 19 Y.36 cg1362935 3.46E-6.3124 MRGPRX2 11 N.34 cg294382 4.19E-6.3586 IL23A 12 N.22 cg8768421 4.49E-6.365 GDA 9 Y.24 cg2144298 5.77E-6.4468 CEBPA 19 Y.31 cg263991 8.23E-6.687 ANKRD43 5 Y.31 cg23363832 1.21E-5.6963 RBP1 3 Y.36 cg112757 1.36E-5.6963 RBP1 3 Y.37 cg272 1.55E-5.6963 MGC134 11 Y.13 cg625653 1.4E-5.6963 WNT7A 3 Y.31 cg63164 1.52E-5.6963 KCNQ4 1 Y.33 cg161488 1.3E-5.6963 TRPA1 8 Y.31 cg3556497 1.31E-5.6963 SLC32A1 Y.22 cg497257 1.42E-5.6963 ADCY2 5 Y.32 cg7657776 1.21E-5.6963 UBE3B 12 N.63 cg146722 1.51E-5.6963 CALCA 11 Y.33 cg14117297 1.11E-5.6963 MGC23244 19 N. cg18342279 1.31E-5.6963 ZAR1 4 Y.33 cg1867498 1.54E-5.6963 CA3 8 Y.29 cg215393 1.58E-5.6963 EMP2 16 Y.31 cg25823578 1.51E-5.6963 PTGER2 14 Y.37 cg715629 1.94E-5.8299 ERBB4 2 Y.33 cg8539991 2.26E-5.8866 ZBTB32 19 N.39 cg651311 2.25E-5.8866 TRIM15 6 N.26 cg11781389 2.26E-5.8866 LOC89944 11 Y.37 cg2719612 2.29E-5.8866 COG7 16 Y.31 cg13692433 2.47E-5.924 NCAM1 11 Y.28 cg26796283 2.56E-5.924 MSX2 5 Y.3 cg4623837 2.54E-5.924 HCG9 6 Y.3 cg2258173 2.68E-5.9365 THBS1 15 Y.27 cg8818784 2.71E-5.9365 KLK1 19 Y.35 cg23273897 2.76E-5.9365 MME 3 N.25 cg26524899 2.84E-5.9419 AKAP5 14 Y.35 cg9595479 3.7E-5.9973 PRPH 12 Y.31 cg8949296 3.23E-5.191 JPH1 8 Y.34 cg9688546 3.21E-5.191 GLRB 4 Y.37 cg14187678 3.62E-5.11114 TBR1 2 N.29 cg5829479 3.88E-5.11467 C6orf141 6 Y.3

cg1731149 3.81E-5.11467 CYBRD1 2 Y.26 cg699298 3.95E-5.11471 RASD1 17 Y.32 cg4645342 4.18E-5.11924 NEGR1 1 Y.31 cg7533148 5.14E-5.12665 TRIM58 1 Y.26 cg654318 4.96E-5.12665 RBP1 3 Y.25 cg133311 5.4E-5.12665 PTHLH 12 N.28 cg14383135 5.29E-5.12665 NPAS2 2 Y.34 cg15321211 5.21E-5.12665 HNRPF 1 Y.25 cg512279 5.26E-5.12665 SLC18A2 1 Y.3 cg65775 5.6E-5.12665 DHDDS 1 Y.23 cg86674 4.62E-5.12665 PAPPA 9 N.28 cg935141 5.12E-5.12665 PPM1F 22 Y.37 cg15878317 4.97E-5.12665 NMNAT3 3 Y.25 cg23547429 4.54E-5.12665 SLC43A3 11 N.27 cg2134676 5.53E-5.12667 TGFBI 5 Y.26 cg25782229 5.47E-5.12667 WT1 11 Y.27 cg1889852 5.4E-5.12667 PDE8B 5 Y.27 cg247176 5.67E-5.1281 ABCG2 4 Y.23 cg1331933 6.E-5.13375 RORA 15 Y. cg1535453 6.24E-5.13535 ACADS 12 Y.34 cg83715 6.18E-5.13535 ST3GAL4 11 Y.24 cg1833369 7.19E-5.15397 PADI4 1 N.26 cg19221959 7.5E-5.15854 PPP1R9A 7 Y.31 cg3391568 7.92E-5.16511 PTHR1 3 N.25 cg2522573 8.9E-5.16667 KCNK13 14 Y.26 cg24354652 8.45E-5.17176 PTAFR 1 N.4 cg2341627 8.78E-5.17635 CH25H 1 Y.24 cg11738543 8.93E-5.17719 SOCS2 12 Y.29 cg1151699 9.1E-5.17843 CACNG2 22 Y.25 cg218677 9.6E-5.18598 GABRA2 4 Y.28 cg1813774.12.19338 CECR6 22 Y.3 cg263371.12.19338 TACR1 2 Y.38 cg7699362.19.318 GPX3 5 Y.32 cg21715963.112.665 C1orf51 1 Y.29 cg27457941.114.928 RBP1 3 Y.37 cg796846.118.21252 STK11 19 Y.17 cg4434339.119.21252 ST6GAL2 2 Y.25 cg26898336.127.2213 TEKT3 17 Y.36 cg21727574.126.2213 ZNF137 19 N.52 cg9416313.129.22283 MATK 19 Y.34 cg1127165.13.22283 STEAP4 7 Y.22 cg25384595.138.22324 LILRA1 19 N.24 cg13756879.132.22324 IGF2 11 Y.26 cg431614.133.22324 FLJ1117 4 N.43 cg16523424.139.22324 TIMP1 X N.19 cg18489434.136.22324 VASH1 14 Y.26 cg22759686.137.22324 ARSD X Y.22 cg37566.146.23238 ESRRG 1 Y.3 cg8383315.157.24732 RIC3 11 Y.18 cg758475.171.25939 SEMA3B 3 N.65 cg152557.17.25939 C1orf16 1 Y.32 cg19188612.168.25939 CTHRC1 8 Y.67 cg19478743.169.25939 CXCL16 17 Y.25 cg793426.173.2671 ABCA11 4 Y.3 cg91458.177.26473 GAP43 3 Y.34 cg16785.184.26774 SLC5A6 2 N.24 cg14724613.184.26774 GRM3 7 Y.25 cg14812492.183.26774 DGKH 13 Y.3

cg25965576.189.273 CST4 N.31 cg9811393.9.2995 SEMA3B 3 Y.42 cg578689.9.2995 CKB 14 Y.3 cg762584.9.2995 PRSS12 4 Y.33 cg13843613.8.2995 FAM5B 1 Y.24 cg26516759.213.29171 BMP7 Y.26 cg12249575.212.29171 TITF1 14 Y.27 cg11762346.2.29699 HKDC1 1 N.49 cg699736.221.29699 VAX2 2 Y.26 cg15645.231.3839 APC 5 N.34 cg37194.234.3943 GSTM2 1 N.3 cg133582.238.31255 MFAP4 17 N.33 cg596686.24.31299 STS X N.53 cg26812418.243.31317 CPE 4 Y.21 cg4418492.246.31567 CYP7B1 8 Y.24 cg21237418.263.31691 RAB34 17 Y.31 cg261781.255.31691 MATN3 2 Y.35 cg465284.257.31691 LRRTM1 2 Y.28 cg137443.253.31691 DGKQ 4 Y.3 cg1698981.258.31691 Corf39 Y.33 cg21814.263.31691 PRSS12 4 Y.35 cg22334665.26.31691 SLC22A16 6 Y.23 cg22692158.262.31691 PRB4 12 N.67 cg1734665.267.3191 ATP1A 15 Y.34 cg251243.271.32145 MRPL48 11 Y.36 cg1169812.288.33372 CD38 4 N.51 cg13468685.288.33372 PLEK 2 N.34 cg16155382.289.33372 GRHL3 1 Y.27 cg566118.287.33372 TNC 9 Y.17 cg1199721.295.3381 GCN1L1 12 Y.22 cg2489251.31.33956 ZNF415 19 Y.22 cg275179.3.33956 ERBB2 17 Y.23 cg16584573.316.35414 FGF8 1 Y.37 cg21513385.318.35414 LOC57228 12 Y.29 cg4498739.323.3574 PDK4 7 Y.27 cg2137143.325.35762 MYBPC3 11 N.49 cg1188544.338.36675 FKBP9L 7 Y.22 cg149376.34.36675 NALP4 19 Y.7 cg22598744.34.36675 MLANA 9 N.57 cg24813212.345.3695 TEKT2 1 Y.29 cg58689.366.36993 KCNV1 8 Y.27 cg149559.36.36993 KCNMB1 5 N.26 cg18554.367.36993 CACNB2 1 Y. cg9437522.354.36993 GNAS Y.49 cg9967877.368.36993 SYT12 11 Y.36 cg1688991.361.36993 DLX3 17 Y.27 cg15736338.353.36993 FAM19A2 12 Y.28 cg16998213.355.36993 METRN 16 Y.32 cg25462291.366.36993 HEYL 1 Y.36 cg25996835.359.36993 BBS4 15 Y.27 cg561515.375.37471 ARPP-21 3 N.49 cg26831415.49.4576 EFHA2 8 Y.21 cg46288.421.41555 ZBTB16 11 Y.28 cg1837719.43.496 FUT9 6 Y.27 cg778788.434.42244 SLCO2A1 3 Y. cg176532.437.4227 ZNF256 19 Y.18 cg785271.442.42298 MMP24 N.54 cg2289294.441.42298 CBX2 17 Y.54

cg11919.451.42863 AZGP1 7 N.29 cg3573747.474.43388 ADIPOQ 3 N.47 cg696435.47.43388 FLJ25773 14 N.3 cg7862358.475.43388 MYO1 5 Y. cg1548978.474.43388 C1orf27 1 N.35 cg16382256.472.43388 EPHB3 3 Y.37 cg17398613.468.43388 SLC37A1 21 Y.56 cg1986374.459.43388 PARVG 22 N.33 cg1479785.481.43643 SFTPC 8 N.42 cg25886284.483.43643 ZNF545 19 Y.17 cg1358918.55.4581 FAM5B 1 Y.21 cg285335.53.4581 KCNF1 2 Y.19 cg2467598.57.4581 FLJ23577 5 Y.17 cg2415431.516.45632 IGLL1 22 N.22 cg7537523.522.45877 BCAT1 12 Y.1 cg12359315.526.45964 SLC6A 3 Y.25 cg7792737.533.46187 NPIP 16 N.69 cg7525445.535.46187 TPM1 15 Y.33 cg27574244.537.46187 TBCD 17 Y.26 cg23769143.54.46242 TIMP4 3 N.21 cg18815943.549.46477 FOXE3 1 Y.37 cg17532978.547.46477 NEUROD4 12 N.27 cg4486568.559.4669 ETS2 21 Y.15 cg1459963.558.4669 GPR19 12 Y.64 cg14681767.556.4669 ARHGEF1 8 Y.33 cg18589624.566.46995 INMT 7 N.41 cg2469559.57.4777 HNRPL 19 Y.15 cg14824983.589.48382 SEMA3B 3 N.4 cg72729.597.48775 FLJ1925 7 Y.65 cg1373941.64.4933 AKAP7 6 N.52 cg177331.66.4933 C1orf16 1 Y.27 cg821616.613.4925 ZNF52 3 Y.25 cg18453621.615.4925 LMX1B 9 Y.28 cg2394336.619.49342 LDLR 19 Y.21 cg17527798.625.49538 LTF 3 Y.33 cg22392276.627.49538 CKB 14 Y.27 cg6747888.631.4964 TBR1 2 Y.36

Supplementary Table S2: Preferential overlap analysis between genomic locations of the 7 p-dmr array probes and genomic locations of histone modifications and chromatin states from the ENCODE project 1 in comparison to the remaining probes of the HumanMethylation27 array. Analysis was performed using the MCFDR scheme for Monte Carlo based p-value computation on the Genomic HyperBrowser platform (http://hyperbrowser.uio.no). 2,3 P-values <.5 support an overlap between datasets more than expected by chance. Chromatin ENCODE dataset ENCODE cell type p value modification or binding factor Poised promoter Chromatin State Segmentation by GM12878 (lymphatic).5 HMM from ENCODE/Broad 4 H1hESC (stem cell).5 H3K27me3 H3K27me3 from ENCODE/Broad GM12878 (lymphatic).5 H1hESC (stem cell).5 EZH2 H3K27me3 from ENCODE/Broad GM12878 (lymphatic).5 H1hESC (stem cell).5 Supplementary Table S3: Overrepresentation of overlap between genomic locations of the 7 p-dmr probes and transcription binding sites in the lymphoblastoid cell line GM12878 as provided in the ENCODE dataset was calculated using the MCFDR scheme for Monte Carlo based p-value computation on the Genomic HyperBrowser platform. 2,3 P-values <.5 indicate and overlap between datasets of more than expected by chance. Transcription Factor ENCODE dataset Cell type p value SP1 Hudson Alpha GM12878 <.1 EGR1 Hudson Alpha GM12878.1 NFKB Stanford GM12878 (TNFα-stimulated).8 Supplementary References 1. Consortium EP. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 11;9(4):e1146. 2. Sandve GK, Gundersen S, Rydbeck H, et al. The Genomic HyperBrowser: inferential genomics at the sequence level. Genome Biol. 1;11(12):R121. 3. Sandve GK, Ferkingstad E, Nygard S. Sequential Monte Carlo multiple testing. Bioinformatics. 11;27(23):3235-3241. 4. Ernst J, Kheradpour P, Mikkelsen TS, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 11;473(7345):43-49.

Supplementary Figure S1. Kaplan-Meier plots for overall survival and scatterplots indicating the correlation between methylation and expression for the pd-dmrs mapping to RASD1, CD38, NCAM1, PDK4. In the right column, grey shading indicates samples with high methylation (Materials and Methods) Overall Survival Correlation Methylation and Expression 1 8 22.7 (n=1) 46.9 (n=149) Log-rank p<.1 6 RASD1 4 4 6 8 1 1 8 59.1 (n=73) 32.9 (n=86) Log-rank p=.3 6 CD38 4 4 6 8 1 1 8 21.9 (n=8) 46.4 (n=151) Log-rank p<.1 6 NCAM1 4 4 6 8 1 1 8 25.6 (n=24) 47.7 (n=135) Log-rank p=.3 6 PDK4 4 4 6 8 1

Supplementary Figure S2. Kaplan-Meier plots for overall survival for the prognostically independent pd-dmrs. Analysis was performed separately for the subgroups of the intensive (younger, fitter patients) and non-intensive (elderly, unfit patients) treatment arms of the MRC Myeloma IX trial. Intensive Treatment Arm Non-Intensive Treatment Arm 1 8 13.2 (n=5) 65.3 (n=8) Log-rank p=.169 1 8 25.5 (n=7) 35.7 (n=67) Log-rank p=.53 6 6 GPX3 4 4 4 6 8 1 4 6 8 1 1 8 4.8 (n=1) 8. (n=75) Log-rank p=.99 1 8 16.5 (n=16) 38.5 (n=58) Log-rank p=.14 6 6 RBP1 4 4 4 6 8 1 4 6 8 1 1 8 16.7 (n=14) 88. (n=71) Log-rank p<.1 1 8 22.4 (n=15) 35.7 (n=59) Log-rank p=.172 6 6 SPARC 4 4 4 6 8 1 4 6 8 1 1 8 38.3 (n=14) 88. (n=71) Log-rank p=.2 1 8 25.5 (n=15) 38.5 (n=59) Log-rank p=.588 6 6 TGFBI 4 4 4 6 8 1 4 6 8 1

Supplementary Figure S3. Kaplan-Meier plot for overall survival for the pd-dmr mapping to SPARC. The analysis was performed in the subgroup of patients with a hyperdiploid genotype. 1 8 32.6 (n=1) 6.6 (n=52) Log-rank p=.33 6 4 4 6 8 1 Supplementary Figure S4. Kaplan-Meier plot for overall survival for the four independent pd-dmrs mapping to SPARC, TGFBI, RBP1 and GPX3. Cases were grouped regarding the number of the four pd- DMRs showing high methylation. 1 8 "" meth pd-dmrs None: 57.1 (n=14) 1-2: 39.1 (n=44) 3-4: 13.2 (n=11) Log-rank p<.1 6 4 None 1-2 3-4 4 6 8 1