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Supplemental Figure S1 Differentially Methylated Regions (Dmrs Supplemental Figure S1 '$$#0#,2'**7+#2&7*2#"0#%'-,11 #25##,"'1#1#122#1 '!2-0'*"#.'!2'-,-$122&#20,1'2'-,$0-+2- !"Q !"2-$%," $ 31',% 25-$-*" !&,%# ," ' 0RTRW 1 !32V-$$ !0'2#0'T - #.0#1#,22'-, -$ "'$$#0#,2'**7+#2&7*2#"%#,#11',.0#,2&#1#1,"2&#'0 #&4'-022&#20,1'2'-, #25##,"'$$#0#,2"'1#1#122#1T-*!)00-51',"'!2#&7.#0+#2&7*2#"%#,#1Q%0700-51 &7.-+#2&7*2#"%#,#1Q31',%25-$-*"!&,%#,"'0RTRW1!32V-$$!0'2#0'T-%#,#1 +#22&# -4#!0'2#0'22&#20,1'2'-,$0-+$%2-$Q5#2&#0#$-0#*1-',!*3"#" %#,#15'2&V4*3#0RTRWT$$#!2#"%#,10#&'%&*'%&2#" 712#0'1)1#T Supplemental Figure S2 Validation of results from the HELP assay using Epityper MassarrayT #13*21 $0-+ 2&# 1$ 117 5#0# !-00#*2#" 5'2& /3,2'22'4# +#2&7*2'-, ,*78#" 7 '13*$'2#11007$-04V-,"6U-%#,#.0-+-2#00#%'-,1T11007 51.#0$-0+#"31',%**4'* *#1+.*#1T S Supplemental Fig. S1 A unique hypermethylated genes (methylation sites) 454 (481) 5693 (6747) 120 (122) NLMGUS NEWMM REL 2963 (3207) 1338 (1560) 5 (5) unique hypomethylated genes (methylation sites) B NEWMM 0 (0) MGUS 454 (481) 0 (0) NEWMM REL NL 3* (2) 2472 (3066) NEWMM 2963 REL (3207) 2* (2) MGUS 0 (0) REL 2 (2) NEWMM 0 (0) REL Supplemental Fig. S2 A B ARID4B DNMT3A Methylation by MassArray Methylation by MassArray 0 0.2 0.4 0.6 0.8 1 1.2 0.5 0.6 0.7 0.8 0.9 1 2 0 NL PC MGUS 1.5 -0.5 NEW MM 1 REL MM -1 0.5 -1.5 0 -2 -0.5 -1 -2.5 -1.5 -3 Methylation by HELP Assay Methylation by HELP Methylation by HELP Assay Methylation by HELP -2 -3.5 -2.5 -4 Supplemental tables "3..*#+#,2*6 *#"SS 9*','!*!&0!2#0'12'!1-$.2'#,21+.*#1 DZ_STAGE Age Gender Ethnicity MM isotype PCLI Cytogenetics t[4:14] t[11:14] Hyper- del13 del17p t[14:16] # prior Plt Hb Prot ALb CRP B2M Cr IgG IgA IgM SFK SFL FLCratio diploid treatments LC LC MGUS6 57 M caucasian IgG kappa ND 46,XY[20] ND ND ND ND ND ND 0 200 13.9 8.3 4.2 156 ND 3.1 1.1 1410 96 218 1.85 1.81 1.02 MGUS5 69 M caucasian IgG kappa 0 46,XY[20] 0 0 0 0 0 ND 0 134 12.4 7.9 4.5 150 ND 3.2 1.8 1310 262 62 25.2 28.9 0.87 MGUS4 64 M caucasian IgG lambda 0 46,XY[20] ND ND ND ND ND ND 0 253 12 6.3 3.2 145 0.7 4.49 2 876 145 139 19.2 24.6 0.78 MGUS11 48 M caucasian IgG kappa 0 46,XY[30] ND ND ND ND ND ND 0 186 14.3 9.4 4.3 156 0.6 1.94 1.1 3260 41 68 1.75 0.65 2.69 MGUS7 71 F caucasian IgG Kappa ND - No 46,XX[20] ND ND ND ND ND ND 0 274 13.1 8.4 3.7 434 ND 1.9 0.6 2040 54 527 3.83 1.16 3.3 monotypic PC MGUS1 59 F african IgG lambda 0 46 xy[20] ND ND ND ND ND ND 0 190 14.3 7.5 4.38 182 ND 2.53 1.3 1350 219 70 23.7 48.6 0.49 american MGUS3 56 f caucasian IgG lambda 0 46,XX[20] ND ND ND ND ND ND 0 192 10.2 6.9 3.4 213 ND 9.41 2.1 1320 180 74 36 52.9 0.68 MGUS2 72 M caucasian IgG kappa 0 46,XY[20] ND ND 0 1 0 ND 0 74 13.2 7.9 4.15 160 ND 3.51 1.1 2010 227 120 24.9 24.9 1 MGUS10 32 M hispanic IgG lambda ND - No 46,XY[20] ND 0 0 0 ND ND 0 188 13.4 9.4 3.7 154 0.5 5.9 1.2 2980 169 780 7.88 6.64 1.19 monotypic PC MGUS9 58 F caucasian IgM kappa ND - No 46,XX[20] ND ND ND ND ND ND 0 306 14.5 8 4.2 178 0.6 ND 0.8 834 127 384 1.05 1.39 0.76 monotypic PC MGUS8 63 F caucasian IgG kappa ND - No 46,XX,del(20)(q ND 0 1 0 0 1 0 111 7.9 7 3 223 0.5 5.91 1.2 1830 138 32 5.76 2.03 2.84 monotypic PC 11.2q13.3)[4]/46 ,XX[16] NEWMM13 61 F caucasian IgG lambda 0.7 46,XX[20] 1 0 1 1 0 0 0 194 10.6 10.1 4.17 167 0.6 2.97 0.62 5380 16 10 0.82 3.81 0.22 NEWMM11 69 F hispanic Lambda 0 46,XX[20] 0 0 1 0 0 0 0 198 10.2 8.3 4.3 178 ND 7.86 1.2 1760 28 7 ND ND ND Light chain NEWMM8 72 M caucasian Lambda 0 46,XY[20] ND 1 1 0 0 ND 0 227 10.1 7.9 3.4 ND ND 24 2.7 582 43 8 1.04 256 0 Light chain 0 NEWMM7 63 M caucasian IgA lambda 0.3 45,der(X)add(X) 1 0 0 0 0 ND 0 211 8.4 10.4 3 99 0.9 6.31 1.3 300 396 6NDND ND (p22.1)add(X)(q 0 22),Y,- 7,add(8)(q24.1), psu dic(?;12)(?;p11. 2),add(17)(q25), add(18)(q23),ad d(22)(q11.2)[3]/ 46,XY[27] NEWMM6 57 F caucasian IgG lambda 0.4 54,XX,+5,+5,+7, 0 0 1 1 0 ND 0 357 12.6 7.2 3.2 148 0 3.46 3.46 1490 85 70 ND ND ND +9,+9,13,+15,+ 15,+19,+21[1]/4 6,XX[29] NEWMM5 56 F african Kappa Light ND 46,XX[20] ND ND ND ND ND ND 0 264 8.3 7.6 4.82 ND ND 2.36 0.9 881 24 17 ND ND ND american chain NEWMM9 63 M caucasian Kappa Light 1 46,XY[20] 0 0 1 0 0 ND 0 304 12.5 6.8 3.9 159 ND 3.02 1.17 279 11 15 862 0.06 14366.67 chain NEWMM12 84 M caucasian IgA kappa 1.6 46,XY[20] 0 0 1 0 0 ND 0 237 10.4 9.3 3.9 123 ND 4.83 1.3 405 279 11 7.16 0.93 7.7 0 NEWMM10 46 M hispanic Lambda 0.4 46,XY[20] ND 1 0 0 0 ND 0 357 13.4 5.4 3.2 210 3.73 3.73 0.79 431 38 17 0.91 63.2 0.01 Light chain NEWMM3 68 M caucasian IgA kappa 0 46,XY[7]/45X,- ND 1 1 0 0 ND 1 250 12.3 7.7 2.8 130 0.6 2.61 1.2 261 261 4150.04340.91 Y[4] 0 NEWMM1 61 F caucasian free kappa ND - No 46xx[20] ND ND ND ND ND ND 0 285 8.5 6.8 3 119 1.7 41.4 11.3 574 15 14 280 23.6 1186 LC monotypic PC 00 NEWMM2 74 F caucasian IgG kappa ND - No 46,XX[20] ND ND ND ND ND ND 0 259 12.2 8.1 3.9 152 0.6 2.18 0.6 1800 66 16 8.46 21.8 0.39 monotypic PC NEWMM4 57 F caucasian IgG kappa 0.5 46,XX[30] 1 ND 0 1 0 ND 0 304 11 10 3.85 150 0.9 2.25 0.9 5090 62 43 9.25 36.9 0.25 REL9 68 M hispanic IgG kappa, 1 46,XY[20] 0 0 1 1 1 ND 5 158 11.3 7.2 3.1 155 0.8 2.38 0.9 2020 12 5 ND ND ND Kappa light chain REL10 60 F caucasian Lambda 0.6 46,XX,del(20)(q ND 1 1 0 0 ND 11 55 8.7 6.4 3.38 195 3 8.94 1.34 222 9 9 0.14 665 0 Light chain 11.2q13.1)[5]/46 ,XX,- 5,+r[5]/53,XX, t(1;12)(p13;q15) ,+6,t(8;14)(q24. 1;q32),+9, der(9)t(9;11)(q3 4;q13)x2,+add(1 1)(q13),del(13)( q12q22), der(14)t(11;14)( q13;q32),+15,+ 18,+20,+22[4]/4 6,XX[6]. REL4 53 M caucasian IgG lambda 0 46,XY[20] 1 0 0 1 0 ND 6 191 12.7 8.8 2.2 205 ND 2.5 0.8 5040 21 15 ND ND ND REL11 44 M african IgG kappa, ND - No 46,XY,t(1;8)(p1 ND 1 0 0 0 ND 2 39 10.4 6.6 3.2 170 6.7 12.3 1.65 474 35 11 0.12 303 0 american IgG lambda, monotypic PC 3;q24.1),t(11;14 free kappa )(q13;q32)[16]/4 6,XY[4] REL12 65 M caucasian IgG lambda 2.6 46,XY[20] 0 0 1 0 0 ND 3 226 9.7 9.5 2.7 145 ND 4.63 1.4 3890 20 39 0.81 3.33 0.24 REL13 73 M caucasian IgG kappa, 5.2 ND 1 0 0 1 0 ND 4 40 8 5.3 1.3 156 8.7 8.78 3.62 1030 27 24 0.63 95.8 0.01 Kappa light chain REL15 69 M hispanic IgG kappa, 2.2 46,XY[20] 0 0 1 1 1 ND 8 193 7.9 7.9 2.8 218 1.4 7.44 0.9 3240 0 <4 28 0.22 127.27 Kappa light chain REL16 60 M caucasian IgG lambda 0 46,XY[20] 1 0 0 1 0 0 2 141 13.7 10 3.64 123 0 2.6 1.1 5570 26 26 0.78 2.57 0.3 REL17 49 M caucasian IgG kappa 0.8 46,XY[20] ND 1 0 0 0 ND 6 187 11.8 9.7 3.98 145 ND 3.67 1.1 4160 23 24 9.69 0.86 11.27 REL18 62 M caucasian IgG lambda 0 46,XY[20] 1 ND 0 1 0 ND 4 163 9.6 9.4 3 137 8.7 4.18 1.3 4090 26 31 0.89 293 0 REL5 52 F caucasian IgG lambda ND 46,XX[30] ND ND ND ND ND ND 2 179 11.6 6.9 3.9 238 0 2.41 0.72 612 10 53 0.2 5.64 0.04 REL6 62 M caucasian IgG lambda 0 46,XY[20] 1 ND 0 1 0 ND 3 199 11.4 8 3.7 142 1 2.74 1.3 2220 26 33 0.68 75.4 0.01 REL14 67 M asian IgG kappa 6.3 41- 0 0 1 1 1 ND 4 61 8.2 10.2 3.23 219 0 4.66 1.1 6470 110 46 16 0.99 16.16 51,XY,+1[3],dic( 1;19)(p13;q13.3 )[3],t(1;20)(p13; q13.3), +del(2)(q31)[2], +7[8],+add(7)(p 13)[5],- 8[14],iso(8)(q10 )[3], +9[16],- 11[3],+del(11)(p 11.1)[14],- 13[12], der(16)t(11;16)( q13;p13.3)[2],ad d(17)(p11.2)[14] ,+18[14], +19[3],+add(19) (q13.1)[4],- 22,+1- 3mar[cp17]/46, XY[3] REL2 74 M caucasian faint IgG 0 46,XY[20] 0 0 1 0 1 ND 2 328 11.1 7.5 3.4 167 ND 5.11 1.7 1150 186 83 13.6 20.5 0.66 lambda REL8 50 M caucasian Kappa Light 0 46,XY[20] ND 1 0 1 0 ND 5 365 14.2 6.5 3.7 167 ND 2.62 1 207 11 31 38.6 23.4 1.65 chain REL7 48 M caucasian IgG kappa 0 46,XY[20] ND ND ND ND ND ND 3 444 4 7.7 3.9 173 nd 2.77 1 1250 181 10 750 27.7 27.08 REL3 48 M caucasian IgG kappa 0.2 46,XY[20] 0 0 1 ND ND ND 3 251 12.6 7.4 4.1 161 ND 1.77 1.1 1060 55 69 33.1 14.4 2.3 REL1 51 F caucasian free kappa 0 46,XX[20] ND 1 0 0 0 ND 4 228 12.5 6.5 3.7 165 ND 2.4 0.8 382 0 44 303 3.04 996.71 LC 0 REM2 66 M caucasian IgG kappa ND - No 46,XY[20] ND ND ND ND ND ND 6 152 12.6 6.7 3.97 169 0 2.44 0.94 408 10 11 0.23 0.89 0.23 monotypic PC REM1 50 M caucasian IgG kappa ND - No 46,XY[20] ND ND ND ND ND ND 2 275 11.6 6.9 3.7 213 0 2.39 0.83 889 0 12 1.55 0.33 4.7 monotypic PC SMM2 66 F african IgG kappa ND 46,XX[20] ND ND ND ND ND ND 0 190 13.6 8 3.6 128 2.1 3.64 0.7 1670 177 396 ND ND ND american SMM6 70 M caucasian IgG lambda ND - No 45,X,-Y[11], ND 1 0 0 0 ND 0 223 13.6 8.3 3.4 180 ND 2.65 0.93 2260 68 51 1.33 18.8 0.07 monotypic PC 46,XY[9] SMM1 76 M caucasian IgA lambda 0 46,XY[20] 0 0 1 0 0 ND 0 219 12.1 7 3.7 135 ND 5.21 1.7 706 900 27 ND ND ND SMM8 64 F asian IgG kappa ND 46,XX[20] 1 0 1 1 0 0 0 349 12.6 9.2 3.4 211 0.5 2.12 0.8 2970 45 23 17 0.83 20.48 "3..*#+#,2*6 *#"T A) NL vs.
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