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Supplementary Table 1. Assignment of Hyperdiploidy by FISH and Clinical Parameters of Group 1 Patients

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Supplementary Table 1. Assignment of Hyperdiploidy by FISH and Clinical Parameters of Group 1 Patients Supplementary table 1. Assignment of hyperdiploidy by FISH and clinical parameters of Group 1 patients FISH Based Trisomy Index MAYO T3 T9 T11 T15 T19 TC class Heavy Chain Light Chain Status 13 VH/CH PCLI GEP Cluster Albumin B2M ISS Stage Bone Disease M003 ND + + + ND D1 G Kappa Relapse 0 0 4.2 1 3.4 4.16 II - M029 ND + - + ND D1 G lambda Relapse 0 0 3 1 2.74 7.29 III Y M037 ND + + - ND D2 G Kappa New 1 0 0.2 2 2.77 6.54 III Y M051 ND + - + ND D2 G Kappa Relapse 1 0 4.8 1 3.24 8.46 III Y M058 ND + + + ND D1 G lambda New 1 0 0 4 3.15 7.18 III N M059 ND + - + ND D1 L Kappa New 0 1 0 4 3.94 2.28 I Y M061 + + - - - D1 L Kappa New 0 0 0 2 2.67 2.61 II Y M082 ND + + - ND D2 A Kappa Relapse 1 0 5.8 1 2.76 - - Y M113 + + - - - D1 G lambda Relapse 0 0 2.2 4 3.79 11.6 III Y M123 ND + - + ND D1+D2 G Kappa Relapse 1 1 1.2 2 4.28 1.7 I Y M128 ND + + + ND D1 L Kappa Relapse 0 1 2.3 4 4.17 7.4 III Y M131 ND - + + ND D1 G Kappa Relapse 0 0 4.4 4 4.88 8.74 III Y M135 ND + + + ND D1 G Kappa New 0 0 0 3 4.01 5.23 II Y M142 ND + + - ND D1 A Kappa New 0 0 0.2 3 3.92 5.23 II Y M163 ND + + + ND D1 A Kappa New 0 0 0.4 3 2.96 2.06 II N M198 ND + + + ND D1 A Kappa New 0 0 0.4 2 3.1 3.3 II Y M200 ND + + - ND D2 A Kappa New 0 0 3.8 1 2.5 3.16 II Y M218 ND + + + ND D1 A lambda New 0 0 0 3 3.6 4.31 II Y M227 ND - + + ND D1 L Kappa New 1 0 0 3 3.9 2.76 I Y M229 ND - + + ND D1 G Kappa Relapse 0 0 3.8 1 4.3 8.77 III Y M230 ND + + - ND D1 A Kappa New 1 1 1 4 3.6 6.94 III Y M235 ND + + + ND D1 G Kappa Relapse 0 0 0.2 2 4 2.37 I Y M245 ND + - + ND D1 G Kappa New 0 0 0 4 3.9 2.11 I Y M249 ND + + + ND D1 A Kappa New 1 0 5.1 1 3 5.32 II Y M254 ND + + + ND D1 G Kappa Relapse 0 0 2.6 4 4 2.01 I Y M264 ND + + + ND D1 G Kappa New 1 0 0.6 2 4 6.55 III N M276 ND + + + ND D1 G Kappa Relapse 0 0 4.7 1 4.1 - - Y M279 + + - - - D1 A Kappa New 0 0 1.2 2 3.9 6.31 III Y M288 ND + - + ND NONE G lambda New 0 0 9.4 1 2.3 1.74 II Y M300 ND + + + ND NONE G Kappa New 1 1 1.2 3 3.8 2.59 I N M304 ND + + + ND D1+D2 G lambda New 0 0 0 2 3.6 3.34 I N M307 ND + + - ND D1+D2 A lambda New 0 0 0 1 3.7 6.22 III Y M315 ND + + + ND D1 G Kappa Relapse 0 1 2.4 4 3.7 3.39 I Y M318 ND + + + ND D1 L lambda New 0 1 4 4 3.8 2.76 I Y M337 + - + - - D1 A Kappa New 1 0 0 2 3.8 5.12 II Y M338 ND + + + ND D1 G Kappa New 0 0 2.8 4 3.3 1.96 II Y M359 ND + + + ND D1 G Kappa New 0 0 0.2 3 3.8 4.35 II Y M370 ND + - + ND D1 G Kappa New 1 0 0 2 4 9.67 III N M373 ND + + + ND D1 G lambda New 0 0 0 4 3.5 1.31 I Y M380 ND + + + ND D1 G Kappa New 0 0 2 3 3.9 2.11 I Y M383 ND + + + ND D1 G Kappa New 0 0 0.2 1 3.3 4.73 II Y M407 ND + + + ND D1 A Kappa New 0 0 0.6 4 4.3 1.65 I Y M410 ND + - + ND NONE A Kappa New 0 0 0 3 3.6 2.14 I Y M412 ND + + - ND D1 G Kappa New 0 0 0.2 3 2.9 3.43 II Y M444 ND + + + ND D1 G Kappa Relapse 0 0 0.4 4 4 5.45 II Y M467 ND + + + ND D1 A lambda New 0 0 0 3 3.9 1.91 I N M490 ND + + + ND D1 G Kappa Relapse 0 1 4 3 3.82 4.45 II Y M687 ND + + + ND D2 L lambda New 1 1 0 3 3.7 2.74 I N M700 ND + + + ND D1 G Kappa New 1 1 0.8 2 3.6 2.4 I Y M789 ND + + + ND D1 G Kappa Relapse 0 0 1 4 5 - - Y M790 ND + + + ND D1 G Kappa New 0 0 0.8 3 2.9 3.97 II Y M806 ND + + + ND D1 G Kappa New 0 0 0 2 2.4 - - N M822 ND + + + ND D1+D2 A lambda New 1 0 2.2 1 3.9 2.25 I N Abbreviation: ND = not done; M = Male; F = Female; L = light chains only; T3, T9. T11. T15. T19 = trisomies of chromosomes 3,9,11,15 and 19 respectively. Supplementary table 2. Genes lists used for each recursive clustering. 1st Recursive Clustering 2nd Recursive Clustering 3rd Recursive Clustering 4th Recursive Clustering Probe ID Gene Name Probe ID Gene Name Probe ID Gene Name Probe ID Gene Name 200602_at APP 200602_at APP 200602_at APP 200602_at APP 200799_at 200799_at 200799_at 200799_at 200951_s_at CCND2 200951_s_at CCND2 200951_s_at CCND2 200953_s_at CCND2 200953_s_at CCND2 200953_s_at CCND2 201005_at CD9 201005_at CD9 201005_at CD9 201005_at CD9 201105_at LGALS1 201105_at LGALS1 201105_at LGALS1 201105_at LGALS1 201131_s_at CDH1 201131_s_at CDH1 201131_s_at CDH1 201131_s_at CDH1 201160_s_at CSDA 201160_s_at CSDA 201160_s_at CSDA 201160_s_at CSDA 201161_s_at CSDA 201161_s_at CSDA 201161_s_at CSDA 201161_s_at CSDA 201170_s_at BHLHB2 201170_s_at BHLHB2 201170_s_at BHLHB2 201417_at SOX4 201417_at SOX4 201417_at SOX4 201417_at SOX4 201565_s_at ID2 201565_s_at ID2 201565_s_at ID2 201565_s_at ID2 201839_s_at TACSTD1 201839_s_at TACSTD1 201839_s_at TACSTD1 201839_s_at TACSTD1 201939_at PLK2 201939_at PLK2 201939_at PLK2 201939_at PLK2 202075_s_at PLTP 202075_s_at PLTP 202075_s_at PLTP 202208_s_at ARL7 202208_s_at ARL7 202208_s_at ARL7 202363_at SPOCK 202363_at SPOCK 202391_at BASP1 202391_at BASP1 202391_at BASP1 202391_at BASP1 202551_s_at CRIM1 202551_s_at CRIM1 202551_s_at CRIM1 202733_at P4HA2 202790_at GABARAP 202790_at GABARAP 202790_at GABARAP 202790_at GABARAP 202826_at SPINT1 202826_at SPINT1 202826_at SPINT1 202839_s_at NDUFB7 203029_s_at PTPRN2 203029_s_at PTPRN2 203029_s_at PTPRN2 203029_s_at PTPRN2 203153_at IFIT1 203153_at IFIT1 203186_s_at S100A4 203186_s_at S100A4 203186_s_at S100A4 203186_s_at S100A4 203215_s_at MYO6 203215_s_at MYO6 203215_s_at MYO6 203215_s_at MYO6 203421_at TP53I11 203421_at TP53I11 203421_at TP53I11 203476_at TPBG 203476_at TPBG 203476_at TPBG 203476_at TPBG 203559_s_at ABP1 203828_s_at NK4 203887_s_at THBD 203888_at THBD 203962_s_at NEBL 203962_s_at NEBL 203962_s_at NEBL 203962_s_at NEBL 204103_at CCL4 204103_at CCL4 204103_at CCL4 204114_at NID2 204114_at NID2 204114_at NID2 204114_at NID2 204271_s_at EDNRB 204271_s_at EDNRB 204271_s_at EDNRB 204271_s_at EDNRB 204285_s_at PMAIP1 204285_s_at PMAIP1 204285_s_at PMAIP1 204285_s_at PMAIP1 204286_s_at PMAIP1 204286_s_at PMAIP1 204286_s_at PMAIP1 204288_s_at ARGBP2 204288_s_at ARGBP2 204288_s_at ARGBP2 204288_s_at ARGBP2 204374_s_at GALK1 204374_s_at GALK1 204430_s_at SLC2A5 204430_s_at SLC2A5 204430_s_at SLC2A5 204430_s_at SLC2A5 204439_at C1orf29 204439_at C1orf29 204439_at C1orf29 204439_at C1orf29 204469_at PTPRZ1 204469_at PTPRZ1 204469_at PTPRZ1 204560_at FKBP5 204560_at FKBP5 204560_at FKBP5 1st Recursive Clustering 2nd Recursive Clustering 3rd Recursive Clustering 4th Recursive Clustering Probe ID Gene Name Probe ID Gene Name Probe ID Gene Name Probe ID Gene Name 204641_at NEK2 204661_at CDW52 204661_at CDW52 204661_at CDW52 204661_at CDW52 204748_at PTGS2 204748_at PTGS2 204748_at PTGS2 204748_at PTGS2 204766_s_at NUDT1 204766_s_at NUDT1 204766_s_at NUDT1 204777_s_at MAL 204777_s_at MAL 204777_s_at MAL 204798_at MYB 204798_at MYB 204798_at MYB 204823_at NAV3 204823_at NAV3 204823_at NAV3 204836_at GLDC 204836_at GLDC 204836_at GLDC 204960_at PTPRCAP 204960_at PTPRCAP 204960_at PTPRCAP 204960_at PTPRCAP 205081_at CRIP2 205081_at CRIP2 205081_at CRIP2 205081_at CRIP2 205110_s_at FGF13 205110_s_at FGF13 205110_s_at FGF13 205110_s_at FGF13 205114_s_at CCL3 205114_s_at CCL3 205114_s_at CCL3 205122_at TMEFF1 205122_at TMEFF1 205122_at TMEFF1 205124_at MEF2B 205124_at MEF2B 205124_at MEF2B 205363_at BBOX1 205363_at BBOX1 205363_at BBOX1 205363_at BBOX1 205399_at DCAMKL1 205399_at DCAMKL1 205399_at DCAMKL1 205399_at DCAMKL1 205404_at HSD11B1 205433_at BCHE 205449_at HSU79266 205449_at HSU79266 205449_at HSU79266 205848_at GAS2 205848_at GAS2 205848_at GAS2 205902_at KCNN3 205902_at KCNN3 205902_at KCNN3 205902_at KCNN3 205967_at HIST1H4F 205968_at KCNS3 205968_at KCNS3 205968_at KCNS3 205968_at KCNS3 205983_at DPEP1 205983_at DPEP1 205997_at ADAM28 205997_at ADAM28 205997_at ADAM28 205997_at ADAM28 206045_s_at NOL4 206045_s_at NOL4 206045_s_at NOL4 206204_at GRB14 206204_at GRB14 206204_at GRB14 206204_at GRB14 206255_at BLK 206255_at BLK 206255_at BLK 206359_at SOCS3 206359_at SOCS3 206363_at MAF 206363_at MAF 206363_at MAF 206363_at MAF 206372_at MYF6 206372_at MYF6 206372_at MYF6 206394_at MYBPC2 206394_at MYBPC2 206394_at MYBPC2 206394_at MYBPC2 206456_at GABRA5 206461_x_at MT1H 206461_x_at MT1H 206461_x_at MT1H 206525_at GABRR1 206574_s_at PTP4A3 206574_s_at PTP4A3 206574_s_at PTP4A3 206574_s_at PTP4A3 206595_at CST6 206595_at CST6 206595_at CST6 206595_at CST6 206626_x_at SSX1 206640_x_at GAGE5 206762_at KCNA5 206762_at KCNA5 206762_at KCNA5 206762_at KCNA5 206834_at HBD 206834_at HBD 206834_at HBD 206834_at HBD 206843_at CRYBA4 206843_at CRYBA4 206843_at CRYBA4 206843_at CRYBA4 206897_at GAGEB1 206991_s_at CCR5 206991_s_at CCR5 206991_s_at CCR5 206991_s_at CCR5 207076_s_at ASS 207076_s_at ASS 207076_s_at ASS 207076_s_at ASS 207086_x_at GAGE5 207100_s_at VAMP1 207100_s_at VAMP1 207100_s_at VAMP1 1st Recursive Clustering 2nd Recursive Clustering 3rd Recursive Clustering 4th Recursive Clustering Probe ID Gene Name Probe ID Gene Name Probe ID Gene Name Probe ID Gene Name 207101_at VAMP1 207101_at VAMP1 207101_at VAMP1 207104_x_at LILRB1 207104_x_at LILRB1 207104_x_at LILRB1 207191_s_at ISLR 207191_s_at ISLR 207191_s_at ISLR 207337_at CTAG2 207339_s_at LTB 207339_s_at LTB 207339_s_at LTB 207339_s_at LTB 207414_s_at PACE4 207493_x_at SSX2 207663_x_at GAGE3 207666_x_at SSX3 207666_x_at SSX3 207666_x_at SSX3 207706_at USH2A 207706_at USH2A 207738_s_at NCKAP1 207738_s_at NCKAP1 207738_s_at NCKAP1 207739_s_at GAGE2 207826_s_at ID3 207826_s_at ID3 207826_s_at ID3 207918_s_at TSPY1 208029_s_at LAPTM4B 208029_s_at LAPTM4B 208029_s_at LAPTM4B 208112_x_at EHD1 208112_x_at EHD1 208155_x_at GAGE5 208235_x_at GAGE5 208456_s_at RRAS2 208456_s_at RRAS2 208456_s_at RRAS2 208502_s_at PITX1 208502_s_at PITX1 208502_s_at PITX1 208502_s_at PITX1 208553_at HIST1H1E 208553_at HIST1H1E 208553_at HIST1H1E 208553_at HIST1H1E 208580_x_at HIST1H4J 208580_x_at HIST1H4J 208580_x_at HIST1H4J
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