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(E, F). Ovarian Clear Cell Carcinomas Harbouring Amplification of 19Q13.2

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(E, F). Ovarian Clear Cell Carcinomas Harbouring Amplification of 19Q13.2 Supplementary Material Supplementary Figure S1: Validation of amplicons using fluorescence in situ hybridisation with probes for 19q13.2 (A, B), 20q13.13 (C, D) and 20q13.31-q13.32 (E, F). Ovarian clear cell carcinomas harbouring amplification of 19q13.2, 20q13.13 and 20q13.31-q13.32 (A, C and E, respectively) and lacking amplification of these genomic regions (B, D and F, respectively). Images were captured with 3 channels (DAPI, FITC and Cy3) by using a TCS SP2 confocal microscope (Leica Milton Keynes, UK) (630X Immersion Oil). Supplementary Table S1: Summary of recurrent regions (at least 5/50 tumours, i.e. ≥10%) of gains (Log2 ratio>0.12) and losses (Log2 ratio<-0.12) and recurrent regions (at least 2/50 tumours, i.e. ≥4%) of high-level gain/ amplification (Log2 ratios>0.4) and known copy number variations (CNV) for all 50 ovarian clear cell carcinomas. NB: This Supplementary Table has been saved in a high resolution PDF format; eighteen A0 pages. Supplementary Table S2: List of genes within regions of recurrent (at least 2/50 tumours) amplification (Log2 ratios>0.4) in 50 ovarian clear cell carcinomas. NB: This Supplementary Table has been saved in a high resolution PDF format; fourteen A0 pages. Supplementary Table S3: Table summarising of the correlations between HER2 amplification as defined by chromogenic in situ hybridisation and HER2 overexpression as defined by immunohistochemistry in ovarian clear cell carcinomas identified as harbouring HER2 gene amplification based on microarray-based comparative genomic hybridisation analysis; the chromogenic in situ hybridisation validation of the presence of 17q21-21.32 amplification as defined by microarray- based comparative genomic hybridisation analysis of ovarian clear cell carcinomas; and the fluorescence in situ hybridisation validation of the presence of 19q13.2, 20q13.13 and 20q13.31-q13.32 amplification as defined by microarray-based comparative genomic hybridisation analysis in ovarian clear cell carcinomas. NB: This Supplementary Table has been saved in a high resolution PDF format; one A4 page. Supplementary Table S4: List of copy number aberrations significantly different in frequency between Cluster-1 and Cluster 2 ovarian clear cell carcinomas using Multi- Fisher’s exact test corrected for false discovery rate (adjusted p<0.05). NB: This Supplementary Table has been saved in a high resolution PDF format; three A0 pages. Supplementary Table 1 Page 1 Supplementary Table 1: Summary of recurrent regions (at least 5/50 tumours, i.e. 10%) of gains (Log2 ratio>0.12) and losses (Log2 ratio<-0.12) and recurrent regions (at least 2/50 tumours, i.e. 4%) of high-level gain/ amplification (Log2 ratios>0.4) and known copy number variations (CNV) for all 50 ovarian clear cell carcinomas. List of regions showing gains in 5 or more cases Chromosome Cytoband Start (bp) End (bp) Maximum Frequency Genes miRNAs aCGH copy number polymorphisms (CNVs) All copy number polymorphisms (CNVs) 1 p36.33-p33 633918 49868708 58% SAMD11, NOC2L, KLHL17, PLEKHN1, C1orf170, HES4, ISG15, AGRN, C1orf159, TTLL10, TNFRSF18, TNFRSF4, hsa-mir-200b, hsa-mir-200a, hsa-mir-429, hsa-mir-551a, hsa-mir-34a, hsa-mir-1290, hsa- V_0001_LC0020_Iafrate et al. (2004), V_0002_LC0028_Iafrate et al. (2004), V_0003_LC0126_Iafrate et al. (2004), V_0001, V_0002, V_0003, V_0004, V_0005, SDF4, B3GALT6, FAM132A, UBE2J2, SCNN1D, ACAP3, PUSL1, CPSF3L, GLTPD1, TAS1R3, DVL1, MXRA8, mir-1256, hsa-mir-1976, hsa-mir-552, hsa-mir-30e, hsa-mir-30c-1 V_0004_LC0152_Iafrate et al. (2004), V_0005_LC0177_Iafrate et al. (2004), V_0006_LC0305_Iafrate et al. (2004), V_0006, V_0256, V_0257, V_0378, V_0379, AURKAIP1, CCNL2, MRPL20, VWA1, ATAD3C, ATAD3B, ATAD3A, C1orf70, SSU72, MIB2, MMP23B, CDC2L2, V_0676_LC0150_Sharp et al. (2005), V_0677_LC0152_Sharp et al. (2005), V_0679_LC0177_Sharp et al. (2005), V_0380, V_0381, V_0382, V_0676, V_0677, SLC35E2, NADK, GNB1, CALML6, TMEM52, C1orf222, KIAA1751, GABRD, PRKCZ, C1orf86, SKI, MORN1, RER1, V_0680_LC0248_Sharp et al. (2005), V_2042_LC0028_Locke et al. (2006), V_2044_LC0177_Locke et al. (2006), V_0679, V_0680, V_0992, V_0993, V_0994, PEX10, PLCH2, PANK4, HES5, TNFRSF14, C1orf93, MMEL1, TTC34, ACTRT2, PRDM16, ARHGEF16, MEGF6, V_2045_LC0219_Locke et al. (2006), V_2046_LC0230_Locke et al. (2006), V_2047_LC0248_Locke et al. (2006), V_0995, V_0996, V_0997, V_0998, V_0999, TPRG1L, WDR8, TP73, CCDC27, LRRC47, KIAA0562, DFFB, C1orf174, AJAP1, NPHP4, KCNAB2, CHD5, RPL22, V_4190_LC0001_Wong et al. (2007), V_4191_LC0001_Wong et al. (2007), V_4192_LC0040_Wong et al. (2007), V_1314, V_1315, V_1316, V_1535, V_1536, RNF207, ICMT, HES3, GPR153, ACOT7, HES2, ESPN, TNFRSF25, PLEKHG5, NOL9, TAS1R1, ZBTB48, KLHL21, V_4193_LC0040_Wong et al. (2007), V_4194_LC0040_Wong et al. (2007), V_4195_LC0040_Wong et al. (2007), V_1537, V_1538, V_1539, V_1540, V_1541, PHF13, THAP3, DNAJC11, CAMTA1, VAMP3, PER3, UTS2, TNFRSF9, PARK7, ERRFI1, SLC45A1, RERE, ENO1, V_4196_LC0040_Wong et al. (2007), V_4197_LC0040_Wong et al. (2007), V_4198_LC0097_Wong et al. (2007), V_2042, V_2044, V_2045, V_2046, V_2047, CA6, SLC2A7, SLC2A5, GPR157, H6PD, SPSB1, SLC25A33, TMEM201, PIK3CD, C1orf200, CLSTN1, CTNNBIP1, V_4199_LC0100_Wong et al. (2007), V_4200_LC0104_Wong et al. (2007), V_4201_LC0106_Wong et al. (2007), V_2294, V_2295, V_2296, V_2297, V_2298, LZIC, NMNAT1, RBP7, UBE4B, KIF1B, PGD, APITD1, DFFA, PEX14, CASZ1, C1orf127, TARDBP, MASP2, SRM, V_4202_LC0106_Wong et al. (2007), V_4203_LC0113_Wong et al. (2007), V_4204_LC0118_Wong et al. (2007), V_2299, V_2300, V_2301, V_2302, V_2303, EXOSC10, FRAP1, ANGPTL7, UBIAD1, PTCHD2, FBXO2, FBXO44, FBXO6, MAD2L2, C1orf187, AGTRAP, V_4205_LC0141_Wong et al. (2007), V_4206_LC0165_W V_2304, V_2305, V_3274, V_3275, V_3276, C1orf167, MTHFR, CLCN6, NPPA, NPPB, KIAA2013, PLO V_3277, V_3278, V_3279, V_3280, V_3281, V_3282, V_3283, V_3284, V_3285, V_3286, V_3287, V_3288, V_3289, V_4190, V_4191, V_4192, V_4193, V_4194, V_4195, V_4196, V_4197, V_4198, V_4199, V_4200, V_4201, V_4202, V_4203, V_4204, V_4205, V_4206, V_4207, V_4208, V_4209, V_4210, V_4211, V_4212, V_4213, V_4214, V_4215, V_4216, V_4217, V_4218, V_4219, V_4220, V_4221, V_4222, V_4403, V_5197, V_5198, V_5200, V_5452, V_5453, V_5454, V_5455, V_5456, V_5457, V_5458, V_5459, V_5460, V_5461, V_5462, V_5463, V_5464, V_5465, V_5466, V_5467, V_5468, V_5469, V_5470, V_5471, V_5472, V_5473, V_5474, V_5475, V_5476, V_5477, V_5478, V_54 1 p33-p32.3 50412265 53048446 14% AGBL4, ELAVL4, DMRTA2, FAF1, CDKN2C, C1orf185, RNF11, TTC39A, EPS15, OSBPL9, NRD1, RAB3B, V_4223_LC0373_Wong et al. (2007), V_4224_LC0373_Wong et al. (2007), V_4225_LC0378_Wong et al. (2007) V_3290, V_4223, V_4224, V_4225, V_5493 TXNDC12, KTI12, BTF3L4, ZFYVE9, CC2D1B, ORC1L, PRPF38A, ZCCHC11 1 p32.3 53700137 54200555 14% MAGOH, LRP8, DMRTB1, GLIS1 V_3291 1 p13.1-p12 116841776 118776756 14% ATP1A1, C1orf203, CD58, IGSF3, C1orf137, CD2, PTGFRN, IGSF2, TTF2, TRIM45, VTCN1, MAN1A2, FAM46C, hsa-mir-320b-1, hsa-mir-942 V_4243_LC0729_Wong et al. (2007) V_3307, V_4243, V_6777 GDAP2, WDR3, SPAG17 1 p12 119335329 119920452 12% TBX15, WARS2, HAO2 V_2323, V_3308, V_9370 1 p12 119875343 120650514 12% HAO2, HSD3B2, HSD3B1, ZNF697, PHGDH, HMGCS2, REG4, ADAM30, NOTCH2 V_4244_LC0743_Wong et al. (2007), V_4245_LC0743_Wong et al. (2007), V_4246_LC0743_Wong et al. (2007) V_1015, V_1552, V_2323, V_3308, V_3309, V_4244, V_4245, V_4246, V_8219, V_9370, V_22949, V_23235 1 q21.1-q31.1 143510356 188484990 48% PPIAL4G, FAM72D, SRGAP2P2, PPIAL4B, NBPF9, PDE4DIP, SEC22B, NOTCH2NL, HFE2, TXNIP, POLR3GL, hsa-mir-554, hsa-mir-190b, hsa-mir-92b, hsa-mir-555, hsa-mir-9-1, hsa-mir-765, hsa-mir- V_0014_LC0941_Iafrate et al. (2004), V_0015_LC0954_Iafrate et al. (2004), V_0685_LC0752_Sharp et al. (2005), V_0014, V_0015, V_0260, V_0261, V_0387, ANKRD34A, LIX1L, RBM8A, GNRHR2, PEX11B, ITGA10, ANKRD35, PIAS3, NUDT17, POLR3C, RNF115, CD160, 556, hsa-mir-921, hsa-mir-1255b-2, hsa-mir-557, hsa-mir-1295, hsa-mir-214, hsa-mir- V_2050_LC0752_Locke et al. (2006), V_2051_LC0752_Locke et al. (2006), V_2052_LC0752_Locke et al. (2006), V_0388, V_0389, V_0390, V_0391, V_0392, PDZK1, GPR89A, GPR89C, NBPF8, NBPF8, NBPF12, PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, 199a-2, hsa-mir-488 V_4249_LC0752_Wong et al. (2007), V_4250_LC0752_Wong et al. (2007), V_4251_LC0752_Wong et al. (2007), V_0393, V_0394, V_0395, V_0396, V_0685, GPR89B, NBPF11, FAM108A2, PPIAL4A, NBPF14, NBPF10, NBPF16, FCGR1C, HIST2H3PS2, FAM72C, V_4252_LC0752_Wong et al. (2007), V_4253_LC0752_Wong et al. (2007), V_4254_LC0752_Wong et al. (2007), V_1016, V_1017, V_1018, V_1019, V_1326, PPIAL4C, FAM91A2, FCGR1A, HIST2H2BF, HIST2H3D, HIST2H4A, HIST2H3C, HIST2H2AA3, HIST2H2AA4, V_4255_LC0752_Wong et al. (2007), V_4256_LC0752_Wong et al. (2007), V_4257_LC0831_Wong et al. (2007), V_1327, V_1328, V_1329, V_1330, V_1331, HIST2H3A, HIST2H4B, HIST2H2BE, BOLA1, HIST2H2AC, HIST2H2AB, SV2A, SF3B4, MTMR11, OTUD7B, V_4258_LC0863_Wong et al. (2007), V_4259_LC0863_Wong et al. (2007), V_4260_LC0878_Wong et al. (2007), V_1332, V_1333, V_1334, V_1335, V_1336, VPS45, PLEKHO1, ANP32E, CA14, APH1A, C1orf54, C1orf51, MRPS21, PRPF3, RPRD2, TARS2, ECM1, V_4261_LC0907_Wong et al. (2007), V_4262_LC0938_Wong et al. (2007), V_4263_LC0946_Wong et al. (2007), V_1337, V_1338, V_1339, V_1340, V_1341, ADAMTSL4, C1orf138, MCL1, ENSA, GOLPH3L, HORMAD1, CTSS, CTSK, ARNT, SETDB1, LASS2, ANXA9, V_4264_LC0975_Wong et al. (2007), V_4265_LC0992_Wong et al. (2007) V_1342, V_1343, V_1344, V_1553, V_1554, FAM63A, PRUNE, BNIPL, C1orf56, CDC42SE1, MLLT11, GABPB2, SEMA6C, TNFAIP8L2, LYSMD1, SCNM1, V_1555, V_1556, V_1557, V_1558,
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