Supplementary Data

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SUPPLEMENTARY FILES – DESCRIPTION AND LEGENDS

Supplementary Data: Validation of amplicons, analysis of grade III IDC-NST of indeterminate phenotype and quantification of PPM1D protein levels by densitometric analysis.

Supplementary Figure 1: Validation of CCND1 and EGFR amplifications in a series of 91 grade III-IDC-NST and CCNE1 amplifications on selected cases. (A) i) H&E ii)

CISH iii) IHC for a) luminal tumour for CCND1 showing amplification and protein over-expression, b) basal-like tumour for CCND1 with normal copy number and no protein expression, c) EGFR non-amplified tumour with no protein expression d)

EGFR amplified tumour showing strong protein expression. Amplification of CCNE1 in basal-like breast cancers. (B) Genome plots of two cases exhibiting amplification with the smallest region of overlap highlighted (i). FISH confirmation of CCNE1 amplification with RP11-327I05 (CCNE1) (red), showing amplification > 5 copies per nucleus (Bii).

Supplementary Figure 2: Microarray-based comparative genomic hybridisation analysis of five grade III invasive ductal carcinomas of no special type of indeterminate phenotype. A) Representative genome plots. Log2 ratios are plotted on the Y axis against each clone according to genomic location on the X axis. The centromere is represented by a vertical dotted line. BACs categorised as displaying genomic gains as defined by aws ratios > 0.08 are highlighted in green and those categorised as genomic losses as defined by aws ratios < -0.08 are highlighted in red. Bi) The proportion of tumours in which each clone is gained (green bars) or lost

(red bars) is plotted (Y axis) for each BAC clone according to genomic location (X axis). Vertical dotted lines represent chromosome centromeres. Bii) The proportion of tumours in which each clone is amplified (green bars) is plotted (Y axis) for each 2

BAC clone according to genomic location (X axis). Vertical dotted lines represent chromosome centromeres.

Supplementary Figure 3: Densitometric analysis of western blots comparing the protein expression levels of PPM1D and β-tubulin. Cell lines harbouring PPM1D gene amplification: MCF-7, KPL-1, MCF-3B, BT474 and ZR-75.3; cell lines with normal PPM1D copy numbers: HeLa, MDA-MB-361, ZR-75.1, CAMA1, T47D and

MDA-MB-231.

Supplementary Table S1: Summary of the results of the immunohistochemical expression of oestrogen receptor, HER2, progesterone receptor, cytokeratins 5/6 and

14, EGFR and p53; chromogenic in situ hybridisation with probes for HER2, EGFR and CCND1; amplification status of PPM1D and mRNA expression levels of PPM1D as defined by qRT-PCR of all grade III invasive ductal carcinomas of no special type subjected to microarray-based comparative genomic hybridisation analysis and used for the construction of tissue microarrays 1 and 2.

Supplementary Table S2: Summary of antibodies, clones, dilutions and scoring systems used for immunohistochemical analysis.

Supplementary Table S3: Results of multi-Fisher’s exact test of gains and losses between basal-like, luminal and HER2 tumours.

Supplementary Table S4: Recurrent amplifications in basal-like breast cancers.

Supplementary Table S5: Results of multi-Fisher’s exact test of gains and losses between basal-like, luminal and HER2 tumours compared in a pair-wise fashion.

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Supplementary Table S6: Results of multi-Fisher’s exact test of amplifications between basal-like, luminal and HER2 tumours.

Supplementary Table S7: Results of multi-Fisher’s exact test of amplifications between basal-like, luminal and HER2 tumours compared in a pair-wise fashion.

Supplementary Table S8: Recurrent amplifications in luminal breast cancers.

Supplementary Table S9: Recurrent amplifications in HER2 breast cancers. Supplementary Table S1 aCGH series sample ER HER 2 PgR ck5/6 ck14 EGFR TP53 basal marker Nielsen groups Genomic pattern HER2 aCGH HER2 CISH CCND1 CCND1 CISH EGFR aCGH EGFR CISH PPM1D aCGH PPM1D expression number aCGH (Taqman) 1004 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified not amplified not amplified not amplified not amplified amplified 3.1256 1005 Positive Negative Positive Negative Negative Negative Positive Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.1132 1008 Positive Negative Positive Negative Negative Negative Positive Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.5775 1010 Negative Negative Negative Positive Positive Negative Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.4085 1011 Positive Negative Positive Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.1381 1012 Negative Positive Negative Negative Negative Negative Negative Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified 1.2885 1013 Negative Positive Negative Negative Negative Negative Positive Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified not amplified 0.6439 1014 Negative Positive Negative Negative Negative Negative Positive Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified amplified 3.3754 1015 Positive Positive Positive Negative Negative Negative Negative Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified not amplified 0.7452 1016 Negative Negative Negative Positive Positive Negative Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.8112 1019 Positive Negative Positive Negative Negative Negative Positive Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1020 Positive Negative Positive Negative Negative Negative Negative Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified 0.8683 1021 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.5526 1022 Positive Negative Negative Negative Negative Negative Negative Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.5418 1024 Positive Negative Positive Negative Negative Negative Negative Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.2073 1025 Positive Positive Negative Negative Negative Negative Negative Negative HER2 amplifier amplified amplified amplified amplified not amplified not amplified amplified 2.0300 1026 Positive Negative Negative Negative Positive Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified not amplified 0.9993 1027 Positive Negative Negative Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1028 Negative Negative Negative Positive Negative Negative Negative Positive Basal sawtooth not amplified not amplified not amplified 0.5787 1029 Positive Negative Negative Positive Negative Negative Negative Positive Luminal simplex not amplified not amplified not amplified 0.5330 1030 Positive Positive Negative Negative Negative Negative Negative Negative HER2 sawtooth amplified amplified amplified not amplified not amplified not amplified not amplified 1.0201 1031 Negative Positive Negative Positive Negative Negative Positive Positive HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified 0.4661 1032 Positive Negative Negative Negative Negative Negative Positive Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified 0.6805 1033 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified not amplified not amplified not amplified not amplified 0.4493 1035 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified not amplified 0.4849 1037 Positive Negative Negative Negative Positive Negative Negative Positive Luminal sawtooth not amplified not amplified amplified amplified not amplified not amplified not amplified 2.4002 1038 Positive Positive Negative Negative Negative Negative Negative Negative HER2 sawtooth amplified amplified not amplified not amplified not amplified not amplified amplified 2.3594 1040 Negative Negative Negative Positive Positive Positive Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified 0.2890 1041 Positive Negative Positive Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified amplified amplified not amplified not amplified not amplified 0.5934 1042 Positive Negative Positive Negative Negative Negative Positive Negative Luminal amplifier not amplified not amplified not amplified not amplified not amplified not amplified amplified 2.7133 1043 Positive Positive Negative Positive Negative Positive Negative Positive HER2 amplifier amplified amplified not amplified not amplified amplified amplified not amplified 0.2306 1044 Positive Negative Negative Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 2.4377 1047 Negative Negative Negative Positive Negative Positive Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.5720 1048 Positive Negative Positive Negative Negative Negative Positive Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1049 Negative Negative Negative Positive Positive Positive Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.2528 1050 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.4690 1051 Negative Positive Negative Negative Negative Positive Negative Positive HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified not amplified 1052 Positive Negative Negative Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified 1.3478 1053 Positive Negative Positive Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.3524 1054 Negative Positive Negative Negative Negative Negative Positive Negative HER2 amplifier amplified amplified amplified amplified not amplified not amplified not amplified 0.6110 1055 Positive Negative Negative Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.6641 1056 Negative Negative Positive Positive Negative Positive Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.1763 1057 Negative Negative Negative Negative Negative Positive Negative Positive Basal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.5899 1058 Positive Negative Positive Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.3556 1061 Negative Negative Negative Negative Positive Negative Positive Positive Basal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.8701 1062 Negative Negative Negative Positive Positive Negative Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.9630 1064 Negative Negative Negative Positive Negative Negative Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1065 Positive Negative Negative Negative Negative Negative Positive Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1066 Positive Negative Positive Negative Negative Negative Positive Negative Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified not amplified 1068 Positive Positive Negative Negative Negative Negative Negative Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified amplified 1069 Positive Positive Negative Negative Negative Negative Negative Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified not amplified 1070 Negative Negative Negative Positive Negative Positive Positive Positive Basal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1071 Positive Negative Negative Positive Negative Negative Negative Positive Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified amplified 1072 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified not amplified 1074 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified not amplified 1076 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified not amplified 1078 Positive Negative Positive Negative Negative Negative Negative Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.0292 1079 Negative Positive Negative Negative Negative Negative Positive Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified not amplified 0.9209 1080 Positive Negative Negative Negative Negative Negative Negative Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1081 Positive Negative Positive Negative Negative Negative Positive Negative Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified not amplified 0.7829 1082 Negative Negative Negative Positive Negative Positive Positive Positive Basal amplifier not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.5577 1083 Positive Positive Positive Negative Negative Negative Negative Negative HER2 amplifier amplified amplified amplified amplified not amplified not amplified not amplified 1084 Negative Negative Negative Negative Negative Positive Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.5952 1085 Negative Positive Negative Negative Negative Negative Positive Negative HER2 amplifier amplified amplified amplified amplified not amplified not amplified not amplified 0.5442 1086 Positive Negative Positive Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.8287 1087 Positive Negative Positive Negative Negative Negative Positive Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.5275 1089 Negative Positive Negative Negative Negative Negative Positive Negative HER2 amplifier amplified amplified amplified amplified not amplified not amplified not amplified 1.9186 1090 Positive Positive Positive Negative Negative Negative Positive Negative HER2 amplifier amplified amplified amplified amplified not amplified not amplified amplified 2.0950 1091 Positive Negative Positive Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.8001 1098 Negative Negative Negative Positive Positive Negative Positive Basal amplifier not amplified not amplified amplified not amplified 1100 Negative Positive Negative Negative HER2 amplifier amplified not amplified not amplified not amplified 1101 Positive Negative Positive Negative Luminal amplifier not amplified amplified not amplified not amplified 1102 Positive Negative Positive Negative Luminal sawtooth not amplified not amplified not amplified not amplified 1104 Negative Positive Negative Negative HER2 amplifier amplified not amplified not amplified not amplified 1105 Positive Negative Negative Negative Luminal simplex not amplified not amplified not amplified not amplified 1106 Negative Negative Negative Negative Positive Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified 1107 Positive Negative Negative Negative Negative HER2 amplifier amplified not amplified not amplified not amplified 1108 Positive Negative Positive Positive Positive Negative Positive Luminal sawtooth not amplified not amplified not amplified not amplified 1109 Positive Negative Positive Negative Positive Negative Positive Luminal sawtooth not amplified not amplified not amplified not amplified 1110 Negative Negative Negative Positive Positive Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified 1111 Negative Positive Negative Positive Positive Negative Positive HER2 amplifier amplified not amplified not amplified not amplified 1112 Positive Negative Negative Negative Positive Negative Positive Luminal amplifier not amplified not amplified not amplified not amplified 1113 Negative Positive Negative Negative Positive Negative Positive HER2 amplifier amplified not amplified not amplified not amplified 1114 Positive Negative Positive Negative Positive Negative Positive Luminal sawtooth not amplified not amplified not amplified not amplified 1115 Positive Negative Positive Negative Luminal sawtooth not amplified not amplified not amplified not amplified 1117 Negative Negative Negative Positive Positive Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified 1118 Positive Negative HER2 amplifier amplified not amplified not amplified not amplified 1119 Negative Negative Negative Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified 1120 Negative Negative Negative Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified 1121 Negative Positive Negative Positive Positive HER2 sawtooth amplified not amplified not amplified not amplified 1122 Negative Negative Negative Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified 1123 Negative Negative Negative Positive Positive Basal simplex not amplified not amplified not amplified not amplified 1124 Negative Negative Negative Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified 1125 Negative Negative Negative Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified 1128 Negative Negative Negative Positive Positive Basal amplifier not amplified not amplified not amplified not amplified

TMA 1 series sample cases subject to number ER HER 2 PgR ck5/6 ck14 EGFR TP53 basal marker Nielsen groups aCGH HER2 CISH CCND1 CISH EGFR CISH 1001 Negative Negative Negative Positive Negative Positive Positive Positive Basal NA not amplified not amplified not amplified 1002 Negative Negative Negative Positive Negative Negative Positive Positive Basal NA not amplified not amplified 1003 Negative Negative indeterminate YES not amplified 1004 Positive Negative Negative Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1005 Positive Negative Positive Negative Negative Negative Positive Negative Luminal YES not amplified not amplified not amplified 1006 Negative Positive Negative Negative Negative Negative Negative Negative HER2 NA amplified not amplified not amplified 1007 Negative Negative Negative Negative Negative Positive Negative Positive HER2 NA amplified not amplified not amplified 1008 Positive Negative Positive Negative Negative Negative Positive Negative Luminal YES not amplified not amplified not amplified 1009 Negative Negative Negative Negative Negative Positive Negative Positive HER2 NA amplified not amplified 1010 Negative Negative Negative Positive Positive Negative Negative Positive Basal YES not amplified not amplified not amplified 1011 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1012 Negative Positive Negative Negative Negative Negative Negative Negative HER2 YES amplified not amplified 1013 Negative Positive Negative Negative Negative Negative Positive Negative HER2 YES amplified not amplified not amplified 1014 Negative Positive Negative Negative Negative Negative Positive Positive HER2 YES amplified not amplified not amplified 1015 Positive Positive Positive Negative Negative Negative Negative Negative HER2 YES amplified not amplified not amplified 1016 Negative Negative Negative Positive Positive Negative Positive Positive Basal YES not amplified not amplified not amplified 1018 Negative Positive Negative Negative Negative HER2 NA amplified not amplified 1019 Positive Negative Positive Negative Negative Negative Positive Negative Luminal YES amplified not amplified not amplified 1020 Positive Negative Positive Negative Negative Negative Negative Positive Luminal YES not amplified not amplified 1021 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1022 Positive Negative Negative Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1023 Negative Negative Negative Negative Negative Negative Negative Negative indeterminate YES not amplified not amplified not amplified 1024 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1025 Positive Positive Negative Negative Negative Negative Negative Negative HER2 YES amplified amplified not amplified 1026 Positive Negative Positive Negative Positive Negative Luminal YES not amplified amplified not amplified 1027 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1028 Negative Negative Negative Positive Negative Negative Negative Positive Basal YES 1029 Positive Negative Negative Positive Negative Negative Negative Positive Luminal YES 1030 Positive Positive Positive Negative Negative Negative Negative Negative HER2 YES amplified not amplified not amplified 1031 Negative Positive Negative Positive Negative Negative Positive Positive HER2 YES amplified not amplified 1032 Positive Negative Negative Negative Negative Negative Positive Negative Luminal YES not amplified not amplified 1033 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified 1035 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified amplified not amplified 1037 Positive Negative Negative Negative Positive Negative Negative Positive Luminal YES not amplified amplified not amplified 1038 Negative Positive Negative Negative Negative Negative Negative Negative HER2 YES amplified not amplified not amplified 1039 Negative Positive Negative Negative Negative Negative Negative Positive HER2 NA amplified not amplified not amplified 1040 Negative Negative Negative Positive Positive Positive Negative Positive Basal YES not amplified not amplified 1041 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified amplified not amplified 1042 Positive Negative Positive Negative Negative Negative Positive Negative Luminal YES not amplified not amplified not amplified 1043 Negative Positive Negative Positive Negative Positive Negative Positive HER2 YES amplified not amplified amplified 1044 Positive Negative Negative Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1047 Negative Negative Negative Positive Negative Positive Negative Positive Basal YES not amplified not amplified not amplified 1048 Positive Negative Positive Negative Negative Negative Positive Negative Luminal YES not amplified not amplified not amplified 1049 Negative Negative Negative Positive Positive Positive Positive Positive Basal YES not amplified not amplified not amplified 1050 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1051 Negative Positive Negative Negative Negative Positive Negative Positive HER2 YES amplified not amplified not amplified 1052 Positive Negative Negative Negative Negative Negative Negative Positive Luminal YES not amplified not amplified 1053 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1054 Negative Positive Negative Negative Negative Negative Positive Negative HER2 YES amplified amplified not amplified 1055 Positive Negative Negative Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1056 Negative Negative Positive Positive Negative Positive Negative Positive Basal YES not amplified not amplified not amplified 1057 Negative Negative Negative Negative Negative Positive Negative Positive Basal YES not amplified not amplified not amplified 1058 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1059 Positive Negative Negative Negative Negative Negative Positive Negative Luminal NA not amplified amplified not amplified 1061 Negative Negative Negative Negative Positive Negative Positive Positive Basal YES not amplified not amplified not amplified 1062 Negative Negative Negative Positive Positive Negative Positive Positive Basal YES not amplified not amplified not amplified 1063 Negative Negative Negative Negative Negative Positive Negative indeterminate YES not amplified not amplified not amplified 1064 Negative Negative Negative Positive Negative Negative Negative Positive Basal YES not amplified not amplified not amplified 1065 Positive Negative Negative Negative Negative Negative Positive Negative Luminal YES not amplified not amplified not amplified 1066 Positive Negative Positive Negative Negative Negative Positive Negative Luminal YES not amplified amplified not amplified 1067 Positive Negative Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 1068 Negative Positive Negative Negative Negative Negative Negative Negative HER2 YES amplified not amplified not amplified 1069 Negative Positive Negative Negative Negative Negative Negative Positive HER2 YES amplified not amplified not amplified 1070 Negative Negative Negative Positive Negative Positive Positive Positive Basal YES not amplified not amplified not amplified 1071 Positive Negative Negative Positive Negative Negative Negative Positive Luminal YES not amplified amplified not amplified 1072 Positive Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1073 Negative Positive Negative Positive Negative Negative Positive Positive HER2 NA amplified not amplified not amplified 1074 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified amplified not amplified 1075 Negative Negative Negative Negative Negative Negative Positive Negative indeterminate YES not amplified not amplified 1076 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1077 Negative Negative Negative Negative Negative Positive Negative indeterminate YES not amplified not amplified not amplified 1078 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1079 Negative Positive Negative Negative Negative Negative Positive Positive HER2 YES amplified not amplified not amplified 1080 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1081 Positive Positive Negative Negative Negative Positive Negative Luminal YES not amplified amplified not amplified 1082 Negative Negative Negative Positive Negative Positive Positive Positive Basal YES not amplified not amplified not amplified 1083 Negative Positive Positive Negative Negative Negative Negative Negative HER2 YES amplified not amplified not amplified 1084 Negative Negative Negative Negative Negative Positive Positive Positive Basal YES not amplified not amplified not amplified 1085 Negative Positive Negative Negative Negative Negative Positive Positive HER2 YES amplified not amplified not amplified 1086 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1087 Positive Negative Positive Negative Negative Negative Positive Negative Luminal YES not amplified not amplified not amplified 1088 Negative Positive Negative Negative Negative Negative Negative Positive HER2 NA amplified not amplified not amplified 1089 Negative Positive Negative Negative Negative Negative Positive Positive HER2 YES amplified amplified not amplified 1090 Negative Positive Negative Negative Negative Negative Positive Negative HER2 YES amplified amplified not amplified 1091 Positive Negative Positive Negative Negative Negative Negative Negative Luminal YES not amplified not amplified not amplified 1092 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 1093 Negative Negative Negative Negative Negative Positive Negative Positive Basal NA not amplified 1094 Negative Negative Negative Negative Negative Positive Positive Positive Basal NA not amplified 1095 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified 1096 Negative Positive Negative Negative Negative Negative Positive Negative HER2 NA amplified not amplified not amplified Supplementary Table S1 TMA 2 series sample cases subject to number ER HER 2 PgR ck5/6 ck14 EGFR TP53 basal marker Nielsen groups aCGH HER2 CISH CCND1 CISH EGFR CISH 2 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified 3 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 4 Positive Negative Positive Positive Positive Negative Negative Positive Luminal NA not amplified not amplified not amplified 8 Positive Positive Positive Negative Negative Negative Negative Negative HER2 NA not amplified not amplified 13 Positive Positive Negative Negative Negative Negative Negative Negative HER2 NA amplified amplified not amplified 15 Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified not amplified 17 Positive Positive Positive Negative Negative Negative Positive Negative HER2 NA amplified not amplified 19 Positive Positive Positive Negative Negative Negative Positive Negative HER2 NA amplified not amplified 22 Positive Negative Negative Negative Negative Negative Negative Negative Luminal NA not amplified amplified not amplified 24 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 25 Negative Negative Negative Positive Positive Positive Positive Positive Basal NA not amplified not amplified not amplified 26 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 27 Negative Negative Negative Negative Negative Negative Positive Negative indeterminate NA not amplified not amplified not amplified 37 Positive Positive Negative Negative Negative Negative Negative Negative HER2 NA amplified not amplified not amplified 39 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 40 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 42 Negative Negative Negative Positive Negative Negative Negative Positive Basal NA not amplified not amplified not amplified 49 Negative Negative Positive Positive Positive Positive Positive Positive Basal NA not amplified not amplified not amplified 53 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified 54 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 56 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 57 Negative Negative Positive Positive Positive Positive Negative Positive Basal NA not amplified not amplified not amplified 59 Positive Negative Positive Positive Negative Negative Negative Positive Luminal NA not amplified not amplified not amplified 60 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 62 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 63 Negative Positive Negative Negative Negative Negative Positive Negative HER2 NA amplified not amplified 64 Negative Negative Negative Negative Positive Negative Negative Positive Basal NA not amplified not amplified not amplified 65 Negative Negative Negative Negative Negative Positive Positive Positive Basal NA not amplified not amplified not amplified 67 Negative Negative Negative Negative Positive Positive Negative Positive Basal NA not amplified not amplified amplified 72 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 84 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 85 Negative Positive Negative Negative Negative Negative Negative Negative HER2 NA amplified not amplified 88 Negative Negative Negative Positive Positive Negative Negative Positive Basal NA not amplified not amplified 89 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified 92 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 93 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 96 Negative Negative Negative Positive Positive Positive Negative Positive Basal NA not amplified not amplified not amplified 97 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 102 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 106 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 107 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified 110 Positive Negative Positive Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 111 Negative Negative Negative Positive Positive Positive Positive Positive Basal NA not amplified not amplified not amplified 113 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified amplified not amplified 114 Negative Negative Negative Positive Negative Negative Negative Positive Basal NA not amplified not amplified not amplified 115 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 128 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 130 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 134 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 139 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 141 Positive Negative Negative Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 142 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 144 Negative Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified amplified not amplified 145 Positive Negative Positive Positive Negative Negative Negative Positive Luminal NA not amplified not amplified not amplified 146 Negative Negative Negative Positive Positive Positive Positive Positive Basal NA not amplified not amplified not amplified 148 Negative Negative Negative Negative Negative Positive Positive Basal NA not amplified not amplified 151 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified amplified not amplified 153 Negative Negative Negative Negative Negative Negative Positive Positive Basal NA not amplified not amplified not amplified 163 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA amplified not amplified not amplified 164 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 165 Negative Negative Positive Positive Positive Positive Positive Positive Basal NA not amplified not amplified not amplified 166 Positive Positive Negative Negative Negative Positive Negative HER2 NA amplified not amplified not amplified 168 Positive Positive Positive Negative Negative Negative Positive Negative HER2 NA amplified not amplified not amplified 169 Positive Negative Positive Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 180 Negative Positive Negative Negative Negative Negative Positive Positive HER2 NA amplified amplified not amplified 182 Positive Positive Positive Negative Negative Negative Negative HER2 NA amplified not amplified 183 Positive Positive Negative Negative Negative Negative Luminal NA not amplified 184 Positive Positive Positive Negative Negative Negative Positive Negative HER2 NA amplified not amplified 186 Negative Negative Negative Positive Positive Positive Positive Positive Basal NA not amplified not amplified not amplified 188 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 192 Positive Negative Positive Negative Negative Negative Negative Luminal NA not amplified amplified 196 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 200 Positive Negative Positive Positive Negative Negative Positive Luminal NA not amplified not amplified 202 Negative Negative Negative Positive Positive Positive Positive Positive Basal NA not amplified not amplified not amplified 207 Negative Negative Negative Negative Negative Positive Negative Positive Basal NA not amplified not amplified not amplified 208 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified amplified not amplified 215 Positive Negative Negative Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 217 Negative Negative Negative Positive Positive Positive Positive Positive Basal NA not amplified not amplified not amplified 218 Negative Negative Negative Positive Positive Positive Positive Positive Basal NA not amplified not amplified not amplified 219 Negative Negative Negative Negative Negative Negative Positive Negative indeterminate NA not amplified 220 Positive Negative Negative Negative Negative Negative Negative Negative Luminal NA not amplified amplified 233 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified 234 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 240 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 241 Negative Negative Negative Positive Positive Negative Positive Positive Basal NA not amplified not amplified not amplified 242 Positive Negative Negative Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 244 Negative Negative Negative Positive Positive Negative Positive Positive Basal NA not amplified not amplified not amplified 245 Positive Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified amplified not amplified 247 Negative Negative Positive Positive Negative Positive Positive Positive Basal NA not amplified not amplified not amplified 250 Positive Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified not amplified not amplified 253 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 255 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 257 Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified not amplified 258 Negative Negative Negative Negative Negative Negative Positive Negative indeterminate NA not amplified not amplified not amplified 259 Positive Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified not amplified 264 Positive Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified not amplified not amplified 267 Negative Positive Negative Negative Negative Negative Positive Negative HER2 NA amplified not amplified not amplified 268 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified amplified not amplified 271 Positive Negative Negative Negative Positive Negative Positive Luminal NA not amplified not amplified 275 Positive Positive Positive Negative Negative Negative Positive Negative HER2 NA amplified not amplified not amplified 277 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 280 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 283 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 285 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 293 Positive Negative Positive Negative Negative Negative Negative Luminal NA 302 Positive Negative Negative Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 304 Positive Negative Negative Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 309 Negative Positive Negative Negative Negative Positive Negative Positive HER2 NA amplified not amplified amplified 310 Positive Negative Positive Negative Negative Negative Positive Negative Luminal NA not amplified not amplified not amplified 313 Positive Positive Negative Negative Negative Negative Positive Negative HER2 NA not amplified not amplified not amplified 316 Positive Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified not amplified not amplified 319 Negative Negative Negative Negative Negative Negative Negative Negative indeterminate NA not amplified not amplified 324 Positive Positive Positive Negative Negative Negative Positive Negative HER2 NA amplified not amplified not amplified 327 Negative Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified not amplified 328 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 330 Positive Negative Positive Negative Negative Negative Negative Positive Luminal NA not amplified amplified not amplified 331 Positive Negative Positive Negative Negative Negative Negative Negative Luminal NA not amplified not amplified not amplified 343 Positive Negative Positive Positive Positive Negative Positive Positive Luminal NA not amplified not amplified not amplified 345 Positive Positive Positive Negative Negative Negative Negative Negative HER2 NA amplified not amplified not amplified 348 Negative Positive Negative Negative Negative Negative Positive Negative HER2 NA amplified amplified not amplified Supplementary Table S2

Antibody Species Clone Supplier Dilution Antigen retrieval method Threshold CK14 Mouse LL02 Novocastra 1:25 Citrate, 2´ Pressure Cooker >1% CK5/6 Mouse D5/16 B4 DAKO 1:25 Citrate, 2´ Pressure Cooker >1% EGFR Mouse 113 Novocastra 1:10 Citrate, 2´ Pressure Cooker >1% ER Mouse 1D5 Novocastra 1:30 Citrate, 2´ Pressure Cooker >5% HER2 Herceptest DAKO Citrate, 40´ Water Bath 3+ PR Mouse 1A6 Novocastra 1:30 Citrate, 2´ Pressure Cooker >5% p53 Mouse DO7 Novocastra 1:50 Citrate, 2´ Pressure Cooker >30% Ki-67 Mouse Mib-1 DAKO 1:30 Citrate, 2´ Pressure Cooker >15% Supplementary Table S3

Gains and losses - Multi-Fisher's adjusted p value <0.05 basal-like chromosome start (kb) end (kb) cytoband frequency basal (%) frequency luminal/ HER2 (%) gains 1 16638.36 16782.71 p36.13 24 2 1 84024.29 98002.00 p31.1-p21.3 24 3 1 101021.44 102077.11 p21.2-p21.1 28 6 1 118122.56 120432.22 p12 32 8 1 147045.34 148001.85 q21.1-q21.2 72 36 2 37693.75 39101.52 p22.2-p22.1 28 6 2 48074.43 64014.72 p16.3-p14 28 4 6 11402.23 30407.41 p24.1-p21.33 52 37 6 32491.65 35203.56 p21.32-p21.31 32 17 6 37477.47 62238.52 p21.2-q11.1 36 8 6 69075.85 81529.04 q12-q14.1 40 10 6 83710.43 93108.18 q14.1-q16.1 40 10 6 97300.09 112490.71 q16.1-q21 44 23 7 64803.84 67100.78 q11.21-q11.22 28 6 7 112723.95 116108.49 q31.1-q31.2 44 11 7 128144.14 140560.97 q32.1-q34 36 5 8 131034.34 142175.68 q24.21-q24.3 88 50 9 29.04 38765.15 p24.3-p13.1 52 6 9 68293.66 71253.76 q12-q21.11 32 4 10 63.26 30633.10 p15.3-p11.23 64 10 10 33507.24 35205.87 p11.22-p11.21 40 10 10 43309.69 45220.28 q11.21 28 3 10 49041.70 52255.29 q11.22-q11.23 28 4 10 54451.55 60976.62 q21.1 32 6 10 70574.90 72032.18 q21.3-q22.1 24 5 12 5316.58 5919.34 p13.31 48 13 12 7044.43 10899.98 p13.31-p13.2 28 13 12 75474.27 78635.99 q21.2 0 27 17 45153.71 47886.76 q21.33-q22 0 28 17 59834.15 60370.96 q23.3-q24.1 12 45 18 3824.82 4422.18 p11.31 12 46 18 58219.61 60222.87 q21.33-q22.1 24 3 18 62868.28 64777.47 q22.1 24 3 18 72500.62 73124.10 q23 24 3 19 32474.89 33056.22 q12 33 5 19 41211.64 41702.24 q13.12 28 3 22 27836.60 28911.82 q12.1-q12.2 24 3

losses 2 214813.26 227038.33 q34-q36.3 36 15 2 231168.95 232628.96 q37.1 52 18 2 235394.33 241743.17 q37.2-q37.3 60 25 4 3576.56 11338.70 p16.2-p15.33 56 24 4 15054.35 17861.12 p15.33-p15.32 40 13 4 25003.96 38234.26 p15.2-p14 40 10 4 181557.34 183371.31 q34.3-q35.1 40 13 4 187017.38 190149.17 q35.1-q35.2 40 13 5 2003.47 3462.11 p15.33 28 4 5 51454.84 99504.48 q11.2-q21.1 44 13 5 108924.80 119565.05 q21.3-q23.1 40 10 5 120815.52 150811.98 q23.1-q33.1 40 10 5 153791.79 157349.37 q33.2-q33.3 44 11 5 159190.89 180730.04 q33.3-q35.3 44 11 6 106203.67 109833.27 q21 40 30 6 124074.65 140131.79 q22.31-q24.1 0 26 7 6688.62 9874.74 p22.1-p21.3 24 2 7 20049.42 57627.19 p15.3-p11.1 16 0 9 7273.08 24066.18 p24.1-p21.3 4 30 10 103823.34 111591.42 q24.32-q25.1 60 26 12 49237.79 51672.89 q13.13 40 10 12 52695.89 60627.57 q13.13-q14.1 44 14 12 62468.97 66295.67 q14.2-q15 24 3 12 71562.51 78635.99 q21.1-q21.2 24 3 12 92946.08 95294.19 q22-q23.1 24 3 12 97452.36 120069.20 q23.1-q24.31 32 6 12 123242.69 132289.53 q24.31-q24.33 50 17 14 96748.60 101273.80 q32.2-q32.31 56 24 15 19970.52 60689.70 q11.2-q22.2 56 24 16 4441.46 28171.00 p13.3-p11.2 44 12 16 31483.61 33001.32 p11.2 56 28 17 23534.99 25346.39 q11.2 56 22 20 38218.81 38785.66 q12 36 10 X 2969.15 14018.66 p22.33-p22.2 56 24 X 21548.00 23807.50 p22.12-p22.11 48 18 X 26492.37 28164.74 p21.3 48 18 X 36807.31 40784.28 p21.1-p11.4 48 18

luminal chromosome start (kb) end (kb) cytoband frequency luminal (%) frequency basal-like/ HER2 (%) gains 5 55546.77 61661.50 q11.2-q12.1 20 4 5 64847.60 68820.84 q12.3-q13.2 20 0 5 70212.48 78375.13 q13.2-q14.1 22 2 5 94521.09 95934.20 q15 27 4 5 101825.14 119542.00 q21.1-q23.1 22 2 5 121724.99 127383.51 q23.2-q23.3 24 2 5 134188.79 137252.04 q31.1-q31.2 22 2 5 142315.63 142910.61 q31.3 22 2 5 159226.96 159723.36 q33.3 18 0 6 4000.55 8360.90 p25.2-p24.3 9 32 6 13204.02 30456.68 p24.1-p21.33 11 42 6 32392.47 33195.77 p21.32 2 26 6 37775.58 39009.74 p21.2 0 20 6 42260.79 57744.37 p21.1-p11.2 7 32 7 130781.98 135655.01 q32.3-q33 0 22 9 29.04 37849.98 p24.3-p13.2 2 36 10 63.26 30633.10 p15.3-p11.23 10 38 10 43201.65 44876.38 q11.21 0 18 10 49345.88 58518.78 q11.22-q21.1 0 20 10 64274.92 68526.27 q21.2-q21.3 0 22 11 73706.36 74438.64 q13.4 29 8 11 76260.08 76998.74 q13.5-q14.1 29 10 12 7145.69 9137.59 p13.31 2 28 16 6160.70 7877.53 p13.3-p13.2 30 6 16 16057.52 18780.92 p13.11-p12.3 33 6 16 19795.49 20637.04 p12.3-p12.2 36 8 16 23323.21 23865.45 p12.1 28 8 17 34003.22 35720.00 q12-q21.2 2 50 17 50186.41 51318.73 q22 40 10 20 35577.41 37030.94 q11.23 38 6 20 38231.28 39577.47 q12 40 10 20 41887.69 43112.81 q13.12 42 14

losses 4 3576.56 11948.95 p16.2-p15.33 16 50 5 52301.59 61513.87 q11.2-q12.1 9 38 5 62741.97 63759.65 q12.1-q12.3 7 34 5 64728.98 72527.85 q12.3-q13.2 7 36 5 132519.21 142806.68 q31.1-q31.3 11 46 12 102410.62 103080.74 q23.3 10 30 16 4952.29 24091.83 p13.3-p12.1 2 30 16 31736.16 33001.32 p11.2 18 50 17 41087.30 42878.16 q21.31-q21.32 27 60 17 50530.40 51902.77 q22 7 36

HER2 chromosome start (kb) end (kb) cytoband frequency (%) HER2 frequency luminal/ basal-like (%) gains 17 23374.39 25931.27 q11.2 44 2 17 32864.72 35891.50 q12-q21.2 62 4 17 44672.65 46507.87 q21.32-q21.33 60 16

losses 17 34781.21 35522.38 q12-q21.1 0 50 17 50733.37 51623.83 q22 52 14 Supplementary Table S4

Recurrent amplification in basal-like tumours chromosome start (kb) end (kb) cytobands Copy Number Polymorphism* genes miRNA 1 48800.76 49356.83 p33 C1orf165,AGBL4 1 58030.88 59581.72 p32.2-p32.1 V_4226_LC0413_Wong et al. (2007) LOC644928,TACSTD2,MYSM1,FLJ10986,JUN,OMA1,DAB1 1 60890.30 61556.86 p32.1-p31.3 NFIA 1 63733.28 64333.96 p31.3 PGM1,ROR1,KIAA1799,ITGB3BP 1 66380.63 66710.23 p31.3 PDE4B 1 87268.08 87418.68 p22.3 HS2ST1 1 120249.99 120792.19 p12-p11.2 V_4246_LC0743_Wong et al. (2007) LOC440607,NOTCH2 1 142803.53 143548.63 q21.1 V_4248_LC0752_Wong et al. (2007) PPIAL4,NBPF20 1 143900.68 144162.83 q21.1 V_2050_LC0752_Locke et al. (2006), NOTCH2NL,TXNIP,HFE2 V_4250_LC0752_Wong et al. (2007), V_4251_LC0752_Wong et al. (2007), V_4252_LC0752_Wong et al. (2007) 1 144514.03 145134.53 q21.1 LOC728932,FMO5,LOC653519,PRKAB2,FAM108A2,NBPF11 1 145351.62 147039.95 q21.1 V_2051_LC0752_Locke et al. (2006), LOC728932,PPIAL4,NBPF14,NBPF15,GJA5,GPR89A,BCL9,ACP6,GJA8,NBPF10,NBPF11 V_4253_LC0752_Wong et al. (2007) 1 147192.89 148144.66 q21.1-q21.2 V_2052_LC0752_Locke et al. (2006), PPIAL4,H4/o,HIST2H2AA,HIST2H2AB,FCGR1A,HIST2H2AC,HIST2H4,BOLA1,HIST2H2BE,HIST2H2BF,SV2A,H2A/R,H3/o,HIST2H3C V_4254_LC0752_Wong et al. (2007), V_4255_LC0752_Wong et al. (2007), V_4256_LC0752_Wong et al. (2007) 1 149849.65 151903.02 q21.3 S100A7L2,RORC,SNX27,LCE3A,LCE3B,LCE3C,LCE3D,C1orf42,LCE3E,HRNR,C1orf45,LELP1,SPRR2A,SMCP,SPRR2B,SPRR2D,SPRR2E,SPRR2F,S100 A7A,SPRR2G,TCHH,FLG2,LCE4A,TDRKH,PGLYRP3,PGLYRP4,CRNN,TNRC4,LOR,S100A10,S100A11,S100A12,S100A13,S100A14,S100A16,LCE1A,LC E1B,LCE1C,LCE1D,LCE1E,LCE1F,SNAPAP,LCE5A,OAZ3,ILF2,TCHHL1,MRPL9,LINGO4,LCE2A,LCE2B,LCE2C,LCE2D,THEM4,THEM5,SPRR1A,SPRR1 B,S100A1,S100A2,S100A3,C1orf77,SPRR3,FLG,S100A4,SPRR4,S100A5,S100A6,IVL,S100A7,S100A8,S100A9 1 152389.87 153580.03 q21.3-q22 V_4257_LC0831_Wong et al. (2007) GBA,SHC1,ADAM15,SCAMP3,C1orf43,ADAR,RAG1AP1,KRTCAP2,CHRNB2,THBS3,ZBTB7B,DCST1,DCST2,TDRD10,HCN3,PBXIP1,HAX1,C1orf104,PKL hsa-mir-92b R,AQP10,TPM3,EFNA1,EFNA3,EFNA4,ASH1L,NUP210L,C1orf2,KCNN3,PMVK,C1orf189,IL6R,UBE2Q1,UBAP2L,MTX1,FDPS,CLK2,CKS1B,PYGO2,TRIM 1 155007.58 156501.72 q23.1 ARHGEF11,KIRREL,PEAR1,PRCC,FCRL1,FCRL2,FCRL3,C1orf92,FCRL4,FCRL5,NTRK1,INSRR,CD1A,CD1D,CD5L,ETV3,FLJ16478,SH2D2A hsa-mir-765 1 157996.99 158759.30 q23.2 CCDC19,KCNJ10,ATP1A2,ATP1A4,VSIG8,SLAMF6,SLAMF8,SLAMF9,IGSF8,PEX19,IGSF9,FCRL6,PIGM,COPA,KCNJ9,PEA15,VANGL2,WDR42A,NHLH1 ,TAGLN2,DUSP23,CASQ1,NCSTN 1 162887.42 163883.30 q23.3-q24.1 RXRG,MGST3,PBX1,LMX1A,LRRC52 1 171969.03 174198.57 q25.1 V_0014_LC0941_Iafrate et al. (2004), ZBTB37,SERPINC1,CACYBP,DARS2,RFWD2,TNN,TNR,KLHL20,GPR52,C1orf155,MRPS14,RC3H1,RABGAP1L U44,U80,U47,U81,U74,U75,U76,U77, V_4263_LC0946_Wong et al. (2007) U78,U79 1 191506.14 194595.12 q31.2-q31.3 V_2053_LC1052_Locke et al. (2006) KCNT2 1 195446.77 198105.82 q31.3-q32.1 PTPRC,NEK7,C1orf53,DENND1B,ATP6V1G3,FLJ20054,LHX9,CRB1 hsa-mir-181a-1,hsa-mir-181b-1 1 204335.92 209369.43 q32.1-q32.2 V_2091_LC1120_Locke et al. (2006), CAMK1G,IL10,CR1,CR2,LAMB3,SRGAP2,IL19,TRAF3IP3,CD34,CTSE,IL20,IRF6,LGTN,IL24,G0S2,C1orf107,CD46,PFKFB2,SYT14,PIGR,C1orf186,PLXNA hsa-mir-29b-2,hsa-mir-205,hsa-mir- V_4268_LC1117_Wong et al. (2007), 2,C4BPA,C4BPB,MAPKAPK2,FAIM3,HSD11B1,CR1L,C1orf116,AVPR1B,CD55,DYRK3,RASSF5,FCAMR,IKBKE,YOD1,C1orf74,HHAT,KCNH1,SERTAD4 29c V_4269_LC1125_Wong et al. (2007) 1 246570.68 246944.05 q44 V_0017_LC1401_Iafrate et al. (2004), OR2T10,OR2T11,OR2G6,OR5BU1,OR5BF1,OR2T27,OR2T29,OR2T1,OR2T2,OR2T3,OR2T4,OR2T5,OR2T6,OR2T34,OR2T35 V_2056_LC1401_Locke et al. (2006) 3 140772.86 142075.13 q23 V_0036_LC3666_Iafrate et al. (2004) NMNAT3,CLSTN2,TRIM42 3 148766.99 149322.93 q24 3 152709.13 154220.81 q25.1-q25.2 V_0037_LC3745_Iafrate et al. (2004), AADAC,SUCNR1,P2RY1,AADACL2,MBNL1 V_4357_LC3748_Wong et al. (2007) 3 157888.17 159140.95 q25.31-q25.32 PTX3,VEPH1,TIPARP,FLJ16641,CCNL1 3 170138.87 170844.14 q26.2 V_4362_LC3840_Wong et al. (2007) EVI1,MDS1 5 3825.95 4733.45 p15.33-p15.32 V_4430_LC6506_Wong et al. (2007) 5 9159.07 12159.24 p15.2 V_2082_LC6572_Locke et al. (2006) TAS2R1,LOC134145,LOC134147,SEMA5A,CCT5,MARCH6,ROPN1L,DAP,CTNND2 5 14141.34 14576.93 p15.2 TRIO 5 15446.92 16593.11 p15.1 FLJ20152,ZNF622,FBXL7 6 13348.49 14858.45 p24.1-p23 GFOD1,C6orf114,NOL7,CD83,TBC1D7,PHACTR1,RANBP9,SIRT5,RNF182,C6orf79 6 15430.44 15789.54 p23-p22.3 JARID2,DTNBP1 6 16514.54 17207.71 p22.3 ATXN1 6 18231.81 19438.31 p22.3 IBRDC2,DEK,AOF1,TPMT hsa-mir-548a-1 6 38953.98 41211.02 p21.2-p21.1 DNAH8,BZRPL1,GLP1R,DAAM2,KIF6,C6orf64,C6orf130,FLJ41649,KCNK5,NFYA,MOCS1,UNC5CL,KCNK16,APOBEC2,LRFN2,KCNK17 6 43851.26 44223.55 p21.1 MRPL14,VEGF,MGC45491,TMEM63B 6 45496.37 46160.23 p12.3 V_0078_LC8319_Iafrate et al. (2004) CLIC5,RUNX2 6 46648.84 47013.87 p12.3 PLA2G7,TDRD6,CYP39A1,MEP1A,GPR116,SLC25A27 6 47836.39 48542.85 p12.3 V_4494_LC8335_Wong et al. (2007), OPN5,FLJ41841,LOC442213 V_4495_LC8337_Wong et al. (2007) 6 49856.37 52774.05 p12.3-p12.1 TRAM2,IL17,GSTA1,GSTA2,PKHD1,CRISP1,EFHC1,TMEM14A,PAQR8,MCM3,PGK2,IL17F,DEFB110,DEFB111,DEFB112,DEFB113,DEFB114,TFAP2B,T hsa-mir-133b,hsa-mir-206 6 53635.14 54244.98 p12.1 LRRC1,KLHL31,C6orf142 6 55583.71 56650.79 p12.1 BMP5,DST,COL21A1 6 160912.55 161110.58 q26 V_4514_LC8985_Wong et al. (2007) LPA,PLG 6 79508.88 79782.29 q14.1 PHIP,IRAK1BP1 8 36772.94 37077.53 p12 FKSG2 8 37517.26 37934.27 p12 GOT1L1,PROSC,BRF2,ZNF703,RAB11FIP1,GPR124,SPFH2 8 38529.21 39152.22 p11.23 V_4589_LC10531_Wong et al. (2007) TM2D2,ADAM9,ADAM32,HTRA4,TACC1 8 40916.54 42777.72 p11.21 VDAC3,SFRP1,CHRNB3,ANK1,GOLGA7,PLAT,POLB,FLJ25169,SLC20A2,SLD5,DKK4,C8orf40,AGPAT6,IKBKB,MYST3,CHRNA6,AP3M2 hsa-mir-486 8 49380.20 50105.41 q11.21 V_4591_LC10578_Wong et al. (2007) SNAI2,EFCAB1 8 52846.52 55191.94 q11.23 RB1CC1,UNQ9433,PCMTD1,LYPLA1,ST18,ATP6V1H,RGS20,PXDNL,OPRK1,NPBWR1,TCEA1 8 55286.41 56688.36 q11.23-q12.1 XKR4,RP1,SOX17 8 58245.50 60194.17 q12.1 V_4594_LC10611_Wong et al. (2007) CYP7A1,LOC137886,C8orf72,NSMAF,TOX,SDCBP 8 73980.95 74869.68 q13.3-q21.11 RPL7,LOC653702,UBE2W,KCNB2,TERF1,RDH10,STAU2,RPESP 8 77429.14 83220.53 q21.11-q21.13 V_0119_LC10711_Iafrate et al. (2004) FABP4,FABP5,PAG1,MRPS28,STMN2,IL7,PXMP3,PERF15,ZFHX4,CHMP4C,C8orf70,ZBTB10,PKIA,HEY1,LOC389672,ZNF704,PMP2,SNX16,ZFAND1,IM 8 86620.60 86899.50 q21.2 V_0121_LC10727_Iafrate et al. (2004), REXO1L1 V_2126_LC10727_Locke et al. (2006), V_4601_LC10727_Wong et al. (2007), V_4602_LC10727_Wong et al. (2007), V_4603_LC10727_Wong et al. (2007), V_4604_LC10727_Wong et al. (2007), V_4605_LC10727_Wong et al. (2007) 8 97279.17 97611.04 q22.1 UQCRB,MTERFD1,PTDSS1,SDC2 8 107896.98 110950.29 q23.1-q23.2 ENY2,ANGPT1,FLJ20366,NUDCD1,EIF3S6,RSPO2,PKHD1L1,TTC35,TMEM74,TRHR,EBAG9 8 116696.62 118892.78 q23.3-q24.11 RAD21,TRPS1,THRAP6,EXT1,EIF3S3,LOC441376,C8orf53,SLC30A8 8 125973.09 127228.37 q24.13 ZNF572,TRIB1,C8orf36,SQLE,KIAA0196 8 128435.76 128894.28 q24.21 V_4609_LC10877_Wong et al. (2007) MYC 8 142097.44 143450.15 q24.3 SLC45A4,PTP4A3,TSNARE1,DENND3,FLJ43860,GPR20 9 4116.88 5335.75 p24.2-p24.1 RCL1,CDC37L1,C9orf68,SLC1A1,RLN1,RLN2,PPAPDC2,AK3,GLIS3,INSL4,INSL6,JAK2 hsa-mir-101-2 9 6837.95 15063.72 p24.1-p22.3 V_4615_LC11143_Wong et al. (2007) PTPRD,C9orf150,CER1,ZDHHC21,JMJD2C,C9orf123,NFIB,FREM1,MPDZ,TYRP1 9 15964.17 16798.69 p22.3-p22.2 LOC648570,BNC2 9 17517.20 20351.13 p22.2-p21.3 FAM29A,DENND4C,ADFP,MLLT3,RRAGA,SLC24A2,ADAMTSL1,SH3GL2,C9orf138,C9orf94,RPS6,ASAH3L U92 10 168.17 4908.73 p15.3-p15.1 V_4664_LC11931_Wong et al. (2007) PITRM1,GTPBP4,LOC399706,DIP2C,IDI1,IDI2,PFKP,ZMYND11,AKR1CL2,ADARB2,WDR37,LARP5,KLF6 10 8115.36 9686.48 p14 FLJ45983,GATA3,LOC389936 10 13551.82 14764.25 p13 V_4666_LC12101_Wong et al. (2007) FAM107B,PRPF18,C10orf30,FRMD4A 10 51600.76 52125.63 q11.23 V_2156_LC12305_Locke et al. (2006) ASAH2,TMEM23 12 1717.99 2518.03 p13.33 V_4765_LC13757_Wong et al. (2007) CACNA2D4,ADIPOR2,LRTM2,CACNA1C,DCP1B 12 2975.97 3791.52 p13.33-p13.32 V_0161_LC13778_Iafrate et al. (2004) PRMT8,MGC4266,PARP11,TSPAN9,TEAD4 12 4892.47 5919.34 p13.32-p13.31 KCNA1,KCNA5,NTF3,TMEM16B 12 9137.49 9466.09 p13.31 A2M,PZP 12 11691.84 12226.88 p13.2 BCL2L14,LRP6,ETV6 12 21890.53 25049.06 p12.1 V_0163_LC13898_Iafrate et al. (2004), SOX5,KIAA0528,CMAS,BCAT1,ABCC9,FLJ32894,ETNK1,ST8SIA1 V_4773_LC13907_Wong et al. (2007) 12 25282.80 28286.49 p12.1-p11.22 FLJ36004,ARNTL2,ITPR2,LOC728858,SSPN,REP15,KRAS,STK38L,PTHLH,MRPS35,SURB7,PPFIBP1,BHLHB3,C12orf11,RASSF8,KLHDC5,FGFR1OP2,T 12 30965.39 31382.37 p11.21 TSPAN11,DDX11,FAM60A,OVOS2 19 8736.73 8860.00 p13.2 V_0220_LC18794_Iafrate et al. (2004), MUC16,MBD3L1,ZNF558 V_2240_LC18794_Locke et al. (2006), V_5081_LC18794_Wong et al. (2007), V_5082_LC18794_Wong et al. (2007), V_5083_LC18794_Wong et al. (2007) 19 34329.17 35419.26 q12 POP4,C19orf12,PLEKHF1,UQCRFS1,CCNE1,C19orf2 19 35814.10 36161.85 q12 19 38449.07 39365.16 q13.11 CHST8,LSM14A,KCTD15,CEBPA,CEBPG,PEPD 19 45118.57 45531.36 q13.2 PSMC4,ZNF546,AKT2,FLJ36888,TTC9B,FCGBP,FLJ13265,LOC284323,LOC163131,MAP3K10 hsa-mir-641 20 58796.90 59346.16 q13.33 CDH4 20 16177.20 17072.48 p12.1 V_0224_LC19418_Iafrate et al. (2004), OTOR,SNRPB2,C20orf23 V_5127_LC19406_Wong et al. (2007) 21 18228.67 18691.77 q21.1 CHODL,PRSS7 21 41225.04 43166.90 q22.2-q22.3 TSGA2,PLAC4,WDR4,PRDM15,ABCG1,ZNF295,RIPK4,PDE9A,SLC37A1,MX1,MX2,TMPRSS2,TMPRSS3,UMODL1,UBASH3A,C21orf25,C21orf129,BACE 21 44518.52 46424.00 q22.3 V_5163_LC20269_Wong et al. (2007) POFUT2,KRTAP12-1,KRTAP12-2,KRTAP12-3,KRTAP12-4,PFKL,LRRC3,PTTG1IP,AIRE,C21orf56,ADARB1,C21orf2,COL18A1,KRTAP10-10,KRTAP10- 11,KRTAP10-12,PCBP3,KRTAP10-1,FTCD,KRTAP10-2,KRTAP10-3,KRTAP10-4,KRTAP10-5,KRTAP10-6,KRTAP10-7,C21orf123,KRTAP10-8,KRTAP10- 9,C21orf29,TRPM2,C21orf67,C21orf69,PRED57,SLC19A1,COL6A1,COL6A2,C21orf70,ITGB2,SUMO3,UBE2G2 23 112713.52 115622.72 q23 LOC203413,SLC6A14,LUZP4,IL13RA2,HTR2C,PLS3,LRCH2,AGTR2 HBI-36,hsa-mir-448 23 121800.91 122716.87 q25 V_0252_LC21078_Iafrate et al. (2004) GRIA3,THOC2 hsa-mir-220 23 123085.05 124261.78 q25 SH2D1A,ODZ1

*: copy number polymorphism according to http://projects.tcag.ca/variation/ Supplementary Table S5

gains and losses - Multi-Fisher's adjusted p value<0.05 basal-like vs luminal chromosome start (kb) end (kb) cytoband frequency basal (%) frequency luminal (%) gains 1 86724.68 91569.19 p22.3-p22.2 24 2 2 36223.91 39009.62 p22.3-p22.1 24 0 5 57025.10 58982.91 q11.2-q12.1 0 27 6 4779.57 30456.68 p25.1-p21.33 40 7 6 32392.47 33659.18 p21.32-p21.31 40 2 6 37477.47 62379.41 p21.2-q11.1 30 0 6 79716.02 81451.01 q14.1 44 9 6 83875.19 93108.18 q14.1-q16.1 40 4 6 100503.60 102048.17 q16.3 44 10 6 104842.56 105820.88 q21 40 7 6 107535.32 112359.30 q21 40 9 7 64803.84 67077.05 q11.21-q11.22 28 2 7 97453.12 101421.40 q21.3-q22.1 28 2 7 109586.36 116108.49 q31.1-q31.2 36 4 7 128144.14 137204.31 q32.1-q33 32 2 7 140038.69 140846.95 q34 40 7 8 137000.22 138270.35 q24.23 88 51 8 139080.97 140772.15 q24.23-q24.3 88 51 9 29.04 38723.85 p24.3-p13.1 56 0 9 68462.85 71253.76 q12-q21.11 32 2 10 63.26 36519.69 p15.3-p11.21 64 10 10 43201.65 45651.74 q11.21 28 0 10 49041.70 61247.18 q11.22-q21.2 28 0 10 63505.23 72032.18 q21.2-q22.1 28 0 12 7044.43 10338.71 p13.31-p13.2 44 4 12 75229.08 78635.99 q21.2 0 30 19 41211.64 41702.24 q13.12 28 2 19 43929.36 44352.70 q13.2 24 2 20 35577.41 36794.28 q11.23 4 38

loss 2 237608.77 239999.81 q37.3 64 27 4 358.14 2486.41 p16.3 44 11 4 3537.55 22601.81 p16.2-p15.31 56 16 4 25178.22 37125.35 p15.2-p14 44 11 5 1866.64 3171.98 p15.33 24 2 5 51454.84 99318.46 q11.2-q21.1 50 9 5 109144.16 119565.05 q21.3-q23.1 44 9 5 121600.61 180730.04 q23.2-q35.3 44 9 6 127832.71 140131.79 q22.33-q24.1 0 24 7 21755.34 56295.46 p15.3-p11.2 20 0 10 77123.72 78742.05 q22.2-q22.3 44 11 10 83256.34 87535.13 q23.1 40 11 10 93154.09 96513.91 q23.32-q23.33 52 20 10 101583.59 111591.42 q24.2-q25.1 56 20 11 111694.88 115609.21 q23.1-q23.3 24 62 11 121312.64 126114.30 q24.1-q24.2 32 69 12 53037.24 60370.34 q13.13-q14.1 30 4 12 62468.97 66295.67 q14.2-q15 24 2 12 71562.51 73546.99 q21.1 24 2 12 74768.75 78635.99 q21.2 24 0 12 89758.71 90170.08 q21.33 24 0 12 90421.92 91463.48 q21.33-q22 24 2 12 92435.96 95294.19 q22-q23.1 24 2 12 96365.77 119877.98 q23.1-q24.31 45 2 12 123242.69 132289.53 q24.31-q24.33 52 13 15 20523.63 50457.06 q11.2-q21.2 60 27 16 4193.49 28380.36 p13.3-p11.2 50 4 16 31649.04 32226.04 p11.2 60 20 16 32439.73 33207.28 p11.2 60 18 17 44137.17 44978.29 q21.32-q21.33 52 18 21 38218.81 39520.69 q22.13-q22.2 36 7 X 9343.73 11011.53 p22.31-p22.2 60 24

basal-like vs HER2 chromosome start (kb) end (kb) cytoband frequency basal (%) frequency HER2 (%) gains 6 44796.92 45131.56 p21.1 64 20 6 47549.29 48136.64 p12.3 68 20 6 56250.57 56650.79 p12.1 68 20 6 101544.66 102350.09 q16.3 40 0 6 104216.43 106179.77 q16.3-q21 40 0 9 1965.29 3286.37 p24.3-p24.2 60 12 9 4116.88 5479.24 p24.2-p24.1 56 12 9 6486.02 6896.34 p24.1 52 12 9 8065.05 8801.96 p24.1 52 8 9 14750.64 16051.20 p22.3 52 8 9 16535.57 17437.71 p22.3-p22.2 48 4 9 19026.98 19374.00 p22.1 44 8 9 25425.79 26788.45 p21.3-p21.2 52 8 10 13978.83 14693.65 p13 68 20 10 15606.89 16011.34 p13 68 20 10 17714.94 18587.26 p12.33 64 16 17 23374.39 25657.34 q11.2 4 56 17 33326.85 35720.00 q12-q21.2 4 65 17 55328.12 55924.55 q23.1-q23.2 8 60 17 56267.77 57048.02 q23.2 8 60 17 57363.41 57842.00 q23.2 8 52 17 59297.09 60307.16 q23.3-q24.1 12 56 losses 2 102909.43 103722.90 q12.1 36 0 2 106278.15 107554.55 q12.2-q12.3 36 0 7 41765.65 43687.91 p14.1-p13 36 0 9 21966.89 23363.24 p21.3 4 44 12 50199.83 50728.84 q13.13 48 4 12 51001.65 51330.43 q13.13 56 12 15 35892.66 44239.32 q14-q21.1 64 16 15 48080.31 50457.06 q21.2 56 8 15 53319.10 54172.91 q21.3 52 8 15 55114.36 56651.55 q21.3-q22.1 52 8 15 59278.14 60689.70 q22.2 52 8 16 9148.95 10777.99 p13.2-p13.13 52 4

luminal vs HER2 chromosome start (kb) end (kb) frequency luminal (%) frequency HER2 (%) gains 17 32864.72 35720.00 q12-q21.2 4 65 17 44725.68 44978.29 q21.32-q21.33 18 60 17 44816.03 46825.75 q21.33 18 60 losses 8 37418.78 37710.30 p12 25 50 8 38922.35 39768.41 p11.23-p11.22 9 44 8 40275.99 41238.82 p11.21 10 48 11 25297.21 25756.02 p14.3 0 24 17 41087.30 41719.58 q21.31 27 68 17 49994.53 51902.77 q22 10 48 Supplementary Table S6

Multi-Fisher's test for Amplifications - adjusted p value<0.05 basal-like chromosome start (kb) end (kb) cytoband Frequency (%) basal Frequency (%) luminal and HER2 (%) adj p value Copy Number Polymorphism* genes miRNA genes expression correlated with amplification Neve 1 142803.53 143328.57 q21.1 20 3 0.0215 V_4248_LC0752_Wong et al. (2007) PPIAL4,NBPF20 V_2050_LC0752_Locke et al. (2006), V_4250_LC0752_Wong et al. (2007), V_4251_LC0752_Wong et al. (2007), PDZK1,LIX1L,RBM8A,FAM108A2,POLR3C,ANKRD34,ANKRD35,NBPF11,NUDT17,LOC728932 1 143900.68 144960.77 q21.1 20 1 0.0076 V_4252_LC0752_Wong et al. (2007) ,NOTCH2NL,POLR3GL,HFE2,CD160,ITGA10,PIAS3,PEX11B,LOC653519,TXNIP,ZNF364 POLR3C, PEX11B 1 146329.02 147039.95 q21.1 20 3 0.0215 V_2051_LC0752_Locke et al. (2006) PPIAL4,NBPF14,NBPF15,NBPF10 V_0037_LC3745_Iafrate et al. (2004), 3 152709.13 154220.81 q25.1-q25.2 12 0 0.0277 V_4357_LC3748_Wong et al. (2007) AADAC,MBNL1,AADACL2,SUCNR1,P2RY1 3 170138.87 170844.14 q26.2 12 0 0.0277 EVI1, MDS1 3 170655.62 170844.14 q26.2 12 0 0.0277 MDS1 6 44011.63 44165.11 p21.1 16 14 0.0273 MGC45491 6 44124.32 44223.55 p21.1 12 0 0.0277 TMEM63B,MRPL14 8 128339.38 128894.28 q24.21 50 21 0.0157 V_4609_LC10877_Wong et al. (2007) MYC MYC 8 131208.10 137015.73 q24.21-q24.23 36 11 0.0208 V_0123_LC10906_Iafrate et al. (2004), LRRC6,KHDRBS3,WISP1,PHF20L1,KCNQ3,OC90,ST3GAL1,ADCY8,TG,NDRG1,ZNF406,SLA, hsa-mir-30d,hsa-mir-30b KIAA0143, PHF20L1, ST3GAL1 9 4116.88 5335.75 p24.2-p24.1 12 0 0.0277 RLN1,RLN2,RCL1,CDC37L1,C9orf68,PPAPDC2,SLC1A1,AK3,GLIS3,INSL4,INSL6,JAK2 hsa-mir-101-2 CDC37L1 9 6837.95 15063.72 p24.1-p22.3 12 0 0.0277 V_4615_LC11143_Wong et al. (2007) ZDHHC21,JMJD2C,PTPRD,NFIB,FREM1,C9orf123,MPDZ,C9orf150,CER1,TYRP1 JMJD2C, MPDZ 10 168.17 908.11 p15.3 12 0 0.0277 V_4664_LC11931_Wong et al. (2007) ZMYND11,LARP5,DIP2C 10 1465.37 3344.64 p15.3-p15.2 12 0 0.0277 PFKP,PITRM1,ADARB2 11 68767.97 69297.66 q13.2-q13.3 0 20 0.0165 V_4755_LC13316_Wong et al. (2007) CCND1,ORAOV1,FGF19,MYEOV,FGF4 CCND1, CTTN, FADD,PPF1A1 11 69336.69 70008.69 q13.3 0 20 0.0298 PPFIA1,CTTN,FADD,FGF3,TMEM16A,SHANK2 SHANK2 12 1717.99 2518.03 p13.33 12 0 0.0272 V_4765_LC13757_Wong et al. (2007) LRTM2,CACNA1C,CACNA2D4,DCP1B,ADIPOR2 12 2975.97 3791.52 p13.33-p13.32 12 0 0.0076 V_0161_LC13778_Iafrate et al. (2004) TEAD4,MGC4266,PRMT8,PARP11,TSPAN9 TEAD4 DYRK4,KCNA1,KCNA5,KCNA6,AKAP3,TMEM16B,GALNT8,NDUFA9,C12orf4,NTF3,VWF,RAD5 12 4474.48 6104.17 p13.32-p13.31 12 0 0.0277 1AP1 C12orf4, NDUFA9m, DYRK4 12 9137.49 9279.58 p13.31 16 0 0.0067 A2M,PZP 12 11691.84 12260.88 p13.2 12 0 0.0277 LRP6,BCL2L14,ETV6 12 13450.37 13749.85 p13.1 12 0 0.0277 GRIN2B

V_0163_LC13898_Iafrate et al. (2004), KRAS,FLJ32894,ETNK1,SOX5,FLJ36004,KIAA0528,CASC1,LYRM5,CMAS,LRMP,BCAT1,ST8S 12 21890.53 25685.79 p12.1 16 1 < 0.0272 V_4773_LC13907_Wong et al. (2007) IA1,ABCC9 KLHDC5,FGFR1OP2,STK38L,PTHLH,C12orf11,LOC728858,PPFIBP1,MRPS35,TM7SF3,ARNT 12 26326.61 28286.49 p11.23-p11.22 16 1 < 0.0277 L2,ITPR2,SURB7,REP15 RPS3 12 30965.39 31382.37 p11.21 12 0 0.0277 DDX11,FAM60A,OVOS2,TSPAN11

PNMT,NR1D1,ZPBP2,NEUROD2,ERBB2,PSMD3,PERLD1,GSDML,CSF3,ORMDL3,PPARBP,T 17 34781.21 35522.38 q12-q21.1 0 36 < 0.0157 HRAP4,C17orf37,PPP1R1B,GSDM1,FBXL20,TCAP,GRB7,THRA,ZNFN1A3,STARD3,CRKRS ERBB2, GRB7, GSDML, PERLD1, STARD3, THRAP4, PSMD3, THRA, TCAP, PNMT, THRA 19 33858.00 34130.59 q12 12 0 0.0272 19 34636.25 34914.35 q12 16 1 0.0272 PLEKHF1,POP4,C19orf12 PLEKHF1, POP4

19 45118.57 45531.36 q13.2 12 0 0.0277 ZNF546,FLJ13265,AKT2,PSMC4,LOC284323,LOC163131,FLJ36888,TTC9B,MAP3K10,FCGBP hsa-mir-641

luminal chromosome start (kb) end (kb) cytoband Frequency (%) luminal Frequency (%) basal and HER2 (%) adj p value Copy Number Polymorphism* genes miRNA genes expression correlated with amplification Neve 1 199215.67 199761.74 q32.1 11 0 0.0355 DKFZp434B1231,PHLDA3,TMEM9,CACNA1S,TNNT2,KIF21B,CSRP1,TNNI1,LAD1,PKP1 KLHL12,C1orf37- DUP,PPFIA4,RABIF,JARID1B,ADORA1,CHI3L1,MYOG,C1orf37,PPP1R12B,CYB5R1,SYT2,ADI 1 200702.52 201433.63 q32.1 11 0 0.0355 V_4267_LC1097_Wong et al. (2007) POR1,MYBPH ADIPOR1, RABIF, JARI1B, C1orf37, RCL1 TMEM81,SOX13,TMCC2,RIPK5,PIK3C2B,ETNK2,RBBP5,NUAK2,GOLT1A,NFASC,KLHDC8A, 1 202282.06 203577.17 q32.1 15 0 < 0.0355 REN,KISS1,LRRN5,MDM4,CNTN2,PPP1R15B,PLEKHA6 1 207547.77 208097.15 q32.2 20 4 0.0378 CAMK1G,IRF6,LAMB3,G0S2,TRAF3IP3,C1orf74,C1orf107,HSD11B1 hsa-mir-205 IRF6 8 37560.50 37710.30 p12 24 6 0.0309 8 37923.66 38189.05 p12 16 2 0.0418 ASH2L,BAG4,STAR,EIF4EBP1,LSM1,ADRB3 ASH2L, BAG4, LSM1 10 8115.36 8864.08 p14 16 4 0.0465 GATA3,FLJ45983 U15A,U15B,hsa-mir-326 11 69685.40 69901.80 q13.3 22 4 0.0193 ZNF703 11 69978.31 70204.38 q13.4 18 2 0.0203 PPFIA1,TMEM16A,FADD 11 74182.42 77290.15 q13.4-q14.1 15 0 < 0.0418 SHANK2 CLNS1A, HBXAP, PTD015 12 27928.45 28200.29 p11.22 20 2 0.0464 PTHLH 17 45024.20 46380.31 q21.33 28 0 < 0.0465 V_5017_LC17552_Wong et al. (2007) CA,ITGA3,CHAD,HILS1,MRPL27,SPOP,TAC4,ABCC3,CROP,SAMD14,MYCBPAP,TOB1,EPN3, CROP, DLX4, ITAG3, MYST2, RSAD1, SLC35B1, XYLT2, SPOP, EPN3, TOB1, PDK2, TG, FLJ20920

HER2 chromosome start (kb) end (kb) cytoband Frequency (%) HER2 Frequency (%) luminal and basal (%) adj p value Copy Number Polymorphism* genes miRNA genes expression correlated with amplification Neve 14 29027.12 30483.79 q12 12 0 0.0279 SCFD1,KIAA1333,COCH,PRKD1,STRN3 14 31203.56 32086.19 q12-q13.1 12 0 0.0279 AKAP6,NUBPL,ARHGAP5 14 63996.81 64415.59 q23.2-q23.3 12 0 0.0279 ZBTB25,HSPA2,PLEKHG3,ZBTB1,SPTB,AKAP5,C14orf50 TOP2A,WIPF2,NR1D1,MSL- 1,THRA,IGFBP4,GJC1,RARA,RAPGEFL1,DKFZp586B1922,CDC6,TNS4,L47277,DKFZp686J17 17 35496.35 35891.50 q21.1-q21.2 100 0 0.0000 211,CASC3 ERBB2, GRB7, GSDML, PERLD1, STARD3, THRAP4, PSMD3, THRA, TCAP, PNMT, THRA V_0804_LC17530_Sharp et al. (2005), KPNB1,PNPO,NPEPPS,MRPL10,SKAP1,COPZ2,CDK5RAP3,OSBPL7,NFE2L1,C17orf57,SP2,T 17 42833.68 43788.75 q21.32 13 0 < 0.0272 V_2229_LC17530_Locke et al. (2006) BKBP1,TBX21,SP6,SCRN2,CBX1,SNX11,LRRC46,ATAD4 hsa-mir-152 PNPO SNF8,LOC81558,MBTD1,PHB,SLC35B1,RSAD1,B4GALNT2,ITGA3,CHAD,MRPL27,SPOP,NGF R,TAC4,ABCC3,CROP,SAMD14,TOB1,EPN3,WFIKKN2,CACNA1G,SPATA20,DLX3,DLX4,NME V_0208_LC17538_Iafrate et al. (2004), 1,HOXB13,NME2,LRRC59,MYST2,TMEM92,PRAC,ZNF652,NXPH3,XYLT2,FLJ20920,CA10,UB V_5016_LC17543_Wong et al. (2007), E2Z,PHOSPHO1,ANKRD40,UTP18,HOXB3,HOXB4,SGCA,HOXB5,TTLL6,HOXB6,HILS1,HOXB V_5017_LC17552_Wong et al. (2007), 7,HOXB8,SPAG9,HOXB9,ATP5G1,IGF2BP1,GNGT2,ABI3,MYCBPAP,CALCOCO2,PDK2,PPP1 17 44003.18 47676.82 q21.32-q22 20 3 < 0.0272 V_5018_LC17559_Wong et al. (2007) R9B,NME1-NME2,EME1,GIP,COL1A1 hsa-mir-196a-1,hsa-mir-10a NME1, NME2, PHB, ZNF652, TBX2,TBX4,CA4,C17orf64,APPBP2,INTS2,LOC388407,USP32,BRIP1,PPM1D,ABC1,NACAL,B 17 55503.14 57374.12 q23.1-q23.2 20 4 < 0.0464 V_0805_LC17601_Sharp et al. (2005) CAS3 ACA66 ABC1, ADIPOR1, PPM1D, BCAS3, USP32, BRIP1 DDX42,CD79B,ICAM2,SMARCD2,CCDC47,CSHL1,SCN4A,PSMC5,FTSJ3,GH1,GH2,CSH1,ER 17 59198.39 59495.40 q23.3 20 4 0.0464 V_0210_LC17626_Iafrate et al. (2004) N1,CSH2 DDX2, FTSJ3, SMARCD2

*: copy number polymorphism according to http://projects.tcag.ca/variation/ Supplementary Table S7

Fishers amps groups adj p<0.05 basal-like vs luminal chromosome start (kb) end (kb) cytoband frequency basal (%) frequency luminal (%) adj p value cnv genes miRNA 1 142803.5 143673.8 q21.1 20 2 0.0301 V_4248_LC0752_Wong PPIAL4,NBPF20,PDE4DIP et al. (2007) 1 143900.7 144960.8 q21.1 20 0 <0.0212 V_2050_LC0752_Locke PDZK1,LIX1L,RBM8A,FAM108A2,POLR3C,ANKRD34,ANKRD35,NBPF11,NUDT17,LOC728932, et al. (2006), NOTCH2NL,POLR3GL,HFE2,CD160,ITGA10,PIAS3,PEX11B,LOC653519,TXNIP,ZNF364 V_4250_LC0752_Wong et al. (2007), V_4251_LC0752_Wong et al. (2007), V_4252_LC0752_Wong et al. (2007) 1 146828.7 147039.9 q21.1 20 2 0.0301 NBPF15 8 128435.8 128894.3 q24.21 52 22 0.0427 V_4609_LC10877_Won MYC g et al. (2007) 8 131208.1 132963.4 q24.21-q24.22 36 11 <0.04 ADCY8,DDEF1 8 134707.5 136460.6 q24.22 36 11 0.04 V_0124_LC10922_Iafrat ZNF406 hsa-mir-30d,hsa-mir-30b e et al. (2004), V_4610_LC10912_Won g et al. (2007) 10 8115.361 8864.083 p14 16 0 0.0212 GATA3,FLJ45983 11 68767.97 70008.69 q13.2-q13.3 0 24 <0.333 V_4755_LC13316_Won PPFIA1,CTTN,CCND1,FADD,ORAOV1,FGF19,FGF3,MYEOV,TMEM16A,FGF4,SHANK2 g et al. (2007) 12 9137.487 9466.086 p13.31 16 0 0.0212 A2M,PZP 12 21890.53 25049.06 p12.1 16 0 0.0212 V_0163_LC13898_Iafrat FLJ32894,ETNK1,SOX5,KIAA0528,CMAS,BCAT1,ST8SIA1,ABCC9 e et al. (2004), V_4773_LC13907_Won g et al. (2007) 12 27441.91 28286.49 p11.23-p11.22 20 0 <0.0212 PTHLH,MRPS35,ARNTL2,KLHDC5,PPFIBP1,REP15 19 34636.25 34914.35 q12 16 0 0.0212 PLEKHF1,POP4,C19orf12

basal-like vs HER2 chromosome start (kb) end (kb) cytoband frequency basal (%) frequency HER2 (%) cnv genes miRNA 17 34442.98 35720 q12-q21.2 0 100 <0.01 V_5006_LC17473_Won PNMT,RPL19,NR1D1,WIRE,GSDML,PPARBP,CASC3,FBXL20,GRB7,THRA,RARA,CRKRS,ZPB g et al. (2007) P2,MSL- 1,ERBB2,NEUROD2,PSMD3,PERLD1,PLXDC1,THRAP4,ORMDL3,CSF3,PPP1R1B,C17orf37,CA CNB1,GSDM1,TCAP,STAC2,ZNFN1A3,STARD3,RAPGEFL1,CDC6 17 56350.83 57089.09 q23.2 0 32 <0.014 TBX2,TBX4,LOC388407,NACAL,BCAS3

luminal vs HER2 chromosome start (kb) end (kb) cytoband frequency luminal (%) frequency HER2 (%) cnv genes miRNA 17 32163.47 35891.5 q12-q21.2 0 100 <0.0197 V_2224_LC17457_Lock DUSP14,TOP2A,PNMT,SNIP,RPL19,NR1D1,FBXO47,TBC1D3,WIRE,GSDML,PPARBP,SOCS7,L ACA21 e et al. (2006), OC388381,CASC3,FBXL20,GRB7,THRA,MRPL45,GJC1,RARA,PCGF2,CRKRS,AATF,RPL23,PIP V_5001_LC17457_Won 5K2B,ZPBP2,PSMB3,ACACA,MSL- g et al. (2007), 1,CCDC49,NEUROD2,ERBB2,GPR179,PSMD3,PERLD1,CSF3,ORMDL3,PLXDC1,TADA2L,THR V_5002_LC17457_Won AP4,C17orf37,PPP1R1B,CACNB1,GSDM1,LHX1,DDX52,TCAP,STAC2,LASP1,IGFBP4,ZNFN1A g et al. (2007), 3,C17orf78,STARD3,RAPGEFL1,CDC6,TNS4,AP1GBP1,MLLT6,TCF2 V_5004_LC17457_Won g et al. (2007), V_5005_LC17457_Won g et al. (2007), V_5006_LC17473_Won g et al. (2007) 17 44519.18 46825.75 q21.32-q21.33 2 40 <0.0027 V_5016_LC17543_Won LOC81558,MBTD1,PHB,SLC35B1,RSAD1,B4GALNT2,ITGA3,CHAD,MRPL27,SPOP,NGFR,TAC4 g et al. (2007), ,ABCC3,CROP,SAMD14,TOB1,EPN3,WFIKKN2,CACNA1G,SPATA20,DLX3,DLX4,NME1,NME2,L V_5017_LC17552_Won RRC59,MYST2,TMEM92,NXPH3,ZNF652,XYLT2,FLJ20920,PHOSPHO1,ANKRD40,UTP18,SGC g et al. (2007), A,HILS1,SPAG9,GNGT2,ABI3,MYCBPAP,PDK2,PPP1R9B,NME1-NME2,EME1,COL1A1 V_5018_LC17559_Won g et al. (2007) 17 47115.09 47351.44 q21.33 7 28 0.0402 CA10 17 56350.83 57327.47 q23.2 7 32 <0.0402 TBX2,TBX4,INTS2,LOC388407,BRIP1,NACAL,BCAS3 Supplementary Table S8 Recurrent amplifications in luminal cancers chromosome start (kb) end (kb) cytoband Copy Number Polymorphism* genes miRNA 1 145413.66 146950.77 q21.1 V_2051_LC0752_Locke et al. (2006), V_4253_LC0752_Wong et al. (2007) ACP6,GPR89A,LOC728932,BCL9,PPIAL4,GJA5,GJA8,NBPF10,NBPF11,NBPF14,NBPF15 1 149849.65 152077.20 q21.3 S100A7L2,RORC,SNX27,LCE3A,LCE3B,LCE3C,LCE3D,C1orf42,LCE3E,HRNR,C1orf45,LELP1,SPRR2A,SMCP,SPRR2B,SPRR2D,SPRR2E,SPRR2F,S100A7A,SPRR2G,TCHH,FLG2,INTS3,LCE4A,TDRKH, PGLYRP3,PGLYRP4,CRNN,TNRC4,LOR,S100A10,S100A11,S100A12,S100A13,S100A14,S100A16,LCE1A,LCE1B,NPR1,LCE1C,LCE1D,LCE1E,LCE1F,LCE5A,SNAPAP,ILF2,OAZ3,TCHHL1,MRPL9,GATA D2B,LINGO4,LCE2A,LCE2B,LCE2C,LCE2D,SLC27A3,THEM4,THEM5,SPRR1A,SPRR1B,S100A1,S100A2,C1orf77,S100A3,SPRR3,S100A4,FLG,S100A5,SPRR4,S100A6,S100A7,IVL,S100A8,S100A9

1 155007.58 155533.39 q23.1 ARHGEF11,PEAR1,PRCC,C1orf92,NTRK1,INSRR,ETV3,FLJ16478,SH2D2A hsa-mir-765 1 157996.99 162068.43 q23.2-q23.3 V_4258_LC0863_Wong et al. (2007), V_4259_LC0863_Wong et al. (2007) RGS4,CCDC19,RGS5,UHMK1,KCNJ10,PFDN2,UAP1,PPOX,DEDD,ARHGAP30,FCRLM1,FCRLM2,FCGR3A,FCGR3B,CD244,ATP1A2,NUF2,ATP1A4,SLAMF1,VSIG8,SLAMF6,SLAMF7,SLAMF8,SLAMF9,N hsa-mir-556 R1I3,HSD17B7,APOA2,IGSF8,PEX19,USF1,IGSF9,SDHC,FCRL6,DUSP12,ADAMTS4,PIGM,CD48,COPA,CD84,USP21,KCNJ9,UFC1,HSPA6,PEA15,MPZ,ATF6,VANGL2,TOMM40L,C1orf110,FCER1G,C1orf 111,NDUFS2,WDR42A,NIT1,NHLH1,TAGLN2,NOS1AP,SH2D1B,DUSP23,C1orf192,F11R,CASQ1,NCSTN,PVRL4,LY9,FCGR2A,FCGR2B,KARCA1,FCGR2C,ITLN1,DDR2,B4GALT3,ITLN2,OLFML2B,FLJ131 37 1 163384.21 163862.15 q23.3-q24.1 RXRG,LMX1A,LRRC52 1 166625.84 167465.07 q24.2 XCL1,XCL2,ATP1B1,DPT,NME7 1 170069.07 171022.71 q24.3 FASLG,DNM3,PIGC,C1orf105,C1orf9 hsa-mir-199a-2,hsa-mir-214 1 173658.23 174140.91 q25.1 V_4263_LC0946_Wong et al. (2007) 1 174659.22 175547.25 q25.2 FAM5B,ASTN,PAPPA2 hsa-mir-488 1 176574.92 177359.36 q25.2 C1orf49,FLJ35530,ABL2,ANGPTL1,RASAL2,FAM20B,TOR3A,RALGPS2 1 177945.80 181045.40 q25.2-q25.3 V_4264_LC0975_Wong et al. (2007) RGS8,ZNF648,CEP350,KIAA1614,RNASEL,NPL,ACBD6,IER5,RGS16,CACNA1E,GLUL,MR1,TEDDM1,QSCN6,TOR1AIP1,TOR1AIP2,XPR1,IFRG15,LHX4,C1orf76,STX6 1 181852.78 183125.43 q25.3 V_4265_LC0992_Wong et al. (2007) RGL1,C1orf19,C1orf21,C1orf22,C1orf24,GLT25D2,ARPC5,APOBEC4 1 185538.41 187248.95 q31.1 1 196141.23 197673.50 q31.3-q32.1 PTPRC,NEK7,C1orf53,ATP6V1G3,LHX9 hsa-mir-181a-1,hsa-mir-181b-1 1 199215.67 199761.74 q32.1 DKFZp434B1231,LAD1,PKP1,PHLDA3,CSRP1,TMEM9,KIF21B,CACNA1S,TNNT2,TNNI1 1 200702.52 201433.63 q32.1 V_4267_LC1097_Wong et al. (2007) CHI3L1,ADIPOR1,KLHL12,C1orf37-DUP,PPFIA4,MYOG,JARID1B,ADORA1,CYB5R1,SYT2,MYBPH,RABIF,C1orf37,PPP1R12B 1 203525.99 205161.95 q32.1 V_2091_LC1120_Locke et al. (2006), V_4268_LC1117_Wong et al. (2007) IL10,SRGAP2,IL19,PCTK3,NUCKS1,SLC26A9,CTSE,SLC41A1,IL20,LGTN,IL24,SLC45A3,MFSD4,FLJ32569,C1orf186,MAPKAPK2,RAB7L1,FAIM3,KLHDC8A,LEMD1,AVPR1B,DYRK3,RASSF5,IKBKE,ELK4, hsa-mir-135b NUAK2 1 206365.58 206791.86 q32.2 V_4269_LC1125_Wong et al. (2007) PLXNA2 1 207547.77 208097.15 q32.2 CAMK1G,LAMB3,TRAF3IP3,IRF6,G0S2,C1orf107,HSD11B1,C1orf74 hsa-mir-205 1 208638.52 209204.86 q32.2 HHAT,KCNH1 1 210489.69 210929.50 q32.3 NENF,ATF3,SNFT,FAM71A,C1orf75,PPP2R5A U98b 1 212021.45 212736.37 q32.3-q41 SMYD2,PTPN14,PROX1 1 214172.12 214913.59 q41 ESRRG,USH2A 1 217262.66 217651.60 q41 LYPLAL1 1 218273.47 219396.01 q41 EPRS,BPNT1,C1orf115,RAB3GAP2,IARS2,MARK1,HLX1,MOSC1,MOSC2 hsa-mir-194-1,ACA36B,hsa-mir-215 1 219922.49 220458.40 q41 DUSP10 1 221257.89 221971.47 q41 C1orf65,SUSD4,TLR5,CAPN2 1 226314.82 226794.43 q42.13 TRIM17,OBSCN,GJA12,MRPL55,WNT3A,HIST3H2BB,HIST3H3,C1orf69,GUK1,C1orf35,HIST3H2A,TRIM11,ARF1 1 227960.35 228505.16 q42.13 GALNT2 1 230078.71 231900.00 q42.2 V_0016_LC1285_Iafrate et al. (2004) PCNXL2,KIAA1804,C1orf57,KIAA1383,SIPA1L2,KCNK1,DISC1 1 232294.34 233221.71 q42.2-q42.3 V_4271_LC1296_Wong et al. (2007), V_4272_LC1302_Wong et al. (2007) SLC35F3,TARBP1,IRF2BP2,C1orf31 1 238514.46 240324.82 q43 RGS7,OPN3,GREM2,KMO,EXO1,MAP1LC3C,FH,WDR64,CHML,PLD5,FMN2 1 242009.37 242646.10 q44 AKT3,C1orf100,LOC440742,ZNF238,ADSS 1 243456.79 244139.88 q44 SMYD3,KIF26B 3 24994.82 25433.89 p24.2 3 87707.54 88631.14 p11.2 V_4344_LC3397_Wong et al. (2007) CGGBP1,ZNF654,C3orf38,HTR1F 3 158560.87 159434.06 q25.32 PTX3,VEPH1,SHOX2,RSRC1 3 159866.59 160610.78 q25.32-q25.33 MFSD1,RARRES1,SCHIP1,GFM1,LXN,IQCJ 3 160923.66 161168.89 q25.33 SCHIP1 3 174043.84 175588.08 q26.31 NLGN1,SPATA16 3 178553.14 179681.75 q26.32 V_0040_LC3895_Iafrate et al. (2004) 5 2168.06 2556.94 p15.33 5 5449.10 7983.12 p15.32-p15.31 NSUN2,ADCY2,SRD5A1,FLJ33360,MTRR,TRG20,POLS,LOC134121,MGC5297,KIAA0947 5 8908.06 9719.28 p15.2 TAS2R1,SEMA5A 5 10597.61 10903.32 p15.2 V_2082_LC6572_Locke et al. (2006) DAP 5 13788.92 14689.84 p15.2 TRIO,FAM105A,DNAH5 5 20798.44 20983.59 p14.3 6 8511.01 9840.38 p24.3 6 11242.33 15057.23 p24.1-p23 GFOD1,C6orf114,NOL7,EDN1,CD83,HIVEP1,TBC1D7,PHACTR1,RANBP9,SIRT5,RNF182,NEDD9,C6orf79,C6orf105 6 15430.44 16755.17 p23-p22.3 GMPR,JARID2,MYLIP,DTNBP1,ATXN1 6 107055.69 107424.88 q21 QRSL1,RTN4IP1,AIM1 hsa-mir-587 7 12125.70 14136.22 p21.3-p21.2 TMEM106B,ARL4A,ETV1,SCIN 7 14722.09 15784.19 p21.2-p21.1 MEOX2,FLJ16237,DGKB 7 20438.64 21417.96 p15.3 SP8,ABCB5 7 24805.21 25129.72 p15.3-p15.2 OSBPL3,CYCS 7 25393.84 26260.09 p15.2 CBX3,NFE2L3,HNRPA2B1 hsa-mir-148a 7 29094.25 29626.45 p15.1 LOC222171,CHN2,CPVL 7 30200.33 31082.62 p15.1 INMT,C7orf24,ZNRF2,GARS,FLJ22374,CARD4,CRHR2,GHRHR,AQP1,ADCYAP1R1 hsa-mir-550-1 7 37302.82 38051.70 p14.2-p14.1 SFRP4,GPR141,EPDR1,ELMO1,TXNDC3 7 38504.82 42597.22 p14.1 CDC2L5,C7orf10,C7orf11,VPS41,POU6F2,GLI3,INHBA,RALA,C7orf36,AMPH 7 43097.67 43705.77 p14.1-p13 STK17A,HECW1,FLJ10803 7 64207.80 64577.48 q11.21 ZNF92 7 68636.85 69855.21 q11.22 AUTS2 7 71364.93 71877.34 q11.22-q11.23 CALN1 8 34620.79 35542.63 p12 UNC5D 8 36980.61 37710.30 p12 ZNF703 8 38289.07 39235.33 p12-p11.23 V_4589_LC10531_Wong et al. (2007) FLJ43582,TM2D2,ADAM9,LETM2,ADAM32,HTRA4,WHSC1L1,FGFR1,TACC1 8 40275.99 40830.44 p11.21 ZMAT4 8 41795.49 42777.72 p11.21 VDAC3,CHRNB3,PLAT,POLB,SLC20A2,DKK4,C8orf40,IKBKB,MYST3,CHRNA6,AP3M2 8 49380.20 54499.48 q11.21-q11.23 V_4591_LC10578_Wong et al. (2007), V_4592_LC10583_Wong et al. (2007), RB1CC1,C8orf22,UNQ9433,PCMTD1,SNAI2,SNTG1,ST18,EFCAB1,PXDNL,OPRK1,NPBWR1 V_4593_LC10587_Wong et al. (2007) 8 55777.04 56688.36 q12.1 XKR4 8 57453.47 59077.18 q12.1 V_4594_LC10611_Wong et al. (2007) PENK,C8orf72,IMPAD1 8 75978.34 77193.05 q21.11 V_4599_LC10697_Wong et al. (2007) HNF4G,CRISPLD1 8 80595.34 81295.89 q21.13 MRPS28,STMN2,HEY1,TPD52 8 82629.72 84055.48 q21.13 CHMP4C,SNX16,ZFAND1,IMPA1,SLC10A5 8 86620.60 87896.46 q21.2-q21.3 V_0121_LC10727_Iafrate et al. (2004), V_2126_LC10727_Locke et al. (2006), WWP1,CNGB3,CPNE3,PSKH2,ATP6V0D2,FAM82B,REXO1L1,SLC7A13 V_4601_LC10727_Wong et al. (2007), V_4602_LC10727_Wong et al. (2007), V_4603_LC10727_Wong et al. (2007), V_4604_LC10727_Wong et al. (2007), V_4605_LC10727_Wong et al. (2007) 8 88725.68 91778.19 q21.3 V_4606_LC10731_Wong et al. (2007) RIPK2,C8orf1,DECR1,CALB1,TMEM64,NBN,MMP16,WDR21C 8 93967.30 94588.61 q22.1 V_4607_LC10749_Wong et al. (2007) 8 96297.98 97475.58 q22.1 UQCRB,GDF6,C8orf37,MTERFD1,PTDSS1 8 100057.68 101101.77 q22.2 COX6C,VPS13B,RGS22 hsa-mir-599 8 102624.96 103723.77 q22.3 GRHL2,RRM2B,ODF1,NCALD,EDD1 8 108499.10 109389.98 q23.1 ANGPT1,EIF3S6,RSPO2 8 109729.16 110307.58 q23.1 TMEM74,TRHR 8 117853.65 118356.84 q24.11 RAD21,LOC441376,SLC30A8 8 120711.37 130896.15 q24.12-q24.21 V_4609_LC10877_Wong et al. (2007) HAS2,ZNF572,MTBP,SNTB1,DCC1,NDUFB9,FAM83A,MLZE,ENPP2,FBXO32,WDR67,TRIB1,ZHX1,ZHX2,COL14A1,MRPL13,ANXA13,DERL1,TATDN1,C8orf32,C8ORFK23,C8orf36,FAM84B,ATAD2,C8orf76 hsa-mir-548d-1 ,TMEM65,TRMT12,SQLE,RNF139,FAM91A1,C8ORFK36,TMEM75,MYC,DEPDC6,KIAA0196,MTSS1,C8orf54,TAF2 8 132591.90 134787.06 q24.22 V_0123_LC10906_Iafrate et al. (2004), V_4610_LC10912_Wong et al. (2007) LRRC6,KCNQ3,OC90,ST3GAL1,KIAA0143,WISP1,TMEM71,PHF20L1,TG,NDRG1,SLA 8 139788.74 139958.18 q24.23 COL22A1 8 142202.74 143824.29 q24.3 V_4791_LC10979_Wong et al. (2007) PSCA,BAI1,LY6K,SLC45A4,SLURP1,PTP4A3,TSNARE1,ARC,JRK,DENND3,FLJ43860,GPR20,C8orf55 9 44762.51 45034.48 p11.2 V_0744_LC11330_Sharp et al. (2005), V_2133_LC11330_Locke et al. (2006), V_4629_LC11330_Wong et al. (2007), V_5000_LC11330_Wong et al. (2007) 10 9026.60 9366.97 p14 10 10791.44 11044.63 p14 11 60926.12 62219.42 q12.2-q12.3 V_4749_LC13256_Wong et al. (2007) LOC51035,BSCL2,LOC221091,INTS5,FLJ12529,C11orf66,FADS1,LOC751071,FADS2,FADS3,SCGB2A1,SCGB2A2,LOC790955,SCGB1D1,SCGB1D2,SCGB1D4,AHNAK,ROM1,RBM21,MTA2,RAB3IL1,FLJ2 U99,hsa-mir-611 0487,INCENP,EEF1G,SCGB1A1,ASRGL1,C11orf9,FEN1,FTH1,SYT7,VMD2,C11orf48,EML3,B3GAT3,C11orf10,GANAB,C11orf11 11 67909.03 68463.94 q13.2 CPT1A,IGHMBP2,LRP5,MTL5,MRPL21,SAPS3,GAL 11 68767.97 69297.66 q13.2-q13.3 V_4755_LC13316_Wong et al. (2007) ORAOV1,FGF19,FGF4,CCND1,MYEOV 11 72374.54 73038.99 q13.4 ARHGEF17,TNFRSF19L,P2RY2,P2RY6,KIAA0280,PLEKHB1,FCHSD2 11 75279.95 77918.33 q13.5-q14.1 LOC283219,MYO7A,PAK1,LRRC32,OMP,INTS4,PRKRIR,NDUFC2,AQP11,C11orf30,NARS2,PHCA,KCTD14,CLNS1A,ALG8,THRSP,LRRC54,CAPN5,WNT11,PTD015,GDPD4,USP35,UVRAG,HBXAP,B3GN T6,GAB2 11 79463.52 80464.82 q14.1 11 86479.29 86957.30 q14.2 TMEM135 12 62350.04 62845.05 q14.2 SRGAP1,TMEM5 13 93548.81 93803.60 q31.3-q32.1 GPC6 13 104048.54 104393.09 q33.2 13 105535.35 106665.87 q33.2-q33.3 LOC728215,EFNB2,FLJ10154 13 108795.16 109280.01 q33.3-q34 V_0361_LC15215_Shaw-Smith et al. (2004) IRS2 14 36356.01 37562.08 q13.3-q21.1 FOXA1,TTC6,SLC25A21,MIPOL1 15 83970.62 84687.94 q25.3 V_4908_LC16467_Wong et al. (2007) AKAP13,FLJ32310,KLHL25 15 86251.79 86977.83 q25.3-q26.1 ISG20L1,MRPL46,DET1,NTRK3,MRPS11 hsa-mir-7-2 15 94226.87 97413.93 q26.2-q26.3 V_0192_LC16541_Iafrate et al. (2004), V_4911_LC16537_Wong et al. (2007) FLJ39743,NR2F2,ARRDC4,SPATA8,IGF1R 16 9633.35 10120.86 p13.2 GRIN2A 16 10478.71 11625.74 p13.13 MGC24665,SOCS1,CIITA,KIAA0350,DEXI,LITAF,TNP2,PRM1,PRM2,PRM3,ATF7IP2,LOC780776,EMP2,NUBP1,FLJ32871 16 12151.34 12607.35 p13.13-p13.12 LOC92017 16 16798.85 17356.08 p12.3 V_4929_LC16736_Wong et al. (2007) XYLT1 17 43769.09 44347.53 q21.32 V_0208_LC17538_Iafrate et al. (2004) HOXB13,UBE2Z,TTLL6,SKAP1,PRAC,HOXB1,HOXB2,HOXB3,HOXB4,HOXB5,HOXB6,HOXB7,HOXB8,ATP5G1,HOXB9,CALCOCO2 hsa-mir-10a,hsa-mir-196a-1 17 46892.56 48665.70 q21.33-q22 V_0209_LC17565_Iafrate et al. (2004) CA10 17 50357.48 51204.06 q22 TMEM100,PCTP,HLF,MMD,COX11,STXBP4,TOM1L1 17 51735.96 52294.74 q22 ANKFN1,C17orf67,DGKE,NOG 17 52581.13 53321.73 q22 MRPS23,CUEDC1,MSI2 17 54425.48 56474.01 q22-q23.2 V_0805_LC17601_Sharp et al. (2005) TUBD1,TMEM49,C17orf64,RPS6KB1,APPBP2,DHX40,CLTC,FAM33A,C17orf71,YPEL2,CA4,TRIM37,PRR11,PTRH2,LOC51136,GDPD1,USP32,PPM1D,BCAS3 hsa-mir-21,hsa-mir-301,hsa-mir-454,ACA66 17 57343.94 57724.32 q23.2 V_2230_LC17608_Locke et al. (2006), V_5020_LC17608_Wong et al. (2007) INTS2,THRAP1 17 59459.51 59722.04 q23.3 V_0210_LC17626_Iafrate et al. (2004) ERN1,TEX2 U104,ACA62 17 60667.15 61451.88 q24.1 V_5026_LC17636_Wong et al. (2007) AXIN2,CCDC46 17 63118.03 64432.94 q24.2 NOL11,WIPI1,AMZ2,SLC16A6,ARSG,ABCA8,FAM20A,PRKAR1A,BPTF,C17orf58,PITPNC1,KPNA2 hsa-mir-635 17 65201.41 66782.46 q24.3 V_0211_LC17666_Iafrate et al. (2004) KCNJ16,KCNJ2 17 76130.54 76516.24 q25.3 KIAA1303 19 36394.78 37230.47 q12-q13.11 TSHZ3 20 35284.96 36794.28 q11.23 V_5136_LC19617_Wong et al. (2007) KIAA1219,C20orf77,TGM2,SLC32A1,SRC,CTNNBL1,RPN2,C20orf102,BLCAP,NNAT,KIAA0406,GHRH,MANBAL,BPI,KIAA1755,SMAF1,LBP U71a,U71b,U71c,U71d,ACA60,ACA39 20 44895.11 45114.26 q13.12 EYA2 20 50785.61 52655.57 q13.2 V_0226_LC19822_Iafrate et al. (2004), V_5142_LC19835_Wong et al. (2007), CYP24A1,PFDN4,ZNF217,TSHZ2,DOK5,BCAS1 V_5143_LC19835_Wong et al. (2007) 20 57579.72 58969.91 q13.32-q13.33 FLJ33860,SYCP2,C20orf177,PHACTR3,CDH26,PPP1R3D hsa-mir-646 20 60442.81 61347.72 q13.33 V_5144_LC19966_Wong et al. (2007), V_5145_LC19985_Wong et al. (2007), BIRC7,NTSR1,YTHDF1,OGFR,COL9A3,C20orf166,FLJ30313,DIDO1,BHLHB4,C20orf11,GATA5,C20orf58,C20orf59,TCFL5,C20orf20,SLCO4A1 hsa-mir-124a-3,hsa-mir-133a-2,hsa-mir-1-1 V_5146_LC19985_Wong et al. (2007), V_5147_LC19985_Wong et al. (2007), V_5148_LC19985_Wong et al. (2007) 20 61862.01 62434.35 q13.33 V_2252_LC19985_Locke et al. (2006) LOC284739,UCKL1,SAMD10,OPRL1,PCMTD2,DNAJC5,SOX18,MYT1,TPD52L2,LOC198437,C20orf135,RGS19,PRPF6,BTBD4,NPBWR2,GM632,TCEA2 hsa-mir-647 21 40644.28 41134.11 q22.2 DSCAM 21 6049.31 6552.44 p12-p11.2 21 7394.21 10457.10 p11.2-p11.1 V_2253_LC20054_Locke et al. (2006), V_5151_LC20054_Wong et al. (2007), TPTE,BAGE,BAGE2,BAGE3,BAGE4,BAGE5 V_5152_LC20054_Wong et al. (2007), V_5153_LC20054_Wong et al. (2007), V_5154_LC20054_Wong et al. (2007), V_5155_LC20054_Wong et al. (2007), V_5156_LC20054_Wong et al. (2007) *: copy number polymorphism according to http://projects.tcag.ca/variation/ Supplementary Table S9

Recurrent amplification in HER2 cancers chromosome start (kb) end (kb) cytoband Copy Number Polymorphism* genes miRNA 1 144960.766 146778.005 q21.1 V_2051_LC0752_Locke et al. (2006), V_4253_LC0752_Wong et al. ACP6,PRKAB2,FMO5,GPR89A,LOC728932,BCL9,PPIAL4,CHD1L,GJA5,GJA8,NBPF10,NBPF11,NBPF14 (2007) 1 149888.055 150485.559 q21.3 RORC,SNX27,HRNR,TCHH,TDRKH,TNRC4,S100A10,S100A11,OAZ3,TCHHL1,MRPL9,LINGO4,THEM4,THEM5 1 157296.031 161891.864 q23.1-q23.3 V_4258_LC0863_Wong et al. (2007), V_4259_LC0863_Wong et al. RGS4,CCDC19,RGS5,UHMK1,KCNJ10,PFDN2,IGSF4B,UAP1,PPOX,DEDD,ARHGAP30,FCRLM1,FCRLM2,FCGR3A,FCGR3B,CD244,ATP1A2,NUF2,ATP1 hsa-mir-556 (2007) A4,SLAMF1,CRP,VSIG8,SLAMF6,SLAMF7,SLAMF8,SLAMF9,NR1I3,HSD17B7,APOA2,IGSF8,PEX19,USF1,IGSF9,SDHC,FCRL6,OR10J1,OR10J3,DUSP12 ,ADAMTS4,OR10J5,PIGM,CD48,COPA,CD84,USP21,KCNJ9,UFC1,HSPA6,PEA15,MPZ,ATF6,FCER1A,VANGL2,TOMM40L,C1orf110,FCER1G,C1orf111,N DUFS2,WDR42A,NIT1,NHLH1,TAGLN2,NOS1AP,SH2D1B,DUSP23,DARC,C1orf192,F11R,CASQ1,NCSTN,AIM2,PVRL4,LY9,FCGR2A,APCS,FCGR2B,KAR CA1,FCGR2C,ITLN1,DDR2,B4GALT3,ITLN2,OLFML2B,FLJ13137 5 2003.467 2937.737 p15.33 IRX2,CEI 6 13204.017 15789.536 p24.1-p22.3 GFOD1,C6orf114,NOL7,CD83,JARID2,TBC1D7,PHACTR1,RANBP9,DTNBP1,SIRT5,RNF182,C6orf79 6 21792.185 22273.386 p22.3 6 51798.982 52237.235 p12.2 IL17,PKHD1,MCM3,IL17F hsa-mir-133b,hsa-mir-206 6 53915.758 54244.979 p12.1 C6orf142 6 64287.458 65092.091 q12 V_0082_LC8431_Iafrate et al. (2004) PHF3,PTP4A1 7 28685.131 30382.206 p15.1 LOC222171,CREB5,KIAA0644,ZNRF2,CHN2,PLEKHA8,WIPF3,FKBP14,C7orf41,SCRN1,CPVL hsa-mir-550-1 7 40489.6 41785.096 p14.1 C7orf10,INHBA 7 79564.067 79960.248 q21.11 GNAI1 8 36652.993 37696.334 p12 FKSG2,ZNF703 8 60170.966 66326.122 q12.1-q13.1 V_4595_LC10619_Wong et al. (2007), V_4596_LC10633_Wong et MGC34646,YTHDF3,GGH,CYP7B1,TTPA,FAM77D,BHLHB5,CA8,ASPH,TOX,RAB2,CHD7 hsa-mir-124a-2 al. (2007), V_4597_LC10634_Wong et al. (2007), V_4598_LC10640_Wong et al. (2007) 8 68653.445 71078.708 q13.2-q13.3 CPA6,C8orf34,SLCO5A1,SULF1,DEPDC2 8 73050.988 74139.885 q13.3-q21.11 KCNB2,TERF1,TRPA1 8 78530.552 85471.531 q21.12-q21.2 V_0119_LC10711_Iafrate et al. (2004) FABP4,FABP5,PAG1,MRPS28,STMN2,IL7,PERF15,CHMP4C,C8orf70,ZBTB10,LOC138046,PKIA,HEY1,LOC389672,ZNF704,PMP2,SNX16,ZFAND1,IMPA1, SLC10A5,TPD52 8 86638.084 86899.501 q21.2 V_0121_LC10727_Iafrate et al. (2004), V_2126_LC10727_Locke et REXO1L1 al. (2006), V_4602_LC10727_Wong et al. (2007), V_4603_LC10727_Wong et al. (2007), V_4604_LC10727_Wong et al. (2007), V_4605_LC10727_Wong et al. (2007) 8 91597.271 91900.901 q21.3 EFCBP1,TMEM64 8 92510.674 92998.43 q21.3 8 93562.085 94731.319 q22.1 V_4607_LC10749_Wong et al. (2007) 8 95030.163 95463.144 q22.1 CDH17,GEM,RAD54B 8 97279.168 102013.982 q22.1-q22.3 PABPC1,HRSP12,UQCRB,POLR2K,COX6C,MATN2,POP1,RNF19,OSR2,STK3,NPAL2,RPL30,FBXO43,MTDH,MGC39715,C8orf47,LAPTM4B,TSPYL5,VPS U72,hsa-mir-599 13B,SPAG1,MTERFD1,RGS22,KCNS2,PTDSS1,ANKRD46,PGCP,SDC2,YWHAZ 8 107896.977 108678.924 q23.1 ANGPT1 8 113395.964 114300.771 q23.3 CSMD3 8 115665.287 117325.269 q23.3 TRPS1 8 119121.45 119659.843 q24.11-q24.12 SAMD12,EXT1 8 123692.681 128894.279 q24.13-q24.21 V_4609_LC10877_Wong et al. (2007) ZNF572,NDUFB9,FAM83A,FBXO32,WDR67,TRIB1,ZHX1,ZHX2,ANXA13,DERL1,TATDN1,C8orf32,C8ORFK23,C8orf36,FAM84B,ATAD2,C8orf76,TMEM65,T hsa-mir-548d-1 RMT12,SQLE,RNF139,FAM91A1,C8ORFK36,MYC,KIAA0196,MTSS1,C8orf54 8 133301.247 134544.029 q24.22 V_0123_LC10906_Iafrate et al. (2004) LRRC6,KCNQ3,ST3GAL1,WISP1,TMEM71,PHF20L1,TG,NDRG1,SLA 8 137195.022 138736.966 q24.23 8 140281.871 140281.871 q24.3 10 3634.505 9342.741 p15.2-p14 ITIH2,CALML3,CALML5,KIN,ITIH5,ANKRD16,GDI2,UCN3,FLJ45983,PRKCQ,C10orf18,AKR1CL1,AKR1CL2,RBM17,PFKFB3,GATA3,IL15RA,NET1,SFMBT2 ,ASB13,KLF6,FBXO18,IL2RA,TUBAL3,ATP5C1,TAF3,AKR1C1,AKR1C2,AKR1C3,AKR1C4 10 70997.379 71427.578 q21.3-q22.1 COL13A1,NEUROG3,C10orf35 10 79599.224 80949.616 q22.3 V_2157_LC12477_Locke et al. (2006), V_2158_LC12478_Locke et C10orf56,PPIF,RAI17 al. (2006), V_4704_LC12478_Wong et al. (2007) 11 48959.449 49499.695 p11.12 FOLH1 11 68909.315 69275.624 q13.2-q13.3 V_4755_LC13316_Wong et al. (2007) ORAOV1,FGF19,CCND1 11 77419.227 79073.35 q14.1 V_0151_LC13373_Iafrate et al. (2004), V_4727_LC13373_Wong et LOC283219,NDUFC2,NARS2,ALG8,THRSP,USP35,ODZ4,GAB2 al. (2007) 11 83780.821 84588.697 q14.1 V_0152_LC13403_Iafrate et al. (2004) DLG2 11 87153.912 89142.924 q14.2-q14.3 GRM5,CTSC,TYR,NOX4,PSMAL,RAB38 11 96651.413 97518.886 q21-q22.1 V_4760_LC13485_Wong et al. (2007) 14 18401.055 19432.768 q11.1-q11.2 V_0812_LC15340_Sharp et al. (2005), V_2174_LC15340_Locke et OR11H12,LOC440157,OR4M1,OR4Q3,OR4N2,OR4K2,POTE14 al. (2006), V_2256_LC15340_Locke et al. (2006), V_4822_LC15340_Wong et al. (2007), V_4823_LC15340_Wong et al. (2007), V_4824_LC15340_Wong et al. (2007), V_4825_LC15340_Wong et al. (2007), V_4826_LC15340_Wong et al. (2007), V_0376_LC15340_Bejjani et al. (2005) 14 21305.621 23025.37 q11.2 V_4828_LC15358_Wong et al. (2007), V_4829_LC15358_Wong et SLC7A7,SLC7A8,PRMT5,SLC22A17,C14orf119,ACIN1,OXA1L,ABHD4,KIAA1443,MYH6,MYH7,JUB,MRPL52,C14orf120,BCL2L2,C14orf93,C14orf94,RBM23 hsa-mir-208 al. (2007), V_4830_LC15358_Wong et al. (2007), ,EFS,CEBPE,CDH24,MMP14,PSMB5,REM2,IL17E,LRP10,DAD1,PABPN1,CMTM5 V_4831_LC15358_Wong et al. (2007) 14 24548.293 25467.867 q12 STXBP6 14 29027.121 30483.789 q12 SCFD1,COCH,PRKD1,KIAA1333,STRN3 14 31203.562 32086.193 q12-q13.1 NUBPL,ARHGAP5,AKAP6 14 32994.149 33813.365 q13.1 NPAS3,EGLN3 14 38193.667 38617.892 q21.1 SEC23A 14 38967.497 39596.531 q21.1 FBXO33 14 63996.811 64415.593 q23.2-q23.3 PLEKHG3,C14orf50,HSPA2,ZBTB1,ZBTB25,SPTB,AKAP5 17 21476.421 21834.063 p11.2 V_4998_LC17406_Wong et al. (2007) FAM27L 17 22755.55 23408.572 q11.1-q11.2 NOS2A,NLK,KSR1,LGALS9,LOC201229 17 23883.212 24707.689 q11.2 FLOT2,PHF12,TLCD1,FLJ25006,C17orf63,TRAF4,NEK8,DHRS13,NUFIP2,TIAF1,KIAA0100,SUPT6H,PROCA1,PIGS,PIPOX,ALDOC,RPL23A,CRYBA1,MYO hsa-mir-144,Z17B,hsa-mir- 18A,ERAL1,SDF2,RAB34,LOC647099,UNC119,SEZ6,SPAG5,FOXN1 451,mgh18S-121,U42A,U42B 17 24958.227 25931.269 q11.2 CORO6,ANKRD13B,CCDC55,TMIGD,SLC6A4,FLJ46247,DKFZP434O047,CPD,GOSR1,SSH2,BLMH hsa-mir-423 17 27772.334 28369.711 q11.2 CDK5R1,TMEM98,SPACA3,PSMD11,MYO1D,ACCN1 17 28709.707 29014.335 q11.2-q12 ACCN1 17 29842.549 30526.826 q12 FLJ44815,FNDC8,LIG3,RAD51L3,UNC45B,CCT6B,TMEM132E,RFFL,CCDC16,NLE1 17 32320.52 32782.607 q12 V_5001_LC17457_Wong et al. (2007) ACACA,AATF,LHX1 17 35114.817 35360.385 q12 GSDML,GRB7,ORMDL3,C17orf37,ZNFN1A3,ZPBP2,ERBB2 17 42833.683 43602.175 q21.32 V_0804_LC17530_Sharp et al. (2005), V_2229_LC17530_Locke et TBKBP1,TBX21,KPNB1,MRPL10,COPZ2,OSBPL7,CBX1,LRRC46,ATAD4,SKAP1,SNX11,PNPO,NPEPPS,CDK5RAP3,NFE2L1,C17orf57,SP2,SP6,SCRN2 hsa-mir-152 al. (2006) 17 44426.91 44978.287 q21.32-q21.33 V_5016_LC17543_Wong et al. (2007) B4GALNT2,ZNF652,PHOSPHO1,GNGT2,ABI3,PHB,NGFR,IGF2BP1 17 45651.88 46041.812 q21.33 V_5017_LC17552_Wong et al. (2007) RSAD1,CHAD,TMEM92,XYLT2,MYCBPAP,MRPL27,EPN3,CACNA1G,SPATA20,LRRC59,FLJ20920,EME1 17 46623.828 47676.819 q21.33-q22 MBTD1,CA10,UTP18 17 48311.159 49205.824 q22 17 50530.395 51204.064 q22 TMEM100,PCTP,HLF,MMD,STXBP4 17 54643.7 54973.48 q22-q23.1 C17orf71,YPEL2,GDPD1 17 55328.115 57089.085 q23.1-q23.2 V_0805_LC17601_Sharp et al. (2005) C17orf64,RPS6KB1,APPBP2,NACAL,TBX2,TBX4,CA4,LOC51136,LOC388407,USP32,PPM1D,BCAS3 ACA66 17 59084.371 59823.3 q23.3 V_0210_LC17626_Iafrate et al. (2004) SCN4A,PSMC5,DDX42,ICAM2,ERN1,CSH1,CSH2,GH1,GH2,CD79B,CSHL1,LYK5,SMARCD2,FTSJ3,PECAM1,MAP3K3,CCDC47,TEX2,LIMD2 U104,ACA62 17 60152.895 60690.169 q24.1 V_2231_LC17631_Locke et al. (2006), V_5022_LC17631_Wong et RGS9,FLJ34306,GNA13 al. (2007), V_5023_LC17631_Wong et al. (2007), V_5024_LC17631_Wong et al. (2007) 17 61323.032 61961.765 q24.1-q24.2 V_5026_LC17636_Wong et al. (2007) APOH,PRKCA,CCDC46 17 64587.775 65137.747 q24.2-q24.3 MAP2K6,ABCA5,ABCA6,ABCA10 17 69072.958 69607.17 q25.1 C17orf54 17 73048.388 73582.063 q25.3 TNRC6C,FLJ45079 17 60312.211 60690.169 q24.1 V_2231_LC17631_Locke et al. (2006), V_5022_LC17631_Wong et RGS9,FLJ34306,GNA13 al. (2007), V_5023_LC17631_Wong et al. (2007), V_5024_LC17631_Wong et al. (2007) 17 61323.032 62428.764 q24.1-q24.2 V_2232_LC17640_Locke et al. (2006), V_5026_LC17636_Wong et APOH,PRKCA,CACNG4,CACNG5,CCDC46 hsa-mir-634 al. (2007), V_5027_LC17640_Wong et al. (2007) 17 63854.918 65137.747 q24.2-q24.3 MAP2K6,WIPI1,ARSG,ABCA5,ABCA6,ABCA8,ABCA9,ABCA10,FAM20A,PRKAR1A hsa-mir-635 17 65852.467 66316.735 q24.3 17 69072.958 69607.17 q25.1 C17orf54 17 73048.388 73582.063 q25.3 TNRC6C,FLJ45079 19 58419.319 58762.948 q13.41 BIRC8,ZNF761,ZNF331,LOC91661,ZNF813,ZNF677,VN1R2,VN1R4 21 41851.41 42511.469 q22.3 PRDM15,ABCG1,ZNF295,RIPK4,UMODL1,C21orf25,C21orf129 21 43378.009 43933.917 q22.3 SNF1LK,FLJ41733,HSF2BP,KIAA0179,CRYAA,U2AF1 22 14440.103 15254.802 q11.1 V_0813_LC20342_Sharp et al. (2005), V_2257_LC20342_Locke et ACTBL1,OR11H1 al. (2006), V_4821_LC20342_Wong et al. (2007), V_5164_LC20342_Wong et al. (2007), V_5165_LC20342_Wong et al. (2007), V_5166_LC20342_Wong et al. (2007) 22 19847.992 20261.795 q11.21 V_0816_LC20342_Sharp et al. (2005), V_0817_LC20342_Sharp et LOC375133,LOC220686,UBE2L3,HIC2 al. (2005), V_2262_LC20342_Locke et al. (2006), V_2263_LC20342_Locke et al. (2006), V_5170_LC20342_Wong et al. (2007), V_5171_LC20342_Wong et al. (2007), V_5172_LC20342_Wong et al. (2007), V_5173_LC20342_Wong et al. (2007) *: copy number polymorphism according to http://projects.tcag.ca/variation/