Jung et al. BMC Cancer 2012, 12:382 http://www.biomedcentral.com/1471-2407/12/382 Page 5 of 11 Table 2 Recurrently altered regions in 48 breast cancer specimens RARs Chr Map position Size Cytoband P- value Freq Freq (Mp) (Mp) (Total) (S-I) RAR-G1 1 143,83-144,30 0.47 q21.1 0.04 48% 36% Freq Event* Cancer-related genes (S-II) 51% Earlier TXNIP RAR-G12 16 28,32-31,19 RAR-G2 RAR-G3 RAR-G4 RAR-G5 RAR-G6 RAR-G7 RAR-G8 RAR-G9 RAR-G10 8 RAR-G11 16 RAR-G13 17 RAR-G14 17 RAR-G15 17 RAR-G16 20 RAR-G17 20 RAR-G18 20 RAR-L1 RAR-L2 RAR-L3 RAR-L4 RAR-L5 1 1 1 1 6 8 8 8 8 8 8 16 17 148,12-150,25 150,75-155,11 158,48-159,47 226,10-226,90 64,05-64,75 123,47-124,74 126,23-127,30 140,69-143,86 144,34-146,27 0-3,22 34,97-35,30 70,76-71,21 76,90-78,77 43,84-44,15 60,17-61,61 61,67-62,44 8,14-14,07 15,66-17,12 24,01-26,72 75,79-80,74 10,54-14,10 2.13 4.36 0.99 0.80 0.70 1.27 1.07 3.17 1.93 3.22 2.87 0.33 0.45 1.87 0.31 1.44 0.77 5.93 1.44 2.71 4.95 3.56 q21.2-q21.3 q21.3-q23.1 q23.2-q23.3 q24.13-q24.21 q24.13 q12 q24.13 q24.3 q24.3 p13.3 p11.2 q12 q25.1 q25.3 q13.12 q13.33 q13.33 p23.1-p22 p22 p21.2 q23.1-q23.3 p13.1-p12 0.01 0.04 0.04 0.04 0.00 0.02 0.02 0.02 0.02 0.05 0.05 0.03 0.03 0.03 0.00 0.04 0.04 0.00 0.02 0.02 0.00 0.04 50% 48% 48% 48% 38% 50% 50% 50% 50% 38% 40% 38% 38% 38% 33% 31% 31% 50% 48% 48% 33% 44% 36% 36% 45% 45% 45% 36% 36% 36% 36% 27% 36% 36% 9% 9% 18% 18% 27% 36% 36% 36% 27% 27% 54% 51% 49% 49% 35% 54% 54% 54% 54% 41% 41% 38% 46% 46% 38% 35% 32% 54% 51% 51% 35% 49% UC Earlier Later Later UC UC UC* UC UC Earlier Earlier MCL1, CTSK, ARNT, SETDB1, SELENBP1, S100A10 CREB3L4, TPM3, HAX1, IL6R, PYGO2, SHC1, CKS1B, NES, ADAM15, EFNA1, MUC1, YY1AP1, ARHGEF2, RAB25, CCT3, CRABP2, HDGF, PRCC Earlier F11R, USF1 Earlier WNT9A, WNT3A Earlier - Earlier FAM83A Earlier - Earlier PTK2, PTP4A3, PSCA, LYNX1 Earlier SCRIB, HSF1, SLCA4 MPG, AXIN1, RHOT2, STUB1, MSLN, CACNA1H, IGFALS, GFER, TSC2, PDPK1, MMP25 NUPR1, SULT1A2, SULT1A1, MVP, MAPK3, FUS, PYCARD Earlier PPP1R1B, PNMT, PERLD1, ERBB2, GRB7 HGS, SIRT7, RAC3, FASN, CSNK1D ADRM1, LAMA5, NTSR1, BIRC7, EEF1A2 GRB2 UBE2C, MMP9 TNFRSF6B Earlier CLDN23, PINX1, GATA4, NEIL2, FDFT1, CTSB, DLC1 Earlier TUSC3, MSR1, FGF20 Earlier ADAM28, GNRH1, PPP2R2A, ADRA1A WWOX, DYNLRB2, PLCG2, HSD17B2 MAP2K4, ELAC2 RAR-G: RAR-gain, RAR-L: RAR-loss, Chr: chromosome, Freq: frequency, S-I: stage I, S-II: stage II. Cancer-related genes: Among all RefSeq genes located in the RARs, the genes which can be searched by the keyword “Cancer/Tumor” from NCBI Gene (http://www.ncbi.nlm.nih.gov/gene) are listed as “cancer-related genes”. *Earlier: RARs detected commonly in both stage I and II groups, Later: RARs appearing in <10% of stage I samples, but in >40% of stage II samples, UC: unclassified. TNFRSF6B genes are located in the RAR-Gs while the PPP2R2A, WWOX, TUSC3, MAP2K4, and ELAC2 genes are located in the RAR-Ls (Table 2). High-level CNAs in EBC Of the CNAs identified in our EBC specimens, 191 loci were determined to be high-level CNAs (defined as ≥ 1.5 for amplification or ≤ −1.5 for HD on the log2 scale), with 158 amplifications and 33 HDs (Additional file 1: Table S3). Of the 158 amplifications, 5 were detected in over 10% of the samples: 1q21.3, 8q24.22, 8q24.3, 16p11.2, and 17q12 (Table 3). These five relatively common amplifications overlapped with earlier event RAR-Gs. Amplification on 17q12, where the EBBB2 oncogene is located, was the most frequent occurrence (14/48, 29%), followed by amplification on 1q21.3 and 8q24.22 (both 9/ 48, 19%), where the LCE families and MYC gene are located, respectively. Examples of high copy number changes are illustrated in Figure 3. There was no HD detected in over 10% of the samples. Association of RARs with clinicopathologic features Five clinical variables (age at diagnosis, stage, ER status, PR status, and HER2 status) were analyzed to assess their association with RARs (see Additional file 1). Only RAR-L4 was significantly associated with ER-positivity (P < 0.0001, FDR-corrected P = 0.015) (Additional file 1: Table S4). When we observed the distribution of the RARs by molecular subtypes (Luminal A, Luminal B, HER2 and TNBC), only RAR-G13 was differently distributed among the subtypes (P = 1.77 × 10-4) (Additional file 1: Table S5).