Volume 10, Issue 6, Pages 529-541 (December 2006) Genomic and transcriptional aberrations linked to breast cancer pathophysiologies  Koei Chin, Sandy DeVries, Jane Fridlyand, Paul T. Spellman, Ritu Roydasgupta, Wen-Lin Kuo, Anna Lapuk, Richard M. Neve, Zuwei Qian, Tom Ryder, Fanqing Chen, Heidi Feiler, Taku Tokuyasu, Chris Kingsley, Shanaz Dairkee, Zhenhang Meng, Karen Chew, Daniel Pinkel, Ajay Jain, Britt Marie Ljung, Laura Esserman, Donna G. Albertson, Frederic M. Waldman, Joe W. Gray  Cancer Cell  Volume 10, Issue 6, Pages 529-541 (December 2006) DOI: 10.1016/j.ccr.2006.10.009 Copyright © 2006 Elsevier Inc. Terms and Conditions

Figure 1 Recurrent abnormalities in 145 primary breast tumors A: Frequencies of genome copy number gain and loss plotted as a function of genome location with chromosomes 1pter to the left and chromosomes 22qter and X to the right. Vertical lines indicate chromosome boundaries, and vertical dashed lines indicate centromere locations. Positive and negative values indicate frequencies of tumors showing copy number increases and decreases, respectively, with gain and loss as described in the Experimental Procedures. B: Frequencies of tumors showing high-level amplification. Data are displayed as described in A. C–J: Frequencies of tumors showing significant copy number gains and losses as defined in A (upper member of each pair) or high-level amplifications as defined in B (lower member of each pair) in tumor subtypes defined according to expression phenotype; C and D, basal-like; E and F, ERBB2; G and H, luminal A; I and J, luminal B. Data are displayed as described in A. Cancer Cell 2006 10, 529-541DOI: (10.1016/j.ccr.2006.10.009) Copyright © 2006 Elsevier Inc. Terms and Conditions

Figure 2 Unsupervised hierarchical clustering of genome copy number profiles measured for 145 primary breast tumors Green indicates increased genome copy number, and red indicates decreased genome copy number. The three major genomic clusters from left to right are designated 1q/16q, complex, and amplifying. The bar to the left indicates chromosome locations with chromosome 1pter to the top and 22qter and X to the bottom. The locations of the odd-numbered chromosomes are indicated. The upper color bars indicate biological and clinical aspects of the tumors. Color codes are indicated at the bottom of the figure. Dark blue indicates positive status, and light blue indicates negative status for node, ER, PR, and p53 expression. For Ki67, dark blue indicates fraction >0.1, and light blue indicates fraction <0.1. For size, light blue indicates size <2.2 cm, and dark blue indicates size >2.2 cm. Color codes for the expression bar are as follows: orange, luminal A; dark blue, normal breast-like; light blue, ERBB2; green, basal-like; yellow, luminal B. Cancer Cell 2006 10, 529-541DOI: (10.1016/j.ccr.2006.10.009) Copyright © 2006 Elsevier Inc. Terms and Conditions

Figure 3 Kaplan-Meyer plots showing survival in breast tumor subclasses A: Disease-specific survival in 130 breast cancer patients whose tumors were defined using expression profiling to be basal-like (green curve), luminal A (yellow curve), luminal B (orange curve), and ERBB2 (purple curve) class. B: Disease-specific survival of patients with tumors classified by genome copy number aberration analysis as 1q/16q (green), complex (red), and amplifying (blue). C: Survival of patients with (red curve) and without (green curve) amplification at any region of recurrent amplification. D: Survival of patients whose tumors were defined using expression profiling to be luminal A tumors with (red curve) and without (green curve) amplification at 8p11-12, 11q13, and/or 20q. E: Survival of patients whose tumors were not amplified at 8p11-12 and had normal (green curve) or reduced (red curve) genome copy number at 8p11-12. F: Survival of patients whose tumors had normal (green curve) or abnormal (red curve) genome copy number at 8p11-12. Cancer Cell 2006 10, 529-541DOI: (10.1016/j.ccr.2006.10.009) Copyright © 2006 Elsevier Inc. Terms and Conditions

Figure 4 Results of unsupervised hierarchical clustering of 130 breast tumors using intrinsically variable gene expression but excluding any transcripts whose levels were significantly associated with genome copy number Red indicates increased expression, and green indicates reduced expression. An annotated version is provided as Figure S3. Cancer Cell 2006 10, 529-541DOI: (10.1016/j.ccr.2006.10.009) Copyright © 2006 Elsevier Inc. Terms and Conditions