Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics

Abstract

Introduction: Breast cancer is a profoundly heterogeneous disease with respect to biologic and clinical behavior. Gene-expression profiling has been used to dissect this complexity and to stratify tumors into intrinsic gene-expression subtypes, associated with distinct biology, patient outcome, and genomic alterations. Additionally, breast tumors occurring in individuals with germline BRCA1 or BRCA2 mutations typically fall into distinct subtypes.

Methods: We applied global DNA copy number and gene-expression profiling in 359 breast tumors. All tumors were classified according to intrinsic gene-expression subtypes and included cases from genetically predisposed women. The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was used to identify significant DNA copy-number aberrations and genomic subgroups of breast cancer.

Results: We identified 31 genomic regions that were highly amplified in > 1% of the 359 breast tumors. Several amplicons were found to co-occur, the 8p12 and 11q13.3 regions being the most frequent combination besides amplicons on the same chromosomal arm. Unsupervised hierarchical clustering with 133 significant GISTIC regions revealed six genomic subtypes, termed 17q12, basal-complex, luminal-simple, luminal-complex, amplifier, and mixed subtypes. Four of them had striking similarity to intrinsic gene-expression subtypes and showed associations to conventional tumor biomarkers and clinical outcome. However, luminal A-classified tumors were distributed in two main genomic subtypes, luminal-simple and luminal-complex, the former group having a better prognosis, whereas the latter group included also luminal B and the majority of BRCA2-mutated tumors. The basal-complex subtype displayed extensive genomic homogeneity and harbored the majority of BRCA1-mutated tumors. The 17q12 subtype comprised mostly HER2-amplified and HER2-enriched subtype tumors and had the worst prognosis. The amplifier and mixed subtypes contained tumors from all gene-expression subtypes, the former being enriched for 8p12-amplified cases, whereas the mixed subtype included many tumors with predominantly DNA copy-number losses and poor prognosis.

Conclusions: Global DNA copy-number analysis integrated with gene-expression data can be used to dissect the complexity of breast cancer. This revealed six genomic subtypes with different clinical behavior and a striking concordance to the intrinsic subtypes. These genomic subtypes may prove useful for understanding the mechanisms of tumor development and for prognostic and treatment prediction purposes.

Figure 1

Copy-number alterations (CNAs) observed in 359 breast cancers. Blue regions indicate positions of significant genomic aberrations (n = 133) identified by Genomic Identification of Significant Targets in Cancer (GISTIC) analysis. Green corresponds to loss, and red, to gain. Most common CNAs are observed on chromosomes 1q, 8p, 8q, 11q, and 16q, as indicated in the figure.

Figure 2

High-level amplifications in breast cancer (BC). (a) Coamplification patterns in BC. For each amplification (vertical axis), the fraction of samples with a coamplification (horizontal axis) is indicated in each box. Coamplification fractions smaller than 20% are excluded: for example, 30% of all 12q15-amplified samples also have 8p12 amplification, whereas the fraction of 8p12-amplified samples with 12q15 amplification is < 0.2 and is not displayed. (b) Overview of the coamplification pattern in chromosomes 8p12, 11q13, and 12q15. Amplification pattern is also evident on a gene-expression level, where a number of genes show a significant relation to gene-dosage effects.

Figure 3

Unsupervised analysis of Genomic Identification of Significant Targets in Cancer (GISTIC) regions identifies six CGH subgroups of breast cancer (BC) associated with different clinical and molecular characteristics. (a) Hierarchic clustering of 133 GISTIC regions identifies six subtypes with different clinical and molecular characteristics, and genomic aberrations. Horizontal dashed line for S-phase indicates the average across all samples. (b) Fraction of the genome altered (FGA) for genomic subtypes indicating that basal-complex samples are genomically unstable, whereas luminal-simple tumors are genomically stable. (c) Overall survival (OS) for 339 patients, for whom primary tumors were available, classified according to genomic subtypes, mirrors results obtained for the intrinsic gene-expression subtypes.

Figure 4

Supervised analysis in luminal genomic subtypes. (a) Significant Genomic Identification of Significant Targets in Cancer (GISTIC) regions between BRCA2-mutated and non-BRCA2 tumors within the luminal-complex subtype. (b) Significant GISTIC regions between the luminal-complex and luminal-simple subtypes. (c) Distant metastasis-free survival (DMFS) for luminal A tumors stratified by classification as luminal-simple or non-luminal-simple in a combined Affymetrix gene-expression data set. Significant GISTIC regions were identified by Bonferroni-adjusted Student t test (P < 0.05); red indicates more-frequent gain, and green indicates more-frequent loss, in comparisons between GISTIC regions. Only significant regions with ≥20% CNA frequency are displayed.