Array CGH analysis of breast carcinoma both on BAC array and on oligo array had previously highlighted the genomic heterogeneity of these tumors. The most popular classification distinguishes three classes of tumors. The first one, characterized by only few rearrangements is called “simplex” [1, 27] or “1q/16q” [28, 29], the second, called “complex sawtooth” [27, 30] or “complex” [28, 29], is characterized by a large number of rearrangements, including breakpoints and copy number variations for very small genomic segments. The third one called “complex firestorm” [27, 30] or “mixed amplifier”, [28, 29] is characterized by a phenomenon of gene amplification with a high copy number variation restricted to small genomic regions. Indeed, it is possible to allocate some specific tumors to such a class of genomic profiles and for example, tumor number 83 in our series showed a simplex profile with only a 1q gain and 11q and 16 q losses as sole rearrangements, tumor number 43 showed a typical complex sawtooth profile, and tumor number 100 a mixed amplifier profile. However, a large number of tumors in our series showed intermediary patterns and it was not possible to assign them to a specific class. For example, tumor number 7 showed a relatively flat profile with several amplicons on chromosomes 6 and 17 and tumor number 47 showed an intermediary profile between simplex and complex sawtooth.
In fact, three kinds of genomic rearrangements related to various kinds of genetic instability are detectable by array CGH methodologies. They are: i) whole chromosomal or whole chromosomal arm aneusomies related respectively to mitotic malsegregation or centromeric rearrangement, ii) DNA breakpoints with repair defects resulting in copy number variation for short genomic segments and iii) gene amplification. These three kinds of genomic rearrangements are more or less associated in a single tumor and show a continuous variation with a growing level of intensity from one tumor to another. Thus, a true classification based on genomic alteration criteria remains difficult to implement. The results obtained here suggest that it is possible to distinguish between two groups of tumors. One group shows gain or loss of entire chromosomes or entire chromosomal arms but lack breakpoint within the affected regions. This group corresponds to tumors from the clusters b to e which are characterized by combinations of specific rearranged chromosomal arms. The second group corresponds to tumors from the clusters a and f for which it is not possible to identify a copy number variation affecting an entire chromosome arm, either because of a flat profile (cluster a) or because of a huge number of DNA breakpoints (cluster f). In order to take into account this distinction, we constructed a genomic index based on two parameters representing these two kinds of alterations and showing a continuous distribution of the tumors with a growing level of alterations (Figure 3). Adverse outcome was observed for the most highly rearranged genotypes, corresponding mainly to tumors from clusters e and f.
The transcriptomic intrinsic classification of breast cancer  has led to search for correlations between the Sorlie classes and specific genomic profiles. It was effectively possible to correlate the luminal A class with the simplex profile, the luminal B and the Her2-enriched classes with the amplifier profile and the basal-like class with the complex sawtooth profile [1, 28, 31]. Moreover, a new classification into six classes taking into account these correlations was recently proposed . Such a correlation was also found here between immunohistochemical intrinsic classes and genomic profile. Both the G2I-1 group and the cluster b (1q gain, 16q loss) are mainly composed of luminal A tumors (84% and 80%, respectively). The majority of the tumors belonging to luminal B and Her2-enriched classes show gene amplifications (79% and 90%, respectively). Some results, conversely, are more surprising. If percentages of luminal A tumors decrease progressively from the G2I-1 to the G2I-2 and G2I-3 groups (respectively, 84%, 62.5% and 43%), the fact that 12 luminal A tumors belong to the G2I-3 group was not expected. In the same way, it is surprising that seven of twelve cluster f tumors belong to the luminal A class. Seven tumors belong to the basal-like class. Only one of them appears in the cluster f and in the G2I-3 group. The six other basal-like tumors all belong to the G2I-2 group and to the array CGH cluster a. This cluster, without any specific chromosomal aneusomy, contains in fact two subgroups (Figure 1). The first one (right branch) shows tumors with a flat profile belonging mainly to the luminal A class. The second one (left branch) including the six basal-like tumors shows tumors without chromosomal or chromosomal arm aberrations but with copy number changes affecting small genomic regions that are different from one tumor to another. This profile corresponds to the previously described subtype of high grade ER-negative tumors with low genomic instability index . The fact that six out of seven basal-like tumors did not show metastatic relapse is probably related to a series effect with a small number of cases. It therefore seems that some breast carcinomas of luminal A and luminal B phenotypes, showing important genetic instability with a large number of DNA breakpoints, frequent TP53 mutations, and frequent gene amplification are characterized by very poor outcome.
Prognostic value of genomic alteration in breast cancer has often been reported. Cytogenetic analysis had previously shown the correlation between the unbalanced der(1;16) and good prognosis , whereas homogeneously staining regions or gene amplifications were correlated with poor outcome [35, 36]. These results were confirmed by array CGH approaches that show associations between gene amplification in Her2-enriched and luminal B classes [28, 31, 37, 38], and poor prognosis or between 16q loss in luminal A tumors and good prognosis . Subsequently, copy number variation concerning various genomic regions was shown to be related to outcome as loss on chromosome arms 19 and 18q  or more complex signatures including several regions, either distinct for ER positive and negative tumors , or common for these two kind of tumors . The measurement of genetic instability was not so well documented. A signature of chromosome instability was inferred from transcriptomic data as functional aneuploidy related to a clear deviation in expression of contiguous genes from the same loci . The application of this signature to four different published sets of breast cancer was highly predictive of outcome . The fraction of the genome altered (FGA), calculated as the number of probes affected by gain or loss compared to the total number of probes represented on the array , was shown to correlate with the classification proposed by Jonsson et al. in which a higher level of FGA was observed for “basal complex” and “luminal complex” types of tumors than for the others . The FGA after correction for tumoral cellularity and named “genome instability index” (GII) fails to find such a correlation but identified a subtype of basal like tumor with low instability . In association with a three chromosomal region predictor, the CGH classifier proposed by Gravier et al. in node negative breast cancer used a measurement of genomic complexity corresponding after segmentation to the total number of segmental alterations along the genome with a threshold of 11. Using this single parameter, the prediction of metastatic relapse was highly significant (p = 0.00056) . Recently, an array CGH-based score of genomic complexity called CAAI (Complex arm aberration index) was shown to have overall independent prognostic power . All these data indicate that the type and the level of genetic instability are major determinants of outcome for breast cancer. These characteristics are probably set up very early during tumor development, conserved at late stages and common to any tumoral cell. They can be detected at the level of a primary tumor, even if only some cell clones will acquire metastatic power. The same explanation could be offered for the prognostic significance of transcriptomic signatures obtained from primary tumors that have been shown to be mainly related to the proliferative activity of the tumors .
From a clinical point of view, it is interesting to note that the prognostic value of the G2I is independent of other major prognostic factors except TP53 mutation (Table 5). A faint correlation is also found with others genomic alterations (in particular, the presence of amplicons), with the intrinsic classification and with Mib1 index but not for classical clinico-pathological parameters (Table 5). Moreover, the G2I maintains a strong predictive value in subclasses of tumors showing variable outcomes, such as small tumors, SBR grade 2 and 3 tumors, hormonal receptors positive tumors and tumors in the moderate class of the NPI. These data are in favour of an independent prognostic value for the G2I but evaluation of the benefit in clinical practice will require better definition of the thresholds used to define the groups and validation on an unselected population-based set of tumors. These investigations are currently in progress. The main result concerns the strong predictive value of the G2I in tumors without axillary lymph node involvement since 80% of G2I3 node negative tumors (16 out of 20) relapsed, whereas only 16% of the G2I-1 and G2I-2 node negative tumors (9 out of 55) did so (OR: 17.5 [4.6-66.7] p < 0.001). This information could have major implications for the indication of adjuvant therapies. The paradox of a poor outcome for tumors that do not show any evidence of lymphatic dissemination at the time of local treatment may suggest that these tumors with high genetic instability are not lymphophilic, instead showing a hematogenic mode of diffusion.