Figure 2

Identification of two invasive macropapillary carcinoma genomic subgroups. (A) Unsupervised hierarchical clustering of 39 (IMPC) tumours using Affymetrix Genome-Wide Human SNP 6.0 Array data with Partek software. Each column represents a different tumour, and each row represents single-nucleotide polymorphism (SNP) status (green for losses, red for gains and/or amplifications). Colour coding in lines above the dendrogram: black in top row = Oestrogen receptor–positive (ER+); pink = ERBB2 amplification; brown = ERBB2 overexpression; green = Lymph node metastasis (N+); blue = Lymphovascular invasion–positive (LVI+); pale grey = grade 1; dark grey = grade 2; black in bottom row = grade 3. (B) Frequencies of genome copy number gains and losses plotted as a function of genome location in “Sawtooth/8/16” IMPC (upper panel) and “Firestorm/Amplifier” IMPC (middle panel). Gains and losses are displayed above or below the blue line, respectively, from chromosome 1pter on the left to chromosome Xq on the right. Alternating grey and white bands indicate chromosome boundaries. The regions exhibiting significantly more frequent gains or losses between “Sawtooth/8/16” IMPC and “Firestorm/Amplifier” IMPC are indicated above and below the frequency plots, respectively. Frequency of loss of heterozygosity (LOH) of chromosome 6q assessed on the basis of Affymetrix Genome-Wide Human SNP 6.0 Array profiles observed in the tumours presenting a deletion of the chromosome 6 long arm. The minimal region of deletion is highlighted. cent, Centromere; tel, Telomere. (C) Real-time PCR results of relative expression of SEC63 and FOXO3 genes in samples of IMPC without (n = 6; dark-grey diamond) and with (n = 9; light-grey diamond) chromosome 6q deletion and in invasive ductal carcinoma of no special type (IDC-NST) (n = 11; circle) (in red: median relative value/Tata Binding Protein). w/o, without; w, with. *P ≤ 0.05, **P ≤ 0.001. (D) Summary of the common and distinct genomic alterations between IMPC genomic subgroups and ER+ IDC-NSTs.