Additional file 3 of Breast tumors from CHEK2 1100delC- mutation carriers: genomic landscape and clinical implications

Additional file 3: Unsupervised clustering of array-comparative genomic hybridization (aCGH) and gene-expression (GEX) data. Left, aCGH samples do not cluster according to any of the covariates. Instead, the clustering is based on informative genomic regions and tumors' overall copy-number profiles. Right, unsupervised hierarchical clustering of gene-expression data suggests that estrogen receptor (ER) status and family history of breast cancer have an impact on the tumor's gene-expression profile. The effect of the other variables is likely to be smaller. Replicates that were used as a quality control cluster together as expected. Positions of CHEK2 (checkpoint kinase 2), 1100delC-mutation carrier and control (contr) tumors are indicated by the uppermost color block. NQO1- and NQO1+ stand for samples with germline rs1800566 genotypes: homozygotes of the more common allele (CC) and heterozygotes or homozygotes of the rarer allele (CT or TT), respectively. Frequency of copy-number changes along the genome is depicted with a color scale from blue to red. Blue, few; red, frequent copy-number aberrations. (PDF 115 KB)