Adenoid cystic carcinomas constitute a genomically distinct subgroup of triple‐negative and basal‐like breast cancers

Adenoid cystic carcinoma (AdCC) is a rare form of triple‐negative and basal‐like breast cancer that has an indolent clinical behaviour. Four breast AdCCs were recently shown to harbour the recurrent chromosomal translocation t(6;9)(q22–23;p23–24), which leads to the formation of the MYB–NFIB fusion gene. Our aims were (i) to determine the prevalence of the MYB–NFIB fusion gene in AdCCs of the breast; (ii) to characterize the gene copy number aberrations found in AdCCs; and (iii) to determine whether AdCCs are genomically distinct from histological grade‐matched or triple‐negative and basal‐like invasive ductal carcinomas of no special type (IDC‐NSTs). The presence of the MYB–NFIB fusion gene was investigated in 13 AdCCs of the breast by fluorescence in situ hybridization (FISH) and reverse transcriptase‐PCR (RT‐PCR), and MYB and BRCA1 RNA expression was determined by quantitative RT‐PCR. Fourteen AdCCs, 14 histological grade‐matched IDC‐NSTs, and 14 IDC‐NSTs of triple‐negative and basal‐like phenotype were microdissected and subjected to high‐resolution microarray‐based comparative genomic hybridization (aCGH). The MYB–NFIB fusion gene was detected in all but one AdCC. aCGH analysis demonstrated a relatively low number of copy number aberrations and a lack of recurrent amplifications in breast AdCCs. Contrary to grade‐matched IDC‐NSTs, AdCCs lacked 1q gains and 16q losses, and in contrast with basal‐like IDC‐NSTs, AdCCs displayed fewer gene copy number aberrations and expressed MYB and BRCA1 at significantly higher levels. Breast AdCCs constitute an entity distinct from grade‐matched and triple‐negative and basal‐like IDC‐NSTs, emphasizing the importance of histological subtyping of triple‐negative and basal‐like breast carcinomas. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.