Recurrent copy number alterations inBRCA1-mutated ovarian tumors alter biological pathways

Array CGH was used to identify recurrentcopy number alterations (RCNA) characteristic of eitherBRCA1-related or sporadic ovarian cancer. After pre-processing, both groups of patients were modeled using arecurrent Hidden Markov Model to detect RCNA.RCNA with a probability higher than 80% were called.After removing RCNA present in both groups, the genespresent in the remaining RCNA were investigated forenrichment of pathways from external databases. MoreRCNA were observed in the BRCA1 group, and theydisplay more losses than gains compared to the sporadicgroup. When focusing on the type of RCNA, nosignificant difference in length was seen for the gains,but there was a statistically significant difference for thelosses. In the sporadic group, a great proportion of thealtered regions contain genes known to have a function incell adhesion and complement activation, whereas theBRCA1 samples are characterized by alterations in theHOX genes, metalloproteinases, tumor suppressor genes,and the estrogen-signaling pathways. We conclude thatBRCA1 ovarian tumors present a different type, number,and length of RCNA; a huge amount of the genome islost, resulting in important genomic instability. Moreover,important biological pathways are altered differentiallywhen compared to the sporadic group.Hum Mutat 30:1693–1702,2009. &2009 Wiley-Liss, Inc.KEY WORDS: array CGH; BRCA1; ovarian cancer;hidden Markov model; recurrent copy number alterations