Quantitative copy number analysis by Multiplex Ligation-dependent Probe Amplification (MLPA) of BRCA1-associated breast cancer regions identifies BRCAness

• Published in: Breast cancer research : BCR Vol. 13; no. 5; p. R107
• Main Authors: Lips, Esther H, Laddach, Nadja, Savola, Suvi P, Vollebergh, Marieke A, Oonk, Anne MM, Imholz, Alex LT, Wessels, Lodewyk FA, Wesseling, Jelle, Nederlof, Petra M, Rodenhuis, Sjoerd
• Format: Journal Article
• Language: English
• Published: London BioMed Central 27.10.2011; BioMed Central Ltd
• Subjects: Biomedical and Life Sciences; Biomedicine; BRCA mutations; BRCA1 Protein - genetics; Breast cancer; Breast Neoplasms - drug therapy; Breast Neoplasms - genetics; Cancer Research; Comparative Genomic Hybridization; Female; Gene Dosage; Genetic aspects; Humans; Identification and classification; Mutation; Nucleic Acid Amplification Techniques - methods; Oncology; Predictive Value of Tests; Reagent Kits, Diagnostic; Research Article; Surgical Oncology; BRCA1 Mutation Carrier; Sporadic Breast Cancer; Conventional Dose Chemotherapy; BRCA1 Promoter Methylation; Clinical Genetic Testing
• ISSN: 1465-542X; 1465-5411; 1465-542X
• DOI: 10.1186/bcr3049

Introduction Our group has previously employed array Comparative Genomic Hybridization (aCGH) to assess the genomic patterns of BRCA1-mutated breast cancers. We have shown that the so-called BRCA1-like aCGH profile is also present in about half of all triple-negative sporadic breast cancers and is predictive for benefit from intensified alkylating chemotherapy. As aCGH is a rather complex method, we translated the BRCA1 aCGH profile to a Multiplex Ligation-dependent Probe Amplification (MLPA) assay, to identify both BRCA1-mutated breast cancers and sporadic cases with a BRCA1-like aCGH profile. Methods The most important genomic regions of the original aCGH based classifier (3q22-27, 5q12-14, 6p23-22, 12p13, 12q21-23, 13q31-34) were mapped to a set of 34 MLPA probes. The training set consisted of 39 BRCA1-like aCGH breast cancers and 45 non-BRCA1-like aCGH breast cancers, which had previously been analyzed by aCGH. The BRCA1-like aCGH group consisted of germline BRCA1-mutated cases and sporadic tumours with low BRCA1 gene expression and/or BRCA1 promoter methylation. We trained a shrunken centroids classifier on the training set and validation was performed on an independent test set of 40 BRCA1-like aCGH breast cancers and 32 non-BRCA1-like aCGH breast cancer tumours. In addition, we validated the set prospectively on 69 new triple-negative tumours. Results BRCAness in the training set of 84 tumours could accurately be predicted by prediction analysis of microarrays (PAM) (accuracy 94%). Application of this classifier on the independent validation set correctly predicted BRCA-like status of 62 out of 72 breast tumours (86%). Sensitivity and specificity were 85% and 87%, respectively. When the MLPA-test was subsequently applied to 46 breast tumour samples from a randomized clinical trial, the same survival benefit for BRCA1-like tumours associated with intensified alkylating chemotherapy was shown as was previously reported using the aCGH assay. Conclusions Since the MLPA assay can identify BRCA1-deficient breast cancer patients, this method could be applied both for clinical genetic testing and as a predictor of treatment benefit. BRCA1-like tumours are highly sensitive to chemotherapy with DNA damaging agents, and most likely to poly ADP ribose polymerase (PARP)-inhibitors. The MLPA assay is rapid and robust, can easily be multiplexed, and works well with DNA derived from paraffin-embedded tissues.