Najim Ameziane

This study identifies and characterizes a novel type of splicing mutation in RAD50 deficiency, a rare genetic disorder.

Introduction: BRCA1‐mutated breast carcinomas may have distinct biological features, suggesting the involvement of specific oncogenic pathways in tumor development. The identification of genomic aberrations characteristic for BRCA1‐mutated breast carcinomas could lead to a better understanding of BRCA1‐associated oncogenic events and could prove valuable in clinical testing for BRCA1‐involvement in patients.Methods: For this purpose, genomic and gene expression profiles of basal‐like BRCA1‐mutated breast tumors (n = 27) were compared with basal‐like familial BRCAX (non‐BRCA1/2/CHEK2*1100delC) tumors (n = 14) in a familial cohort of 120 breast carcinomas.Results: Genome wide copy number profiles of the BRCA1‐mutated breast carcinomas in our data appeared heterogeneous. Gene expression analyses identified varying amounts of tumor infiltrating lymphocytes (TILs) as a major cause for this heterogeneity. Indeed, selecting tumors with relative low amounts of TILs, resulted in the identification of three known but also five previously unrecognized BRCA1‐associated copy number aberrations. Moreover, these aberrations occurred with high frequencies in the BRCA1‐mutated tumor samples. Using these regions it was possible to discriminate BRCA1‐mutated from BRCAX breast carcinomas, and they were validated in two independent cohorts. To further substantiate our findings, we used flow cytometry to isolate cancer cells from formalin‐fixed, paraffin‐embedded, BRCA1‐mutated triple negative breast carcinomas with estimated TIL percentages of 40% and higher. Genomic profiles of sorted and unsorted fractions were compared by shallow whole genome sequencing and confirm our findings.Conclusion: This study shows that genomic profiling of in particular basal‐like, and thus BRCA1‐mutated, breast carcinomas is severely affected by the presence of high numbers of TILs. Previous reports on genomic profiling of BRCA1‐mutated breast carcinomas have largely neglected this. Therefore, our findings have direct consequences on the interpretation of published genomic data. Also, these findings could prove valuable in light of currently used genomic tools for assessing BRCA1‐involvement in breast cancer patients and pathogenicity assessment of BRCA1 variants of unknown significance. The BRCA1‐associated genomic aberrations identified in this study provide possible leads to a better understanding of BRCA1‐associated oncogenesis.

Fanconi anemia (FA) is a rare genetic instability syndrome characterized by developmental defects, bone marrow failure, and a high cancer risk. Fifteen genetic subtypes have been distinguished. The majority of patients (≈85%) belong to the subtypes A (≈60%), C (≈15%) or G (≈10%), while a minority (≈15%) is distributed over the remaining 12 subtypes. All subtypes seem to fit within the “classical” FA phenotype, except for D1 and N patients, who have more severe clinical symptoms. Since FA patients need special clinical management, the diagnosis should be firmly established, to exclude conditions with overlapping phenotypes. A valid FA diagnosis requires the detection of pathogenic mutations in a FA gene and/or a positive result from a chromosomal breakage test. Identification of the pathogenic mutations is also important for adequate genetic counselling and to facilitate prenatal or preimplantation genetic diagnosis. Here we describe and validate a comprehensive protocol for the molecular diagnosis of FA, based on massively parallel sequencing. We used this approach to identifyBRCA2,FANCD2,FANCIandFANCLmutations in novel unclassified FA patients.