Received on March 13, 2006
Accepted on May 31, 2006

Molecular Diagnostics and Genetics

Genomic Rearrangements at the BRCA1 Locus in Spanish Families with Breast/Ovarian Cancer

¹ Laboratorio de Oncología Molecular y Servicio de Oncología Médica, Hospital Clínico San Carlos, Madrid, Spain
² Servei de Genética, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
³ Instituto de Biología y Genética Molecular, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
⁴ Departmento de Genética Humana, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
⁵ Unidad de Medicina Molecular, Fundación Pública Galega de Medicina Xenómica, (FPGMX), Hospital Clínico Universitario, Santiago de Compostela, Spain
⁶ Centro de Investigación del Cáncer-Universidad de Salamanca, Salamanca, Spain
⁷ Unidad de Consejo Genético, Servicio de Prevención y Control del Cáncer, Institut Català d'Oncologia, Barcelona, Spain
⁸ Unidad de Medicina Molecular, Fundación Pública Galega de Medicina Xenómica, (FPGMX), Hospital Clínico Universitario, Santiago de Compostela, Spain, and Unidad de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain

^* To whom correspondence should be addressed. E-mail: tcaldes.hcsc{at}salud.madrid.org.

Background: Large genomic rearrangements (LGRs) account for a substantial proportion of the BRCA1 variations identified in families with hereditary breast/ovarian cancer [HB(O)C]. Great differences in the spectrum and prevalence of BRCA1 LGR have been observed among populations. Here we report the first comprehensive analysis of BRCA1 LGRs conducted in Spain.

Methods: We used multiplex ligation-dependent probe amplification (MLPA) to screen for BRCA1 LGRs in the index case individuals of 384 HB(O)C families who previously tested negative for BRCA1 and BRCA2 point variations, small insertions, and deletions. An alternative set of MLPA probes, long-range PCR, and real-time PCR were used to confirm positive results.

Results: We have identified 8 different BRCA1 rearrangements (del exon 1-24, del exon 8-13, del exon 11-15, del exon 14, dup exon 19-20, dup exon 20, exon 21-22 amplification, and del exon 23-24). With the exception of del exon 8-13, they are novel alterations. Overall, BRCA1 LGRs explain 1.4% of the Spanish HB(O)C families, and they account for 8.2% of all BRCA1 pathogenic variations identified in our study population. BRCA1 genetic variants affecting hybridization of commercially available MLPA probes are very rare in our population.

Conclusions: Screening for BRCA1 LGRs should be mandatory in Spanish HB(O)C families. A high proportion of country-specific rearrangements are scattered along the gene. MLPA is a robust method to screen for LGRs in our population. MLPA analysis of positive samples with an alternative set of probes, together with long-range PCR and real-time PCR, is a feasible approach to confirm results in cases in which LGR breakpoints have not been characterized.