Pathogenicity reclassification of two BRCA1/BRCA2 exonic duplications after identification of genomic breakpoints and tandem orientation

• Published in: Cancer genetics 2020-10, Vol.248-249, p.18-24
• Main Authors: Pinheiro, Manuela, Peixoto, Ana, Santos, Catarina, Escudeiro, Carla, Bizarro, Susana, Pinto, Pedro, Santos, Rui, Pinto, Carla, Guerra, Joana, Silva, João, Teixeira, Manuel R.
• Format: Article
• Language: English
• Subjects: Adult; Aged; Alu; BRCA; BRCA1 Protein - genetics; BRCA2 Protein - genetics; Chromosome Breakpoints; Exons; Female; Follow-Up Studies; Gene Duplication; Gene Rearrangement; Genomics; Germ-Line Mutation; HBOC; Hereditary Breast and Ovarian Cancer Syndrome - classification; Hereditary Breast and Ovarian Cancer Syndrome - genetics; Hereditary Breast and Ovarian Cancer Syndrome - pathology; Humans; Middle Aged; Pedigree; Prognosis; Tandem duplication
• ISSN: 2210-7762; 2210-7770
• DOI: 10.1016/j.cancergen.2020.09.001

•Genomic breakpoint characterization is essential to improve variant classification of intragenic duplications.•We report two exonic duplications involving BRCA1 exons 4 to 6 and BRCA2 exons 17 to 18.•These variants occurred in tandem and in direct orientation and are predicted to cause frameshifts that create a premature stop codon.•These two exonic duplications were classified as pathogenic and allowed the molecular diagnosis of HBOC syndrome in two families. The genomic consequence and clinical interpretation of large duplications are difficult to infer without determining the location and orientation of the duplicated sequence. We aimed to characterize two intragenic duplications detected in two hereditary breast and ovarian cancer syndrome (HBOC) families, namely BRCA1 exon 4 to 6 and BRCA2 exon 17 to 18, previously detected by multiplex ligation probe amplification and initially classified as variants of unknown significance. Using long range PCR, with duplication-specific primers, we were able to ascertain the genomic breakpoints and observed that the two rearrangements occurred in tandem and in direct orientation. The BRCA1 c.134+440_441+870dup and BRCA2 c.7806-2083_8332-1512dup duplications here identified are predicted to cause frameshifts that create a premature stop codon and were reclassified as pathogenic. Furthermore, both families present phenotypic traits typical of HBOC syndrome. We also observed that the genomic breakpoints of these two duplications occurred within highly homologous Alu elements. Concluding, we characterized two in tandem BRCA1 and BRCA2 duplications that likely occurred by Alu-mediated homologous recombination, allowing identification of the underlying cause of the HBOC syndrome in these families.