Classification of 15 new BRCA2 exons2-9 splicing variants by hybrid minigenes

Trabajo presentado a la European Human Genetics (ESHG) Conference, celebrada en Milan (Italia) del 16 al 19 de junio de 2018.
The clinical classification of BRCA2 variants of uncertain significance (VUS) poses a challenge in human genetics. Historically, variants have been catalogued from the protein outlook, however, upstream gene-expression mechanisms, such as splicing, could be impaired by changes in the DNA sequence. Disrupted splicing variants could alter the ORF provoking the BRCA2 truncation and be involved in cancer development. Here, we have evaluated the splicing effect of 83 BRCA2 exons 2-9 variants by functional assays using the minigene MGBR2_2-9. The MGBR2_2-9 was built based on the splicing vector pSAD (Patent-P201231427, CSIC). In silico selected BRCA2 variants, from BIC and UMD databases, were introduced into MGBR2_2-9 and assayed in MCF-7 cells. Transcripts were analyzed by capillary electrophoresis and sequenced. After the bioinformatic analysis of 302 BRCA2 variants, 83 were functionally tested. Results showed that 53 variants impaired splicing (26 intronic and 27 exonic). Among them, 36 provoked ¿2/3 of aberrant transcripts. According to the ACMG and ENIGMA criteria, our results support the re-classification of 12 variants from VUS to pathogenic (c.67+1G>T, c.67+3A>G, c.426-12del5, c.441A>G, c.451G>A, c.475+3A>T, c.516+4delAA, c.517-1G>A, c.517G>T, c.631+1G>A, c.632+3A>G and c.632-3G>C) and 3 from VUS to likely pathogenic (c.97G>A, c.100G>A, c.476-3C>A). The reproducibility of this technique was supported by previous studies based on minigenes or/and patient RNA. MGBR2_2-9 is a robust tool which provides RNA data for the clinical interpretation of splicing variants.
Projects FIS PI13/01749 and PI17/00227 (ISCIII, Spanish Ministry of Economy and Competitivity), BIO/VA34/15 (Junta Castilla-León); EF-B is supported by a predoctoral fellowship (University of Valladolid/Banco Santander).