Highlights
- •Whole BRCA1/2 cDNA screening from a large series of 320 unsolved high-risk breast/ovarian cancer cases.
- •Known BRCA1/2 alternative transcripts were detected, together with two novel transcripts: BRCA1 ▼21 and BRCA2 Δ18q_27p.
- •Retrospective RNA analysis detected BRCA2 exon 3 skipping in one patient caused by the insertion of an Alu element in genomic DNA.
- •We identify a potential sQTL in BRCA2 intron 21 (c.8755-66T>C) that modulates ∆22 isoform levels.
- •Our findings can help clinical laboratories to design new studies to test the yield of RNA-based genetic diagnosis of inherited cancer disorders.
Abstract
Germline pathogenic variants in BRCA1 and BRCA2 genes (BRCA1/2) explain an important fraction of hereditary breast/ovarian cancer (HBOC) cases.
Genetic testing generally involves examining coding regions and exon/intron boundaries,
thus the frequency of deleterious variants in non-coding regions is unknown. Here
we analysed BRCA1/2 whole cDNA in a large cohort of 320 unsolved high-risk HBOC cases in order to identify
potential splicing alterations explained by variants in BRCA1/2 deep intronic regions. Whole RNA splicing profiles were analysed by RT-PCR using
Sanger sequencing or high-resolution electrophoresis in a QIAxcel instrument.
Known predominant BRCA1/2 alternative splicing events were detected, together with two novel events BRCA1 ▼21 and BRCA2 Δ18q_27p. BRCA2 exon 3 skipping was detected in one patient (male) affected with breast cancer, caused
by a known Portuguese founder mutation (c.156_157insAluYa5). An altered BRCA2 splicing pattern was detected in three patients, consisting in the up-regulation
of ▼20A, Δ22 and ▼20A+Δ22 transcripts. In silico analysis and semi-quantitative data identified the polymorphism BRCA2 c.8755–66T>C as a potential modifier of Δ22 levels.
Our findings suggest that mRNA alterations in BRCA1/2 caused by deep intronic variants are rare in Spanish population. However, RNA analysis
complements DNA-based strategies allowing the identification of alterations that could
go undetected by conventional testing.
Keywords
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Article info
Publication history
Published online: June 17, 2021
Accepted:
June 9,
2021
Received in revised form:
June 4,
2021
Received:
January 18,
2021
Identification
Copyright
© 2021 Elsevier Inc. All rights reserved.
