Spliceogenic analysis of BRCA1 c.439T>C (rs794727800) variant by High Resolution Melting Analysis
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Correct classification of genomic variants causing potentially aberrant splicing is of utmost importance for patient management, especially in clinically actionable genes such as BRCA1/2. In this article, we report molecular evaluation of the BRCA1 c.439T>C (rs794727800, p.Leu147=) variant based on RNA of a patient suffering with high-grade serous ovarian cancer syndrome, to add new evidence to the only in silico data available for this variant. High Resolution Melting Analysis (HRMA) was used for the first time to investigate the spliceogenicity of a BRCA1 variant. HRMA with Sanger sequencing provided evidence that the c.439C allele does not cause aberrant splicing of the BRCA1 exon 7. In addition, HRMA with Sanger highlighted a different expression of the naturally occurring BRCA1 r.442_444del (c.442_444delCAG, p.Gln148del, at DNA level) isoform between blood and tumor, in this patient. HRMA is an alternative molecular approach to analyze spliceogenic properties of the c.439T>C variant and potentially for all those BRCA1/2 variants affecting splicing sites. These new evidences allowed to classify definitively the c.439T>C variant as benign. Furthermore, the different BRCA1 r.442_444del expression opens the discussion to consider a wider classification criteria for the splicing variants, including molecular evaluation at tissue level, which is an aspect currently scarcely considered in BRCA1/2 variant classification recommendations.
KeywordsSpliceogenic analysis BRCA1/2 genes High Resolution Melting Analysis BRCA1 c.439T>C variant BRCA1 r.442_444del isoform
Hereditary breast and/or ovarian cancer
Poly (ADP-ribose) polymerase
Variants of unknown significance
Evidence-based network for the interpretation of germline mutant alleles
Minor allele frequency
High grade serous ovarian cancer
High-resolution melting analysis
International federation of gynecologists and obstetricians
Next generation sequencing
Variant allele frequency
We would like to thank Franziska M. Lohmeyer for her critical review and English revision.
Compliance with ethical standards
Conflict of interest
The authors declared no potential conflicts of interest.
This study complied with the Ethical Principles for Medical Research Involving Human Subjects according to the World Medical Association Declaration of Helsinki and was certified by the Committee of the Applicable Institution of the Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome.
Informed consent was taken from all participants.
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