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Spliceogenic analysis of BRCA1 c.439T>C (rs794727800) variant by High Resolution Melting Analysis

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Abstract

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.

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Abbreviations

HBOC:

Hereditary breast and/or ovarian cancer

PVs:

Pathogenic variants

BRCA:

BRCA1/2

PARP-1:

Poly (ADP-ribose) polymerase

VUS:

Variants of unknown significance

ENIGMA:

Evidence-based network for the interpretation of germline mutant alleles

MAF:

Minor allele frequency

HGSOC:

High grade serous ovarian cancer

HRMA:

High-resolution melting analysis

FIGO:

International federation of gynecologists and obstetricians

FT:

Fresh tissue

NGS:

Next generation sequencing

VAF:

Variant allele frequency

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Acknowledgement

We would like to thank Franziska M. Lohmeyer for her critical review and English revision.

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Correspondence to Angelo Minucci.

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The authors declared no potential conflicts of interest.

Ethical approval

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.

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Minucci, A., Mazzuccato, G., D’Indinosante, M. et al. Spliceogenic analysis of BRCA1 c.439T>C (rs794727800) variant by High Resolution Melting Analysis. Mol Biol Rep 47, 1513–1520 (2020). https://doi.org/10.1007/s11033-019-05199-3

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Keywords

  • Spliceogenic analysis
  • BRCA1/2 genes
  • High Resolution Melting Analysis
  • BRCA1 c.439T>C variant
  • BRCA1 r.442_444del isoform