The BRCA1 c.788G > T (NM_007294.4) variant in a high grade serous ovarian cancer (HGSOC) patient: foods for thought

Abstract

In this report we described the case of a BRCA1/2 (BRCA) molecular testing performed on tumor sample in a High Grade Serous Ovarian Cancer (HGSOC) patient with two different Next Generation Tumor Sequencing (NGTS) pipelines. The two clinical reports leaded to apparently different BRCA status, providing important foods for thought. After NGTS, the gene sequencing information (i.e., reads) are aligned to the reference gene sequences obtained from public databases, in order to provide an uniform nomenclature for unambiguous variant designation. However, the criteria adopted for variant reporting in tissue test are not always univocal. Particularly, this is the case of rare and unclassified BRCA variants for which the molecular evaluation may be a relevant challenge. Here we described a BRCA1 unclassified variant that may be re-evaluated in the context of alternative BRCA1 transcripts due to its different biological effect. We underlined that an in-depth knowledge of BRCA testing is mandatory for its appropriate use.

This is a preview of subscription content, access via your institution.

Fig. 1

Figure source: https://varsome.com/

Fig. 2

Source: Amplicon Suite software (SmartSeq, Novara, Italy)

Abbreviations

BRCA:

BRCA1/2

BC:

Breast cancer

OC:

Ovarian cancer

PVs:

Pathogenic variants

PARPi:

Poly ADP ribose polymerase inhibitor

VUSs:

Variants of unknown significance

HGSOC:

High grade serous ovarian cancer

tBRCA:

Tumor BRCA

VAF:

Variant allele frequency

MAF:

Minor allele frequency

F1CDx:

FoundationOne®CDx

BRCA1-FL:

BRCA1 full-length

ENIGMA:

Evidence-based network for the interpretation of germline mutant alleles

NLS:

Nuclear localization signal

gBRCA:

Germline BRCA

SNPs:

Single nucleotide variants

CNVs:

Copy number variations

NGS:

Next generation sequencing

MAQ:

Multiplex amplification quantification

MLPA:

Multiplex ligation probe amplification

MSI:

Microsatellite instability

TMB:

Tumor mutational burden

ACMG:

American College of Medical Genetics

References

  1. 1.

    Antoniou A, Pharoah PD, Narod S, Risch HA, Eyfjord JE, Hopper JL, Loman N, Olsson H, Johannsson O, Borg A et al (2003) Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case Series unselected for family history: a combined analysis of 22 studies. Am J Hum Genet 72(5):1117–1130

    CAS  Article  Google Scholar 

  2. 2.

    Anczuków O, Buisson M, Salles MJ, Triboulet S, Longy M, Lidereau R, Sinilnikova OM, Mazoyer S (2008) Unclassified variants identified in BRCA1 exon 11: consequences on splicing. Genes Chromosomes Cancer 47(5):418–426

    Article  Google Scholar 

  3. 3.

    Richards R, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, ACMG Laboratory Quality Assurance Committee (2015) Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17(5):405–424

    Article  Google Scholar 

  4. 4.

    Plon SE, Eccles DM, Easton D, Foulkes WD, Genuardi M, Greenblatt MS, Hogervorst FB, Hoogerbrugge N, Spurdle AB, Tavtigian SV, IARC Unclassified Genetic Variants Working Group (2008) Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. Hum Mutat 29(11):1282–1291

    CAS  Article  Google Scholar 

  5. 5.

    Concolino P, Rizza R, Hackmann K, Paris I, Minucci A, De Paolis E, Scambia G, Zuppi C, Schrock E, Capoluongo E (2017) Characterization of a new BRCA1 rearrangement in an Italian woman with hereditary breast and ovarian cancer syndrome. Breast Cancer Res Treat 164(2):497–503

    CAS  Article  Google Scholar 

  6. 6.

    Marchetti C, Minucci A, D’Indinosante M, Ergasti R, Arcieri M, Capoluongo ED, Pietragalla ACC, Scambia G, Fagotti A (2020) Feasibility of tumor testing for BRCA status in high-grade serous ovarian cancer using fresh-frozen tissue based approach. Gynecol Oncol 158(3):740–746

    CAS  Article  Google Scholar 

  7. 7.

    Bonnet C, Krieger S, Vezain M, Rousselin A, Tournier I, Martins A et al (2008) Screening BRCA1 and BRCA2 unclassified variants for splicing mutations using reverse transcription PCR on patient RNA and an ex vivo assay based on a splicing reporter minigene. J Med Genet 45:438–446

    CAS  Article  Google Scholar 

  8. 8.

    Muller D, Rouleau E, Schultz I, Caputo S, Lefol C, Bieche I et al (2011) An entire exon 3 germ-line rearrangement in the BRCA2 gene: pathogenic relevance of exon 3 deletion in breast cancer predisposition. BMC Med Genet 12:121–112

    CAS  Article  Google Scholar 

  9. 9.

    Peixoto A, Santos C, Rocha P, Pinheiro M, Principe S, Pereira D et al (2009) The c.156_157 insAlu BRCA2 rearrangement accounts for more than one-fourth of deleterious BRCA mutations in northern/central Portugal. Breast Cancer Res Treat 114(1):31–38

    CAS  Article  Google Scholar 

  10. 10.

    Colombo M, Lòpez-Perolio I, Meeks HD, Caleca L, Parsons MT, Li H, De Vecchi G, Tudini E, Foglia C et al (2018) The BRCA2 c.68-7T > A variant is not pathogenic: a model for clinical calibration of spliceogenicity. Hum Mutat 39(5):729–741

    CAS  Article  Google Scholar 

  11. 11.

    de la Hoya M, Soukarieh O, López-Perolio I, Vega A, Walker LC, van Ierland Y, Baralle D, Santamariña M, Lattimore V, Wijnen J et al (2016) Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms. Hum Mol Genet 25(11):2256–2268

    Article  Google Scholar 

  12. 12.

    Colombo M, Blok MJ, Whiley P, Santamariña M, Gutiérrez-Enríquez S, Romero A, Garre P et al (2014) Comprehensive annotation of splice junctions supports pervasive alternative splicing at the BRCA1 locus: a report from the ENIGMA consortium. Hum Mol Genet 23(14):3666–3680

    CAS  Article  Google Scholar 

  13. 13.

    Tammaro C, Raponi M, Wilson DI, Baralle D (2012) BRCA1 exon 11 alternative splicing, multiple functions and the association with cancer. Biochem Soc Trans 40(4):768–772

    CAS  Article  Google Scholar 

  14. 14.

    Raponi M, Smith LD, Silipo M, Stuani C, Buratti E, Baralle D (2014) BRCA1 exon 11 a model of long exon splicing regulation. RNA Biol 11(4):351–359

    Article  Google Scholar 

  15. 15.

    Raponi M, Douglas AGL, Tammaro C, Wilson DI, Baralle D (2012) Evolutionary constraint helps unmask a splicing regulatory region in BRCA1 exon 11. PLoS ONE 7(5):e37255

    CAS  Article  Google Scholar 

  16. 16.

    Qin Y, Xu J, Aysola K, Begum N, Reddy V, Chai Y, Grizzle WE, Partridge EE, Reddy ES, Rao VN (2011) Ubc9 mediates nuclear localization and growth suppression of BRCA1 and BRCA1a proteins. J Cell Physiol 226(12):3355–3367

    CAS  Article  Google Scholar 

  17. 17.

    Maniccia AW, Lewis C, Begum N, Xu J, Cui J, Chipitsyna G, Aysola K, Reddy V, Bhat G, Fujimura Y et al (2009) Mitochondrial localization, ELK-1 transcriptional regulation and growth inhibitory functions of BRCA1, BRCA1a, and BRCA1b proteins. J Cell Physiol 219(3):634–641

    CAS  Article  Google Scholar 

  18. 18.

    Wang Y, Bernhardy AJ, Cruz C, Krais JJ, Nacson J, Nicolas E, Peri S et al (2016) The BRCA1-Δ11q alternative splice isoform bypasses germline mutations and promotes therapeutic resistance to PARP inhibition and cisplatin. Cancer Res 76(9):2778–2790

    CAS  Article  Google Scholar 

  19. 19.

    Høberg-Vetti H, Ognedal E, Buisson A, Vamre TBA, Ariansen S, Hoover JM, Eide GE, Houge G, Fiskerstrand T, Haukanes BI, Bjorvatn C, Knappskog PM (2020) The intronic BRCA1 c.5407-25T>A variant causing partly skipping of exon—a likely pathogenic variant with reduced penetrance? Eur J Hum Genet 28(8):1078–1086

    Article  Google Scholar 

  20. 20.

    Minucci A, Scambia G, Santonocito C, Concolino P, Canu G, Mignone F, Saggese I, Guarino D, Costella A, Molinario R, De Bonis M, Ferrandina G, Petrillo M, Scaglione GL, Capoluongo E (2015) Clinical impact on ovarian cancer patients of massive parallel sequencing for BRCA mutation detection: the experience at Gemelli Hospital and a Literature Review. Expert Rev Mol Diagn 15(10):1383–1403

    CAS  Article  Google Scholar 

  21. 21.

    Minucci A, De Paolis E, Concolino P, De Bonis M, Rizza R, Canu G, Scaglione GL, Mignone F, Scambia G, Zuppi C, Capoluongo E (2017) Competitive PCR-high resolution melting analysis (C-PCR-HRMA) for large genomic rearrangements (LGRs) detection: a new approach to assess quantitative status of BRCA1 gene in a reference laboratory. Clin Chim Acta 470:83–92

    CAS  Article  Google Scholar 

  22. 22.

    Gelli E, Colombo M, Pinto AM, De Vecchi G, Foglia C, Amitrano S, Morbidoni V, Imperatore V et al (2019) Usefulness and limitations of comprehensive characterization of mRNA splicing profiles in the definition of the clinical relevance of BRCA1/2 variants of uncertain significance. Cancers 11(3):295

    CAS  Article  Google Scholar 

  23. 23.

    Bodian DL, Kothiyal P, Hauser NS (2019) Pitfalls of clinical exome and gene panel testing: alternative transcripts. Genet Med 21(5):1240–1245

    CAS  Article  Google Scholar 

  24. 24.

    McCarthy DJ, Humburg P, Kanapin A, Rivas MA, Gaulton K, Cazier JB, Donnelly P (2014) Choice of transcripts and software has a large effect on variant annotation. Genome Med 6(3):26

    Article  Google Scholar 

Download references

Acknowledgements

We would like to thank Franziska M. Lohmeyer for critically reviewing this manuscript.

Funding

This research received no external funding.

Author information

Affiliations

Authors

Contributions

EDP and AM conceived the project and wrote the paper; EDP and MDB performed the experiments and analysed the data; AU contributed to analyses and interpretation of data; AP, AF and GS contributed to patient selection and clinical evaluation. All authors have read and agreed to the published version of the manuscript.

Corresponding author

Correspondence to Angelo Minucci.

Ethics declarations

Confict of interest

The authors declare that they have no conficts 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.

Consent to participate

Written informed consent was obtained from the patient included in this study.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

De Paolis, E., Pietragalla, A., De Bonis, M. et al. The BRCA1 c.788G > T (NM_007294.4) variant in a high grade serous ovarian cancer (HGSOC) patient: foods for thought. Mol Biol Rep 48, 2985–2992 (2021). https://doi.org/10.1007/s11033-021-06243-x

Download citation

Keywords

  • BRCA1/2 genes
  • High grade serous ovarian cancer
  • C.788G > T
  • Tumor BRCA testing
  • Next generation sequencing