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Functional categorization of BRCA1 variants of uncertain clinical significance in homologous recombination repair complementation assays

Bouwman, P., van der Heijden, I., van der Gulden, H., de Bruijn, R., Braspenning, M. E., Moghadasi, S., Wessels, L. F. A., Segers, K., Badoer, C., Vandernoot, I., Hilbert, P., Storm, K., Blaumeiser, B., Claes, K. B. M., Seneca, S., Michils, G., van den Ouweland, A., Collée, J. M., van der Stoep, N., Blok, M. J., Bleeker, F. E., Hogervorst, F. B. L., Mensenkamp, A. R., van der Hout, A. H., Oosterwijk, J. C., van der Luijt, R. B., Koudijs, M. J., Vreeswijk, M. P. G. & Jonkers, J., 16-Jun-2020, In : Clinical Cancer Research. 35 p.

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  • Functional categorization of BRCA1 variants of uncertain clinical significance in homologous recombination repair complementation assays

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DOI

  • Peter Bouwman
  • Ingrid van der Heijden
  • Hanneke van der Gulden
  • Roebi de Bruijn
  • Merel E Braspenning
  • Setareh Moghadasi
  • Lodewyk F A Wessels
  • Karin Segers
  • Cindy Badoer
  • Isabelle Vandernoot
  • Pascale Hilbert
  • Katrien Storm
  • Bettina Blaumeiser
  • Kathleen B M Claes
  • Sara Seneca
  • Geneviève Michils
  • Ans van den Ouweland
  • J Margriet Collée
  • Nienke van der Stoep
  • Marinus J Blok
  • Fonnet E Bleeker
  • Frans B L Hogervorst
  • Arjen R Mensenkamp
  • Annemarie H van der Hout
  • Jan C Oosterwijk
  • Rob B van der Luijt
  • Marco J Koudijs
  • Maaike P G Vreeswijk
  • Jos Jonkers

PURPOSE: Because BRCA1 is a high-risk breast/ovarian cancer susceptibility gene, BRCA1 sequence variants of uncertain clinical significance (VUS) complicate genetic counseling. As most VUS are rare, reliable classification based on clinical and genetic data is often impossible. However, all pathogenic BRCA1 variants analyzed result in defective homologous recombination DNA repair (HRR). Thus, BRCA1 VUS may be categorized based on their functional impact on this pathway.

EXPERIMENTAL DESIGN: 238 BRCA1 VUS - comprising most BRCA1 VUS known in the Netherlands and Belgium - were tested for their ability to complement Brca1 deficient mouse ES cells in HRR, using cisplatin and olaparib sensitivity assays and a DR-GFP HRR assay. Assays were validated using 25 known benign and 25 known pathogenic BRCA1 variants. For assessment of pathogenicity by a multifactorial likelihood analysis method, we collected clinical and genetic data for functionally deleterious VUS and VUS occurring in three or more families.

RESULTS: All three assays showed 100% sensitivity and specificity (95% CI = 83%-100%). Out of 238 VUS, 45 showed functional defects, 26 of which were deleterious in all three assays. For 13 of these 26 variants we could calculate the probability of pathogenicity using clinical and genetic data, resulting in the identification of seven (likely) pathogenic variants.

CONCLUSIONS: We have functionally categorized 238 BRCA1 VUS using three different HRR-related assays. Classification based on clinical and genetic data alone for a subset of these variants confirmed the high sensitivity and specificity of our functional assays.

Original languageEnglish
Number of pages35
JournalClinical Cancer Research
Publication statusE-pub ahead of print - 16-Jun-2020

ID: 127956863