Skip to main content

Advertisement

Log in

Functional coding and non-coding variants in human BRCA1 gene and their use in genetic screening

  • Review Article
  • Published:
Medical Oncology Aims and scope Submit manuscript

Abstract

BRCA1 is involved in double-strand DNA damage repair pathways, and mutations in the gene are associated with hereditary breast and ovarian cancers. With great help of the development of high-throughput DNA sequencing techniques numerous single-nucleotide polymorphisms (SNPs) and insertion deletion (Indel) mutations are detected on both coding and non-coding/regulatory regions of the BRCA1. Mutations may cause pathogenic or benign changes on the protein function or affect its expression. In the last decade, use of genetic screening tests to detect mutations on such genes has become greatly popular. However, it is very important to know the effect of the detected mutations, which is mostly possible by the use of predictive softwares, and also the related family history to be able to correctly analyse the screening results and to inform the patient. Therefore, use of in silico and in vitro techniques to score the pathogenicity of detected variants on genes like BRCA1 is now of great importance. Otherwise, results obtained from screening tests and family history cannot be analysed precisely.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Campbell CD, Eichler EE. Properties and rates of germline mutations in humans. Trends Genet. 2013;29(10):575–84.

    Article  CAS  Google Scholar 

  2. Griffiths AJ, et al. Somatic versus germinal mutation. An introduction to genetic analysis. Stuttgart: W. H. Freeman; 2000.

    Google Scholar 

  3. Wu J, Lu LY, Yu X. The role of BRCA1 in DNA damage response. Protein Cell. 2010;1(2):117–23.

    Article  Google Scholar 

  4. Petrucelli N, Daly MB, Feldman GL. Hereditary breast and ovarian cancer due to mutations in BRCA1 and BRCA2. Genet Med. 2010;12(5):245–59.

    Article  CAS  Google Scholar 

  5. Lippi G, Mattiuzzi C, Montagnana M. BRCA population screening for predicting breast cancer: for or against? Ann Transl Med. 2017;5:13.

    Article  Google Scholar 

  6. Godet I, Gilkes DM. BRCA1 and BRCA2 mutations and treatment strategies for breast cancer. Integr Cancer Sci Ther. 2017. https://doi.org/10.15761/ICST.1000228.

    Article  PubMed  PubMed Central  Google Scholar 

  7. Hassan MM, et al. Bioinformatics approach for prediction of functional coding/noncoding simple polymorphisms (SNPs/indels) in human BRAF gene. Adv Bioinf. 2016. https://doi.org/10.1155/2016/2632917.

    Article  Google Scholar 

  8. Deng N, et al. Single nucleotide polymorphisms and cancer susceptibility. Oncotarget. 2017;8(66):110635–49.

    PubMed  PubMed Central  Google Scholar 

  9. Smigielski EM, et al. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res. 2000;28(1):352–5.

    Article  CAS  Google Scholar 

  10. Thery JC, et al. Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes. Eur J Hum Genet. 2011;19(10):1052–8.

    Article  CAS  Google Scholar 

  11. Esposito MV, et al. A novel pathogenic BRCA1 splicing variant produces partial intron retention in the mature messenger RNA. Int J Mol Sci. 2016;17(12):2145.

    Article  Google Scholar 

  12. López de Silanes I, Paz Quesada M, Esteller M. Aberrant regulation of messenger RNA 3 and M. Esteller, r Intron Retention. Cell Oncol. 2007;29(1):1–17.

    PubMed  PubMed Central  Google Scholar 

  13. Singh P, et al. Global changes in processing of mRNA 3′ untranslated regions characterize clinically distinct cancer subtypes. Cancer Res. 2009;69(24):9422–30.

    Article  CAS  Google Scholar 

  14. Mao G, Pan X, Gu L. Evidence that a mutation in the MLH1 3′-untranslated region confers a mutator phenotype and mismatch repair deficiency in patients with relapsed leukemia. J Biol Chem. 2008;283(6):3211–6.

    Article  CAS  Google Scholar 

  15. Karbassi I, et al. A standardized DNA variant scoring system for pathogenicity assessments in mendelian disorders. Hum Mutat. 2016;37(1):127–34.

    Article  CAS  Google Scholar 

  16. Dorairaj JJ, et al. A germline mutation in the BRCA1 3′ UTR predicts stage IV breast cancer. BMC Cancer. 2014;14:421.

    Article  Google Scholar 

  17. Brewster BL, et al. Identification of fifteen novel germline variants in the BRCA1 3′ UTR reveals a variant in a breast cancer case that introduces a functional miR-103 target site. Hum Mutat. 2012;33(12):1665–75.

    Article  CAS  Google Scholar 

  18. Gochhait S, et al. Implication of BRCA2-26G>A 5′ untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg > Pro polymorphism. Breast Cancer Res. 2007;9(5):R71.

    Article  Google Scholar 

  19. Evans DGR, et al. A dominantly inherited 5′ UTR variant causing methylation-associated silencing of BRCA1 as a cause of breast and ovarian cancer. Am J Hum Genet. 2018;103(2):213–20.

    Article  CAS  Google Scholar 

  20. Sim NL, et al. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res. 2012;40:W452–7.

    Article  CAS  Google Scholar 

  21. Zick A, et al. A BRCA1 frame shift mutation in women of Kurdish Jewish descent. Open Med J. 2015;2:31–6.

    Article  Google Scholar 

  22. Benson JM, Therrell BL Jr. History and current status of newborn screening for hemoglobinopathies. Semin Perinatol. 2010;34(2):134–44.

    Article  Google Scholar 

  23. Kaplan F. Tay–Sachs disease carrier screening: a model for prevention of genetic disease. Genet Test. 1998;2(4):271–92.

    Article  CAS  Google Scholar 

  24. Bozkurt G. Results from the north cyprus thalassemia prevention program. Hemoglobin. 2007;31(2):257–64.

    Article  CAS  Google Scholar 

  25. Lynch J, Venne V, Berse B. Genetic tests to identify risk for breast cancer. Semin Oncol Nurs. 2015;31(2):100–7.

    Article  Google Scholar 

  26. Cline MS, et al. BRCA challenge: BRCA exchange as a global resource for variants in BRCA1 and BRCA2. PLoS Genet. 2018;14(12):e1007752.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Mahmut Çerkez Ergören.

Ethics declarations

Conflict of interest

All authors certify that they have no affiliations with or involvement in any organisation or entity with any financial or non-financial interest in the subject matter or materials discussed in this manuscript.

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

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tuncel, G., Ergören, M.Ç. Functional coding and non-coding variants in human BRCA1 gene and their use in genetic screening. Med Oncol 36, 71 (2019). https://doi.org/10.1007/s12032-019-1294-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12032-019-1294-9

Keywords

Navigation