title: Validation of an NGS Approach for Diagnostic BRCA1/BRCA2 Mutation Testing.
abstract: OBJECTIVE
  Pathogenic mutations in BRCA1/2 tumor suppressor genes increase the lifetime risk for developing breast and ovarian cancer. The aim of the present study was to evaluate the sensitivity and specificity of the Ion Torrent PGM™ for diagnostic mutation screening of BRCA1/2 genes.
  
  
  METHODS
  In the current study we included a cohort of 58 Bulgarian high-risk breast cancer patients to validate a next-generation sequencing approach for diagnostic mutation screening of the BRCA1/2 genes using the Ion Torrent Personal Genome Machine® (PGM™) platform. We have also optimized the workflow by comparing two different library preparation methods and using three software packages: NextGENE, Torrent Suite variantCaller, and Samtools/BCFtools to achieve detection of all variants with high specificity and sensitivity.
  
  
  RESULTS
  We have validated a quick and accurate diagnostic test, with an overall specificity of 95.9% and sensitivity of up to 100%, which can be the first method of choice, followed by confirmation of the identified variants by Sanger sequencing. Our results prove that the Ion AmpliSeq™ BRCA1/2 Community Panel used with the PGM™ platform, and coupled with our variant selection pipeline, is able to detect all sequence variants discovered by Sanger sequencing.
  
  
  CONCLUSIONS
  The application of the new test which outperforms the classical approach in turn-around time and price will have great impact in the clinical practice to identify the mutation carriers and guide the better personalized treatment of the patients, as well as to contribute for the improved prophylaxis in hereditary breast and ovarian cancer families.
authors.affiliation: Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Faculty of Medicine, Medical University of Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria, dacheva@mmcbg.org.
authors.forename: Daniela
authors.initials: D
authors.lastname: Dacheva
authors.forename: Rumyana
authors.initials: R
authors.lastname: Dodova
authors.forename: Ivan
authors.initials: I
authors.lastname: Popov
authors.forename: Teodora
authors.initials: T
authors.lastname: Goranova
authors.forename: Atanaska
authors.initials: A
authors.lastname: Mitkova
authors.forename: Vanio
authors.initials: V
authors.lastname: Mitev
authors.forename: Radka
authors.initials: R
authors.lastname: Kaneva
mesh_terms: D000483:Alleles; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics; D019295:Computational Biology; D005091:Exons; D005260:Female; D015723:Gene Library; D019398:Genes, BRCA1; D024522:Genes, BRCA2; D005820:Genetic Testing / Q000379:methods; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D057188:Workflow