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HBOC multi-gene panel testing: comparison of two sequencing centers.

Christopher Schroeder1, Ulrike Faust2, Marc Sturm2

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Multi-gene panels are effective for hereditary breast and ovarian cancer (HBOC) genetic testing. Expanding beyond BRCA1/2 to include 8 additional genes significantly increases mutation detection rates in large patient cohorts.

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Area of Science:

  • Genetics
  • Oncology
  • Molecular Diagnostics

Background:

  • Multi-gene panels are crucial for identifying genetic causes of hereditary breast and ovarian cancer (HBOC).
  • Comparing diagnostic workflows and next-generation sequencing (NGS) strategies across different centers is essential for optimizing genetic testing.
  • The German consortium for hereditary breast and ovarian cancer (GC-HBOC) facilitates large-scale genetic studies.

Purpose of the Study:

  • To compare the diagnostic workflow and NGS strategies of two centers within the GC-HBOC.
  • To evaluate the concordance and identify potential improvements in NGS-based genetic testing for HBOC.
  • To assess the diagnostic yield of a 10-gene panel compared to standard BRCA1/2 testing.

Main Methods:

  • Sequencing of a 10-gene panel in 620 patients diagnosed with HBOC.
  • Comparative analysis of NGS results from two independent sequencing centers.
  • Exchange of 12 samples between centers to assess inter-center concordance and identify sequencing gaps or coverage issues.

Main Results:

  • High concordance (99.51%) in variant detection between the two centers.
  • Identified one missed non-pathogenic variant at center B due to a sequencing gap, which was subsequently improved.
  • Pathogenic mutations were detected in 12.10% of patients, with significant contributions from BRCA1, BRCA2, CHEK2, and ATM.
  • Expanding testing beyond BRCA1/2 to include 8 additional genes increased the overall mutation detection rate by one-third.

Conclusions:

  • NGS diagnostics for HBOC-related genes are robust, cost-effective, and suitable for large cohort genetic testing.
  • The inclusion of additional genes beyond BRCA1/2 significantly enhances the diagnostic yield for HBOC.
  • Continuous optimization of NGS enrichment strategies is vital for minimizing sequencing gaps and improving diagnostic accuracy.