Sequencing of BRCA1/2-alterations using NGS-based technology: annotation as a challenge

Area of Science:

• Oncology
• Genetics
• Molecular Diagnostics

Background:

• Accurate classification of BRCA1/2 variants is crucial for diagnosing and treating BRCA-associated cancers.
• Existing next-generation sequencing (NGS) platforms may exhibit variability in detecting and annotating these variants.

Purpose of the Study:

• To evaluate and compare the performance of different NGS platforms for the molecular profiling of BRCA1/2 variants in tumor samples.
• To establish guidelines for the interpretation of BRCA1/2 alterations in routine diagnostic settings.

Main Methods:

• Retrospective analysis of 48 samples (45 tumors, 3 non-tumors) using GeneReader, Ion S5™, and MiSeq™ NGS platforms.
• Variant annotation was compared against normal tissue and online databases.
• Comparative analysis of sequencing results, variant detection, and classification across different NGS devices.

Main Results:

• Individual NGS platforms detected varying numbers of BRCA1/2 alterations.
• The GeneReader platform showed inconsistencies in detecting and classifying pathogenic alterations.
• The Ion S5™ platform demonstrated reliable performance in variant detection and classification.

Conclusions:

• The Ion S5™ system, coupled with the Oncomine™ Comprehensive Assay v3, is highly recommended for molecular analysis in routine diagnostics.
• This panel covers additional genes, potentially identifying new therapeutic options for patients based on eligibility criteria.