Clinical impact on ovarian cancer patients of massive parallel sequencing for BRCA mutation detection: the experience at Gemelli hospital and a literature review

Abstract

Objective: Massive parallel sequencing (MPS) is the new frontier for molecular diagnostics. Twenty-four papers regarding BRCA analysis were considered for reviewing all pipelines evaluated in this field. Methods: Proposed here is an integrated MPS workflow able to successfully identify BRCA1/2 mutational status on 212 Italian ovarian cancer patients. The review of literature data is reported. Result: The pipeline can be routinely used as robust molecular diagnostic strategy, being highly sensitive and specific. Conclusion: Literature data report that efforts are being made in order to fully translate MPS-based BRCA1/2 gene assay into routine clinical diagnostics. However, this study highlights the need of an integrated MPS BRCA1/2 molecular workflow fulfilling the standardized requirements needed in the routine clinical laboratory practice.

Keywords:

• bioinformatics NGS analysis
• BRCA1/2 genes
• hereditary breast and ovarian cancer syndrome
• massive parallel sequencing
• next-generation sequencing

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending or royalties.

No writing assistance was utilized in the production of this manuscript.

Key issues

• Massive parallel sequencing is not still completely used in clinical molecular diagnostics due to the issues linked to the complexity of different pipelines. In this regard, no definitive criteria for clinical laboratory routine assays have been established.

• Although MPS is a powerful technology, it needs very standardized chemistries that must be managed by expert and skilled personnel.

• The complete analysis of BRCA1/2 should include both quantitative and qualitative testing in order to correctly identify every type of gene alteration.

• The present paper focuses on a standardized MPS-based pipeline for BRCA1/2 testing that is the result of integration of different strategies able to manage any possible issue regarding these genes. Our pipeline was compared with all data published in this field in the last years, showing superimposable results.

• The present paper summarizes all results deriving from 24 free online accessible papers reporting different methodologies, chemistries and bioinformatics tools for BRCA1/2 testing.

• Bioinformatics analysis is crucial for the annotation of clinical relevant gene variants, above all when BRCA1/2 are considered, these genes are highly polymorphic.

• As evaluated in the present paper, bioinformatics may also be applied for a deeper evaluation of library and chemistries, providing further information able to guarantee the complete evaluation of MPS dynamics.

• Considering that our reviewed literature data show that many laboratories still use home-made pipelines, although when coupled with CE-IVD library kits, a consensus regarding the main parameters and tools needed for ensuring the best BRCA1/2 laboratory reporting is really desirable.