BRCA Testing by Single-Molecule Molecular Inversion Probes

Area of Science:

• Genetics
• Molecular Biology
• Clinical Diagnostics

Background:

• Next-generation DNA sequencing (NGS) tests for single genes need improvement in speed, cost, completeness, and quality.
• Single-molecule molecular inversion probes (smMIPs) offer potential for enhanced clinical genetic testing.
• BRCA1 and BRCA2 gene testing is frequently requested and serves as a model for this study.

Purpose of the Study:

• To develop and validate an automated workflow for clinical genetic testing of BRCA1 and BRCA2 genes using smMIPs.
• To assess the performance of smMIPs in terms of accuracy, speed, and reliability for diagnostic genetic testing.

Main Methods:

• Developed and validated BRCA1 and BRCA2 smMIPs using 166 human genomic DNA samples.
• Established a generic automated workflow for smMIP-based enrichment and sequencing.
• Included CHEK2 c.1100del variant in the automated workflow for comprehensive analysis.

Main Results:

• Achieved 100% analytical sensitivity and specificity for pathogenic and benign variants in a subset of 152 samples.
• Automated workflow correctly identified all true-positive variants (>3000) across 65 in-house and 267 Norwegian samples, with no false positives.
• Reduced turnaround times by 60% to 10-15 days and detected copy number variants with 100% sensitivity and 88% specificity.

Conclusions:

• smMIP-based genetic testing provides an automated and reliable method for analyzing BRCA1 and BRCA2 coding sequences.
• The integrated approach using smMIPs, automation, and sequencing in duplo ensures a robust process and reduces turnaround times.
• smMIPs offer potential to replace independent tools for copy number variation analysis, streamlining genetic testing.