Digital DNA sequencing to confidently detect low-frequency variants

Performance

• Accuracy: Innovative digital sequencing (incorporating molecular barcodes) eliminates PCR duplication and amplification artifacts to detect low-frequency variants with high confidence.
• Specificity: The unique combination of our proprietary primer design algorithm and rigorous testing of every primer assay guarantees high specificity and accurate results.
• Uniformity: The QIAseq Targeted DNA Panel workflow has been optimized to deliver highly uniform sequencing results, to ensure sequencing capacity is utilized very efficiently.
• Sensitivity: Digital DNA sequencing approach is optimized to deliver high confidence in calling low-frequency DNA variants. Over 90% sensitivity for 1% NA12878 SNP and indel on typical coding region with false positive less than 15 per mega base region when variants are detected with tiled primer design to cover complete coding region of each gene.
• Universality: The chemistry used in the QIAseq Targeted DNA Panels and workflow is compatible with both regular and GC-rich genomic regions, allowing one to achieve 100% coverage of genes rich in GC content such as CEBPA and CCND1.
• Flexibility: The QIAseq targeted DNA panels offer a high degree of flexibility in content and sample multiplexing. Several cataloged panels have been developed for a wide range of applications. One can also build a custom panel for a specific content, or extend the contents of an existing cataloged panel. Up to 384 samples can be multiplexed using the QIAseq indexes.

Principle

PCR duplicates are a major issue in targeted DNA sequencing, since, through PCR amplification, they turn unique DNA molecules into identical DNA molecules that cannot be distinguished from each other. In addition, errors from PCR amplification and sequencing process may also be present infinal reads that lead to false positive variants in sequencing results. This, in turn, results in the inability to confidently call DNA variants present at low frequencies in the starting DNA material. To overcome the issue of PCR duplicates and amplification artifacts, the QIAseq Targeted DNA Panels use digital sequencing by incorporating molecular barcodes into the starting DNA material before any amplification takes place, thereby preserving the uniqueness of the starting DNA molecules and overcoming the issues of PCR duplicates, false positives and library bias.

Procedure

The entire workflow of the QIAseq Targeted DNA Panels to go from extracted DNA to sequencing-ready libraries can be completed in 9 hours. Extracted DNA is fragmented, genomic targets are molecularly barcoded and enriched, and libraries are constructed. Sequencing files can be fed into the QIAseq pipeline, a cloud-based data analysis pipeline, which will filter, map and align reads, as well as count unique molecular barcodes associated with targeted genomic regions, and call variants with a barcode-aware algorithm. This data can then be fed into IVA or QCI for interpretation.

Applications

The QIAseq Targeted DNA Custom Panels can be used to call a variety of DNA variants from a wide range of sample types for numerous applications.

DNA variants:

• SNVs
• Small indels
• CNVs

Sample types

• FFPE
• Plasma/serum
• Fresh or frozen tissue
• Cell lines

Applications:

• Profiling of DNA variants in solid and hematologic malignancies
• Hotspot detection in solid tumors
• Examination of variants in mitochondrial DNA
• Pain and ADME Pharmacogenomics
• Human identity and paternity testing
• Assessment of germline mutations for inherited diseases
• Profiling of all exonic bases in BRCA 1 and BRCA2