Oncomine™ Lung cfDNA Assay

The Oncomine™ Lung cfDNA Assay is part of a complete research solution to detect lung tumor-derived DNA (ctDNA) in cfDNA. It provides the reagents for library construction and a single pool of multiplex PCR primers for preparation of amplicon libraries from cell-free DNA (cfDNA) obtained from the plasma fraction of a single tube of whole blood. The assay enables researchers to analyze single nucleotide variants and short indels that are frequently mutated in non-small cell lung cancer (NSCLC). Eleven genes and >150 hotspots are covered (Genes: ALK, BRAF, EGFR, ERBB2, KRAS, MAP2K1, MET, NRAS, PIK3CA, ROS1, and TP53). Through the use of proprietary sequencing technology, a limit of detection (LOD) down to 0.1% can be achieved.

Note: Target and hotspot BED files and User Guide document for cfDNA Variant Analysis with Torrent Suite Software 5.2 can be found below under 'Documents'.

• Optimized amplicon design for short cfDNA (∼170 bp)
• Detection of both single nucleotide variants (SNVs) and short indels down to 0.1% LOD
• Optimized targeted assay design allows highly multiplexed next-generation sequencing (NGS), reducing sequencing costs
• Very high sensitivity and specificity, enabling extremely low levels of detection with minimal false positives
• Efficient workflow, from a single tube of blood to results in just 2 days

Why are pathologists and oncologists interested in liquid biopsy clinical cancer research? Liquid biopsies offer several advantages over conventional solid tumor samples:
• Less invasive to obtain, enabling tumor content to be sampled multiple times
• Lower cost compared to traditional tissue samples
• Faster turnaround time from sample to results
• Help capture more of the heterogeneity of the tumor
• May lead to improvements in standard of care in the future

The entire workflow (figure below) from isolation of cfDNA using the MagMAX™ Cell-Free DNA Isolation Kit to analysis of samples can be accomplished in just 2 days using the Ion Chef™ System and the Ion S5™ XL sequencing system.

Unlike other technologies with low LODs (1-5%), the Oncomine Lung cfDNA Assay has a flexible detection limit down to 0.1% or 1 mutant copy in a background of 1,000 wild-type copies. To achieve 0.1% LOD, 20 ng of input cfDNA is required. Lower amounts of cfDNA can be used, but the resulting LOD will be higher depending on the input amount.

Simplicity, speed, and scalability
The Oncomine Lung cfDNA Assay enables cancer genetic studies from as little as 1 ng of input cfDNA for targeted library construction. The cfDNA assay uses standard PCR equipment and two simple PCR reactions, one for sequencing and the second to amplify the library for high multiplex PCR-based target selection, which minimizes the need for extensive capital investment. Additionally, the Oncomine Lung cfDNA Assay is compatible with FFPE samples for possible concordance studies. Total time to targeted libraries is typically just 3.5 hours. Scalability and flexibility are achieved using the Tag Sequencing Barcode Set 1-24