Circulating tumor DNA panels

Circulating tumor DNA panel

The Gene agnosTic Liquid (GTL) biopsy test is part of a complete solution to detect multiple targets in tumor-derived DNA and RNA isolated from the plasma fraction of whole blood. The assay is sensitive enough to generate information from cell-free total nucleic acid (cfTNA) obtained from the plasma fraction of a single 10-mL tube of whole blood, using targeted next-generation sequencing (NGS). The GTL is based on the platform Thermo Fisher Ion Torrent™.

GTL cell-free assay advantages:
• From a single tube of blood, generates an amplicon library from both DNA and RNA with a detection limit of 0.1% for SNVs. The sensitivity may be increased, when more blood collection is possible.
• Amplicon size optimized for short cfDNA, ensuring the highest possible capture rate
• Tag Sequencing technology minimizes false positives by removing randomly incorporated errors
• Optimized targeted assay design allows highly multiplexed NGS, reducing sequencing costs per sample
• Quick workflow from a single 10-mL tube of blood to report
• Enables cancer genetic studies from just 5 ng of input cfTNA
• Compatible with FFPE samples for possible concordance studies

The 52-gene panel includes:
• Hotspot genes (SNVs) and short indels: AKT1, ALK, AR, ARAF, BRAF, CHEK2, CTNNB1, DDR2,EGFR, ERBB2, ERBB3, ESR1, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, GNA11, GNAQ, GNAS, HRAS, IDH1, IDH2, KIT, KRAS, MAP2K1, MAP2K2, MET, MTOR, NRAS, NTRK1, NTRK3, PDGFRA, PIK3CA, RAF1, RET, ROS1, SF3B1, SMAD4, SMO
• Gene fusions: ALK, BRAF, ERG, ETV1, FGFR1, FGFR2, FGFR3, MET, NTRK1, NTRK3, RET, ROS1
• MET exon 14 skipping
• Copy number genes (CNVs): CCND1, CCND2, CCND3, CDK4, CDK6, EGFR, ERBB2, FGFR1, FGFR2, FGFR3, MET, MYC
• Tumor suppressor genes: APC, FBXW7, PTEN, TP53

These genes have been identified as frequently mutated in multiple cancer types, including bladder, brain and CNS, breast, cervical, colorectal, endometrial, esophageal, gastric, head and neck, kidney, liver, lung, melanoma, ovarian, pancreatic, prostate, sarcoma, and thyroid.

Detection limits:
• SNVs/short indels: a limit of detection (LOD) down to 0.1% allele frequency (AF) can be achieved with a sensitivity of >80% and specificity of >98%*
• TP53 whole-target SNVs/indels: 0.5% AF (looking at all bases within amplicons)
• Fusions and MET exon skipping: LOD down to 1% can be achieved
• CNV targets: detection as low as 1.4-fold change can be achieved

Technology

DNA and cfRNA are found at extremely low concentrations in the plasma fraction of whole blood. Because of this low prevalence, a tag sequencing technology is utilized in this assay. The technology attaches unique molecular tags to the gene-specific primers. After amplification, the tagged molecules are grouped based on the tags. Groups containing the same mutant variant 80% of the time or greater will be called positive. Using this Tag technology, groups that contain random errors generated through the library construction/sequencing process are removed.

Unlike other technologies with LODs of 1-5%, the GTL Pan-Cancer Cell-Free Assay has a flexible detection limit down to 0.1% for SNVs or 1 mutant copy in a background of 1,000 wild-type copies. To achieve 0.1% LOD, 20 ng of input cfTNA is required. Lower amounts of cfTNA can be used, but the %LOD will be higher depending on the input amount.

Liquid biopsies offer several advantages over conventional solid tumor biopsies:
• Liquid biopsy samples are less invasive enabling them to be taken at multiple time points to monitor the progression of the cancer
• Lower cost compared to traditional tissue biopsies
• Faster turnaround time from sample to results
• Better represent tumor heterogeneity

For Research Use Only. Not for use in diagnostic procedures.
https://www.thermofisher.com/order/catalog/product/A37664?SID=srch-srp-A37664

Utility of the comprehensive cancer profiling tests

Cell-free total nucleic acid (cfTNA) is easily accessible in peripheral blood and can be used as biomarkers for cancer diagnostics, prognostics, and therapeutics. The applications of cfTNA in various areas of cancer management are attracting attention. In this review article, we discuss the potential relevance of using cfDNA analysis in clinical oncology, particularly in cancer screening, early diagnosis, therapeutic evaluation, monitoring disease progression; and determining disease prognosis.

For more information please see:
https://www.frontiersin.org/articles/10.3389/fcell.2021.639233/full#B23
https://doi.org/10.1038/s41698-022-00270-y
https://doi.org/10.1038/s41416-022-01776-9