Catalog number: A37664
The Oncomine Pan-Cancer Cell-Free Assay 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 provides the reagents and a single pool of multiplex PCR primers for preparation of an amplicon library from cell-free total nucleic acid (cfTNA) obtained from the plasma fraction of a single 10-mL tube of whole blood. This library can then be used for highly multiplexed targeted next-generation sequencing (NGS).
Oncomine 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
Amplicon size optimized for short cfDNA, ensuring 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
Two-day workflow from single 10-mL tube of blood to report; total time to targeted libraries is just four hours
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
The MagMAX Cell-Free Total Nucleic Acid Isolation Kit (A36716) is highly recommended for isolation of both DNA and RNA from the plasma fraction of whole blood.
Scalability and flexibility are achieved using the Tag Sequencing Barcode Set 1-24 or 25-48 (Cat. Nos. A31830 & A31847 respectively) for multiplexing barcoded samples on the Ion S5 chips.
Analysis of SNVs and short indels can be achieved using Torrent Suite Software 5.2 or higher. In order to analyze SNVs, short indels, fusions, and CNVs, Ion Reporter Software 5.6 (cloud or server based) is required.