Search
Search
View additional product information for Oncomine™ Precision Assay GX - FAQs (A46291)
10 product FAQs found
A number of data formats are available with the Oncomine Precision Assay on the Genexus Integrated Sequencer. A detailed list of those files that are available for download starts on page 153 of the user guide. Some of the data formats (e.g., reports) include already summarized results while others are in data formats that can be used for subsequent analysis (e.g., BAM, FASTQ, etc.).
Run time of the Oncomine Precision Assay will vary depending of number of samples run at once. It can be processed in about 24 hours or less for 2 FFPE tissue samples, ~24 hours for 4 FFPE tissue samples, ~ 25 hours for 8 FFPE tissue samples and ~ 36 hours for 16 FFPE tissue samples, which is the maximum batch size when analyzing DNA & RNA at once. The above specified run times include FFPE sample pre-processing, nucleic acid extraction, quantification, library preparation, templating and sequencing.
The Oncomine Precision Assay includes library reagents that are to be used on the Genexus Integrated Sequencer which automates library preparation workflow, as well as the templating, sequencing and analysis. The assay has not been validated with any other library preparation workflows.
The capacity of the GX5 Chip varies depending on the sample type:
- For plasma cfTNA samples, the workflow is configured to accommodate 1 sample per GX5 Chip lane (or 4 samples on a single GX5 Chip).
- For FFPE DNA+RNA samples, the workflow is configured to accommodate 4 samples per GX5 Chip lane.
- For FFPE DNA-only or RNA-only samples, the workflow is configured to accommodate 8 samples per GX5 Chip lane.
The maximum number of samples that can be analyzed per kit depends upon the type of analysis that you want to perform. Each kit provides the targeted pancancer panel and library reagents sufficient to perform up to 32 sequencing reactions on the Genexus Integrated Sequencer.
- Simultaneous DNA- and RNA-based variant analysis for up to 16 FFPE tissue samples (one DNA reaction and one RNA reaction per sample)
- DNA-only or RNA-only variant analysis for up to 32 FFPE tissue samples
- Cell-free TNA (cfTNA) variant analysis (combined DNA and RNA) for up to 32 plasma samples
For solid tumor samples, the optimal input amount is 10 ng with validated input in the range of 5-15 ng. For liquid biopsy samples, the optimal input amount is 20 ng with validated input in the range of 5-40 ng.
For optimal results, load 20 µL of input with a concentration of ≥0.67 ng/µL for FFPE DNA and FFPE RNA samples and 20 µL of input with a concentration of ≥1.33 ng/µL for cfTNA samples. If the concentration of the sample is lower than optimal, use as much input as possible for each reaction.
Here are the various controls we recommend depending upon the starting material:
FFPE DNA samples
- Structural Multiplex Reference Standard (FFPE), Cat. No. HD789 (Horizon™)
- EGFR Gene-Specific Multiplex Reference Standard (FFPE) 5% AF, Cat. No. HD300 (Horizon™)
- KRAS Gene-Specific Multiplex Reference Standard (FFPE), Cat. No. HD301 (Horizon™)
- Seraseq® Lung & Brain CNV Mix, + 3 copies, Cat. No. 0710-0414 (SeraCare®)
- Seraseq® Breast CNV Mix, + 6 copies, Cat. No. 0710-0412 (SeraCare®)
FFPE RNA samples
- Seraseq® FFPE Tumor Fusion RNA v4 Reference Material, Cat. No. 0710-0496 (SeraCare®)
- Seraseq® FFPE NTRK Fusion RNA Reference Material, Cat. No. 0710-1031 (SeraCare®)
cfTNA samples
- Multiplex I cfDNA Reference Standard Set, Cat. No. HD780 (Horizon™)
Oncomine Precision Assay GX is compatible with solid tumor samples (FFPE DNA or FFPE RNA) as well as liquid biopsy samples (cfTNA).
Oncomine Precision Assay GX is designed for the detection of biomarkers in genes such as EGFR, BRAF, KRAS, ALK, ROS1, NTRK, RET, HER2. The assay analyzes 78 variants, including mutations (45), CNVs (14), and fusion variants (19), across 50 key genes. Included are tumor suppressor genes such as TP53, cancer drivers, and resistance mutations. Content has been carefully curated to include all relevant targets and targets of emerging importance in precision oncology clinical research.
Oncomine Precision Assay GX (Cat. No. A46291) includes the following:
- OPA Pool 1 panel (Part No. A44350)
- Genexus Strip 1, quantity of 8 strips (Part No. A46812)
- Genexus Strip 2-HD, quantity of 8 strips (Part No. A46814)
- The OPA Pool 1 is provided in 8 pairs of tubes, where each tube pair contains one tube with forward (FWD) primers and one tube with reverse (REV) primers.