A40278 - FAQs

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.

The Genexus Primer Pool Tubes kit contains 50 empty assemblies (2 tubes/assembly) of the custom tubes required to deliver primer oligos into the automated library preparation reaction. Each assembly is serialized for traceability and can be used with Ion AmpliSeq- and Ion AmpliSeq HD-based assays. Pipet an aliquot of panel primers from a custom panel or Ion AmpliSeq On-Demand Panel to run the assay on the Genexus Integrated Sequencer. The kit also contains a bag of 100 caps.

Note:
- Assays using Ion AmpliSeq chemistry have primer pools that are loaded in capped tubes in position 1 of the primer pool tube carriers. Empty uncapped tubes are loaded in position 2.
- Assays using Ion AmpliSeq HD chemistry have FWD and REV primer pools that are loaded in capped tubes in both positions of the primer pool tube carrier.

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We recommend storing Genexus Controls at -20 degrees C.

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The Genexus Controls kit provides library and template preparation controls for use with the Genexus Integrated Sequencer. Each kit contains an Ion AmpliSeq-based Genexus Control Panel-AS and a Genexus DNA Control, which can be used to prepare up to 32 automated control libraries. The kit also provides Genexus Control Library-AS, sufficient for four template preparations.

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Remove the templating strips from their boxes in the refrigerator or freezer, and prepare them for loading in the sequencer.
- Genexus Strip 3-GX5 needs to equilibrate to room temperature for 30 mins.
- Genexus Strip 4 needs to thaw on ice for at least 30 mins. Keep the strips on ice until you load them in the sequencer.
Genexus Strip 3-GX5 contains magnetic beads in one or two positions, yellow or brown in color, that sometimes get trapped in the upper "keyhole" of the tube. Dislodge these beads from the keyhole before installing the strip in the sequencer. Use the following procedure for each strip:
- Invert the strip 3-4 times to dislodge beads that are trapped in the keyholes.
- To remove any remaining beads and liquid from the keyholes, grasp the strip at one end with the strip seal facing up, then swing the strip with a rapid, downward centrifugal arm motion, ending with a sharp wrist-flick.
- Grasp the strip at the other end, then repeat the centrifugal motion.
- Check tube positions for significant amounts of beads that are still trapped in keyholes, then repeat the centrifugal motion, if needed. It is acceptable if a few beads remain in the keyhole or on the tube wall, but most should be either in suspension or in a pellet at the bottom of the tube.

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Genexus Strips 3-GX5 (grey) should be stored at 4 degrees C and Genexus Strip 4 (yellow) should be stored at -20 degrees C.

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Genexus Templating Strips 3 and 4-GX5 (Cat. No. A40263) can be used with both Ion AmpliSeq library chemistry and Ion AmpliSeq HD library chemistry runs.

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Genexus Templating Strips 3 and 4-GX5 (Cat. No. A40263) provides eight pairs of strips, required to perform automated template preparation and chip loading of two Ion Torrent GX5 chips using the Genexus Integrated Sequencer. The Genexus sequencer uses 2 strips (Genexus Strip 3-GX5 and Genexus Strip 4) to support template preparation. One template strip pair is required for every lane that is used in a run.

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Genexus Barcodes 1-32 HD provides one plate filled with 32 lyophilized, single-use, dual barcodes (Barcodes HD 1-32) and covered with a pierceable foil seal, eliminating the risk of cross contamination between wells. Each plate supports up to 32 reactions.

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Genexus Barcodes 65-96 AS provides one plate filled with 32 lyophilized, single-use, dual barcodes (Barcodes AS 65-96) and covered with a pierceable foil seal, eliminating the risk of cross contamination between wells. Each plate supports up to 32 reactions.

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Genexus Barcodes 33-64 AS provides one plate filled with 32 lyophilized, single-use, dual barcodes (Barcodes AS 33-64) and covered with a pierceable foil seal, eliminating the risk of cross contamination between wells. Each plate supports up to 32 reactions.

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Genexus Barcodes 1-32 AS provides one plate filled with 32 lyophilized, single-use, dual barcodes (Barcodes AS 1-32) and covered with a pierceable foil seal, eliminating the risk of cross contamination between wells. Each plate supports up to 32 reactions.

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When necessary, the software will alert the user during the run plan setup that not enough barcodes are available.

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Barcodes plates can remain on the instrument deck until all barcodes are used. Once you remove the barcode plate, you cannot put it back on to use again as the instrument has no way of tracking barcode usage.

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The Genexus Barcodes 1-96 AS are supplied in 3 individual plates containing 32 dual barcodes per plate. The barcodes are lyophilized. Each barcode plate can also be ordered individually: Genexus Barcodes 1-32 AS (Cat. No. A40258), Genexus Barcodes 33-64 AS (Cat. No. A40259), and Genexus Barcodes 65-96 AS (Cat. No. A40260).

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12 racks of pipette tips are provided, containing 96 tips per rack. The pipette tips can be stored at room temperature.

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Remove the library strips from their boxes in the refrigerator or freezer, and prepare them for loading in the sequencer.
- Genexus Strip 1 needs to equilibrate to room temperature for 30 mins.
- Genexus Strip 2-HD needs to thaw on ice for at least 30 mins. Keep the strips on ice until you load them in the sequencer. Confirm that the strip contents are completely thawed before installing in the sequencer.
Genexus Strip 1 contains magnetic beads in one or two positions, yellow or brown in color, that sometimes get trapped in the upper "keyhole" of the tube. Dislodge these beads from the keyhole by inverting each strip 3-4 times, before installing the strip in the sequencer.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Genexus Strip 1 (red) should be stored at 4 degrees C and Genexus Strip 2-HD (purple) should be stored at -20 degrees C.

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Genexus Library Strips 1 and 2-HD (Cat. No. A40255) for Ion AmpliSeq HD library-based chemistry provides eight pairs of strips/kit, to perform automated library preparation using the Genexus Integrated Sequencer.

Each library strip is needed to create an Ion Ampliseq HD library and supports up to 4 barcodes.
So 8 strip pairs x 4 = up to 32 DNA or RNA samples/run

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Genexus Library Strips 1 and 2-HD (Cat. No. A40255) for Ion AmpliSeq HD library-based chemistry provides eight pairs of strips/kit, to perform automated library preparation using the Genexus Integrated Sequencer.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Remove the library strips from their boxes in the refrigerator or freezer, and prepare them for loading in the sequencer.
- Genexus Strip 1 needs to equilibrate to room temperature for 30 mins.
- Genexus Strip 2-AS needs to thaw on ice for at least 30 mins. Keep the strips on ice until you load them in the sequencer. Confirm that the strip contents are completely thawed before installing in the sequencer.

Genexus Strip 1 contains magnetic beads in one or two positions, yellow or brown in color, that sometimes get trapped in the upper "keyhole" of the tube. Dislodge these beads from the keyhole by inverting each strip 3-4 times, before installing the strip in the sequencer.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Genexus Strip 1 (red) should be stored at 4 degrees C, and Genexus Strip 2-AS (blue) should be stored at -20 degrees C.

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Genexus Library Strips 1 and 2-AS for standard Ion AmpliSeq library-based chemistry provides eight pairs of strips/kit, to perform automated library preparation using the Genexus Integrated Sequencer.

Each library strip pair is needed to create an Ion AmpliSeq library and supports up to 4 barcodes.
So 8 strip pairs x 4 = up to 32 DNA or RNA samples/run

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Genexus Library Strips 1 and 2-AS for standard Ion AmpliSeq library-based chemistry provides eight pairs of strips/kit, to perform automated library preparation using the Genexus Integrated Sequencer.

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If the number of sample reads is very low, and CF-1 metrics fail QC, there could be a potential issue with the chip/coupler.

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The chip and coupler remain installed on the instrument until all lanes are used or up to 2 weeks, whichever comes first. Once a chip and coupler set is removed from the Genexus platform, it can never be reused.

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The GX5 chip generates 12-15 million sequencing reads per lane, or 48-60 million reads per chip. The four-lane chip design provides maximum flexibility for sample processing, enabling sequencing of one to four lanes per run, with the in-use stability to utilize any remaining lanes within two weeks of the initial run.

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The coupler allows the pipettor to dispense reagents into the desired chip lane and it shuttles the chip between the loading and sequencing area on the Genexus platform. Every time you change the chip, you should change the coupler.

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The GX5 Chip and Genexus Coupler (Cat. No. A40269) contains two GX5 chips and two Genexus couplers, sufficient for up to eight sequencing runs with the Genexus Integrated Sequencer.

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Genexus GX5 Starter Pack-HD (Cat. No. A40280) supplies the following components for Ion AmpliSeq HD library preparation and sequencing using a Genexus-ready assay:
- Genexus Strip 1, 8 strips
- Genexus Strip 2‑HD, 8 strips
- Genexus Strip 3‑GX5, 8 strips
- Genexus Strip 4, 8 strips
- Genexus Barcodes 1-32 HD, 1 plate
- Genexus Pipette Tips, 12 racks
- Genexus Cartridge, 2 cartridges
- Genexus Bottle 2, 4 bottles
- Genexus Bottles 1 and 3, 2 bottles each
Note:
- Genexus Barcodes 1-32 HD (Cat. No. A40261) and Genexus Pipette Tips (Cat. No. A40266) are also orderable individually.
- Library and template strips are orderable separately in paired sets as Genexus Library Strips 1 and 2-HD (Cat. No. A40255) and Genexus Templating Strips 3 and 4-GX5 (Cat. No. A40263).
- The Genexus Cartridge, Genexus Bottle 2, and Genexus Bottles 1 and 3 are orderable as a set in the Genexus Sequencing Kit (Cat. No. A40271).
- For custom assays, Genexus Primer Pool Tubes (Cat. No. A40262) must be ordered separately.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Genexus GX5 Starter Pack-AS (Cat. No. A40279) supplies the following components for Ion AmpliSeq library preparation and sequencing using a Genexus-ready assay:
- Genexus Strip 1, 8 strips
- Genexus Strip 2‑AS, 8 strips
- Genexus Strip 3‑GX5, 8 strips
- Genexus Strip 4, 8 strips
- Genexus Barcodes 1-32 AS, 1 plate
- Genexus Pipette Tips, 12 racks
- Genexus Cartridge, 2 cartridges
- Genexus Bottle 2, 4 bottles
- Genexus Bottles 1 and 3, 2 bottles each
Note:
- Genexus Barcodes 1-32 AS (Cat. No. A40258), Genexus Barcodes 33-64 AS (Cat. No. A40259), Genexus Barcodes 65-96 AS (Cat. No. A40260), Genexus Barcodes 1-96 AS (Cat. No. A40257), and Genexus Pipette Tips (Cat. No. A40266) are also orderable individually.
- Library and template strips are orderable separately in paired sets as Genexus Library Strips 1 and 2-AS (Cat. No. A40252) and Genexus Templating Strips 3 and 4-GX5 (Cat. No. A40263).
- Genexus Cartridge, Genexus Bottle 2, and Genexus Bottles 1 and 3 are orderable as a set in the Genexus Sequencing Kit (Cat. No. A40271).
- For custom assays, Genexus Primer Pool Tubes (Cat. No. A40262) must be ordered separately.


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Yes, the Genexus Sequencing Kit reagents and supplies can be used with both 200-400 base-read Ion AmpliSeq library chemistry and Ion AmpliSeq HD library chemistry runs.

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The Genexus Sequencing Kit consumables are stable on the Genexus instrument for up to two weeks after initialization, allowing flexibility to use the chip lanes according to sample throughput needs.

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The Genexus Sequencing Kit provides the materials required to perform two initializations and automated sequencing of two multilane chips using the Genexus Integrated Sequencer.

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Here are the contents and storage conditions:
- Genexus Cartridge, store at -10 to -30 degrees C
- Genexus Bottle 2, store at room temperature
- Genexus Bottles 1 and 3, store at room temperature

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.