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View additional product information for GX5™ Chip and Genexus™ Coupler - FAQs (A40269)
56 product FAQs found
Remove the templating strips from their boxes in the refrigerator or freezer and get them ready them for loading in the sequencer by equilibrating to/thawing at room temperature for 30 mins. Confirm that the strip contents are completely thawed before loading in the sequencer. If you are delayed in loading, keep the thawed strips on ice or at 4 degrees C until you load them in the sequencer.
Genexus Strip 3B‑GX5 contain 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 using 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 and 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.
Genexus Templating Strips 3B-GX5 and 4-GX5 (Cat. No. A49782) has new Genexus Strip 3B that has the chemistry modified to improve templating and sequencing of GC rich regions.
Genexus Templating Strips 3B-GX5 and 4-GX5 is specifically designed for use with the Oncomine Myeloid GX v2 assay. For all other Genexus assays, please use Genexus Templating Strips 3-GX5 and 4 (Cat. No. A40263).
Genexus Templating Strips 3B-GX5 and 4-GX5 provides 8 pairs of strips per kit - Genexus Templating Strips 3B-GX5 (Part No. A47712) (Orange, 8 strips) and Genexus Templating Strips 4-GX5 (Part No. A46816) (Yellow, 8 strips). Each pair of strips is required to perform automated template preparation and chip loading of two GX5 chips using the Genexus Integrated Sequencer.
Genexus Templating Strips 3B-GX5 (Part No. A47712) (Orange, 8 strips) ships on a gel pack and should be stored at 2 to 8 degrees C. Genexus Templating Strips 4-GX5 (Part No. A46816) (Yellow, 8 strips) ships on dry ice and should be stored at -30 to -10 degrees C.
Detection of somatic variants with the Oncomine Myeloid Research Assay GX has been verified down to 5% allele frequency.
Here is a list of kits that are compatible with Oncomine Myeloid Research Assay GX:
Nucleic acid isolation - RNA samples
- MagMAX mirVana Total RNA Isolation Kit, Cat. No. A27828
- PureLink Total RNA Blood Kit, Cat. No. K156001
- RNaseZap RNase Decontamination Solution, Cat. No. AM9780, AM9782, AM9784
Nucleic acid isolation - DNA samples
- MagMAX DNA Multi-Sample Ultra 2.0 Kit, Cat. No. A36570
- PureLink Genomic DNA Mini Kit, Cat. No. K1820-01
The recommended minimum sample input is 27.75 ng of DNA (1.11 ng/µL minimum concentration) and 14.25 ng of RNA (0.95 ng/µL minimum concentration).
The recommended controls are:
DNA Controls:
- Seraseq® Myeloid Mutation DNA Mix, Cat. No. 0710-0408 (SeraCare®)
- Myeloid DNA Reference Standard, Cat. No. HD829 (Horizon™)
- AcroMetrix™ Oncology Hotspot Control, Cat. No. 969056
RNA Controls:
- Universal Human Reference RNA, Cat. No. 740000 (Agilent™)
- Seraseq® Myeloid Fusion RNA Mix, Cat. No. 0710-0407 (SeraCare®)
Multiplex sequencing of up to 8 Oncomine Myeloid Research Assay GX samples (8 DNA+ 8 RNA) per lane on a GX5 Chip can be performed in a single run. There are 4 lanes on the GX5 Chip, so 32 total samples (32 DNA+ 32 RNA) can be run on one GX5 Chip (8 samples per run).
The Oncomine Myeloid Research Assay GX (Cat. No. A47857) includes the 2-pool DNA panel, the 1-pool RNA panel, Genexus Strip 1, and Genexus Strip 2-AS. The DNA panel is provided in two packs of 8 tubes (4 tubes of Myeloid DNA Pool 1 and 4 tubes of Myeloid DNA Pool 2 per pack). The RNA panel is provided in one pack of 8 tubes (Myeloid RNA Pool 1). Each primer pool in the panel is provided in pairs of tubes, where each tube pair contains one tube with primers in position 1 and one empty uncapped tube in position 2. Three 8-strip packs of the Genexus Strip 1 and Genexus Strip 2-AS (24 total of each strip) are provided with each kit.
The contents of each Oncomine Myeloid Research Assay GX kit are sufficient for up to 32 samples (32 x 3‑pool reactions: 32 x 2‑pool DNA reactions and 32 x 1‑pool RNA reactions).
The Oncomine Myeloid Research Assay GX includes 3 pools of Ion AmpliSeq oligonucleotide primers (a 2-pool DNA panel and a 1-pool RNA panel).
The Oncomine Myeloid Research Assay GX targets key genes and fusions associated with major myeloid disorders, including acute myeloid leukemia (AML), myeloid dysplastic syndrome (MDS), myeloproliferative neoplasms (MPN), chronic myeloid leukemia (CML), chronic myelomonocytic leukemia (CMML), and juvenile myelomonocytic leukemia (JMML). The DNA panel comprises 40 key genes while the RNA panel includes a broad fusion panel of 29 driver genes, enabling detection over 600 unique fusion isotypes. See flyer for gene targets (https://assets.thermofisher.com/TFS-Assets/CSD/Flyers/Oncomine_myeloid_assay_gx_flyer.pdf).
The Oncomine Myeloid Research Assay GX is a comprehensive targeted next-generation sequencing (NGS) assay designed for sensitive detection of myeloid disorder-associated DNA mutations and fusion transcripts in blood and bone marrow samples.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
We recommend storing Genexus Controls at -20 degrees C.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Genexus Strips 3-GX5 (grey) should be stored at 4 degrees C and Genexus Strip 4 (yellow) should be stored at -20 degrees C.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
When necessary, the software will alert the user during the run plan setup that not enough barcodes are available.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
12 racks of pipette tips are provided, containing 96 tips per rack. The pipette tips can be stored at room temperature.
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-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.
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.
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.
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.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The Genexus Sequencing Kit provides the materials required to perform two initializations and automated sequencing of two multilane chips using the Genexus Integrated Sequencer.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
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.