Archer Panel Demo Data

Archer® FusionPlex®, VariantPlex™, Reveal ctDNA™ and Immunoverse™ kits enrich for a panel of gene targets to enable NGS-based detection of fusions, SNVs/indels, and expression levels. Demo data sets using the indicated kits are summarized in the table below. Click on any of these data sets to view the results in Archer Analysis. Results are also available for download by clicking the Download All Files link on the Sample Summary page for each analysis.

All of these demo data sets were obtained from samples that were sequenced on an Illumina™ instrument. Each kit was tested with a negative and positive sample, as indicated.

Archer Kit Sample Name Sample Source Expected Fusions
Immunoverse BCR KET1779 DPD clone CDR3, PBL None
KET1257 Clonal lymphoma FFPE clone None
KET1737 MCF-7 cell line (neg. ctrl) None
Immunoverse TCR Jurkat-spike-in-1-10-rep-1/2 Jurkat clone CDR3, PBL (BioChain #R1234148-10) None
Jurkat-spike-in-1-100-rep-1/2 Jurkat clone CDR3, PBL (BioChain #R1234148-10) None
Jurkat-spike-in-1-1000-rep-1/2 Jurkat clone CDR3, PBL (BioChain #R1234148-10) None
Jurkat-spike-in-1-10000-rep-1/2 Jurkat clone CDR3, PBL (BioChain #R1234148-10) None
FusionPlex ALK, RET, ROS1 v2 AL10_S25_ARR_FP_NEG_R1_001.combined Archer SureShot Negative Control None
Gold_Standard_ARR_FP_POS_L001_R1_001 Archer SureShot ALK, RET, ROS1 Positive Control CCDC6 → RET, EML4 → ALK, SLC34A2 → ROS1
FusionPlex Sarcoma v1 AL21_S36_SARC_FP_NEG_R1_001.combined Archer SureShot Negative Control None
AL11_S26_SARC_FP_POS_L001_R1_001.combined Archer SureShot ALK, RET, ROS1 Positive Control EML4 → ALK, SLC34A2 → ROS1
FusionPlex Oncology Research v1 NM2123_S73_ORP_NEG_R1_001.combined Fresh frozen RNA from normal lung None
AL57_S69_ORP_FP_POS_R1_001.combined Archer SureShot ALK, RET, ROS1 Positive Control CCDC6 → RET, EML4 → ALK, SLC34A2 → ROS1
FusionPlex Solid Tumor v1 AL41_S56_ST_FP_NEG_R1_001.combined Archer SureShot Negative Control None
AL31_S46_ST_FP_POS_R1_001.combined Archer SureShot ALK, RET, ROS1 Positive Control CCDC6 → RET, EML4 → ALK, SLC34A2 → ROS1
FusionPlex CTL v1 NM2414_Normal_Lung_R1 Fresh frozen RNA from normal lung None
NM2404_CD74-ROS1_R1 Clinical FFPE harboring ROS1 fusion CD74 → ROS1

Immunoverse BCR

This demo data contains 3 total samples: One positive control of total RNA from the B cell receptor IGH-expressing DPD tumor cell line (clone CDR3 sequence CARQGGLVGASGRRDYFDYW) diluted into peripheral blood leukocyte RNA (PBL, Clontech, cat#636592). Dilution of DPD:PBL RNA is 1:100 [ng DPD/(ng DPD + ng PBL)]. The resulting library was sequenced on a MiSeq® sequencer using an Illumina® v3 2x300bp kit. Demultiplexed reads were not normalized and received 1,708,329 reads, deduplicated and error-corrected using the "Immune Repertoire" pipeline in Archer Analysis Version Suite_Analysis_v5.0.6.

The second sample is a positive control DLBCL FFPE; 400ng of input was used with the Immunoverse BCR IGH kit. This sample presents with SHM and is also a clonal FFPE sample (clone CDR3 sequence is = CAKLLIGSHGSFHSDQW). Demultiplexed reads were not normalized and received 2,076,167 reads, deduplicated and error-corrected using the "Immune Repertoire" pipeline in Archer Analysis Version Suite_Analysis_v5.0.6.

The third sample is a negative control using breast cancer cell line MCF-7 that does not express the B cell receptor IGH or IGK/L chains; 400ng of MCF-7 input was used with the Immunoverse BCR IGH and BCR IGK/L kit. The resulting library was sequenced on the MiSeq sequencer using an Illumina v3 2x300bp kit. Demultiplexed reads were not normalized and received 218,321 reads, deduplicated and error-corrected using the "Immune Repertoire" pipeline in Archer Analysis Version Suite_Analysis_v5.0.6.

Sample ID Type CDR3 AA Sequence
KET1779 Pos Control / 1:100 Dilution (DPD:PBL) CARQGGLVGASGRRDYFDYW
KET1257 Pos Control / Clonal FFPE (lymphoma) with mutated SHM CAKLLIGSHGSFHSDQW
KET1737 Negative Control (MCF-7) -

Immunoverse TCR

This demo data contains eight total samples: Two replicates of four serial dilutions of total RNA from the T cell receptor α and β-expressing human tumor cell line Jurkat (clone CDR3 sequence is = CASSFSTCSANYGYTF) into peripheral blood lymphocyte RNA (PBL, BioChain, cat# R1234148-10). Dilutions range from 1:10 dilution to 1:10,000 [ng Jurkat / (ng Jurkat + ng PBL)]. Libraries were generated in duplicate in two different laboratories from 400ng aliquots of the same dilution series described above using Archer’s Immunoverse TCR beta/gamma kit. Resulting libraries were sequenced at each laboratory on a MiSeq sequencer using an Illumina v3 2x300bp kit. Demultiplexed reads were normalized to 600,000 reads, deduplicated and error-corrected using the "Immune Repertoire" pipeline in Archer Analysis 4.1.1 to determine TRB clone frequencies.

Sample ID Type CDR3 AA Sequence
Jurkat-spike-in-1-10-rep-1/2 Pos Control / 1:10 Dilution CASSFSTCSANYGYTF
Jurkat-spike-in-1-100-rep-1/2 Pos Control / 1:100 Dilution CASSFSTCSANYGYTF
Jurkat-spike-in-1-1000-rep-1/2 Pos Control / 1:1,000 Dilution CASSFSTCSANYGYTF
Jurkat-spike-in-1-10000-rep-1/2 Pos Control / 1:10,000 Dilution CASSFSTCSANYGYTF

FusionPlex ALK/RET/ROS1 Kit v2

The Archer FusionPlex ALK, RET, ROS1 v2 Kit enriches for ALK, RET and ROS1 proto-oncogenes, which are frequently rearranged in lung cancers as well as a variety of other cancers. The Archer SureShot™ Negative Control is an FFPE-treated cell line that is wild-type with respect to ALK, RET and ROS1 rearrangement. The Archer SureShot ALK, RET, ROS1 Positive Control is an FFPE-treated cell line mixture containing physiologically relevant levels of EML4-ALK, CCDC6-RET, and SLC34A2-ROS1 fusions. Therefore, the FusionPlex ALK, RET, ROS1 v2 Kit is expected to detect ALK, RET, and ROS1 fusions in the SureShot Positive Control.

Negative Control Positive Control
Sample Name AL10_S25_ARR_FP_NEG_R1_001.combined Gold_Standard_ARR_FP_POS_L001_R1_001
Sample source Archer SureShot Negative Control Archer SureShot ALK, RET, ROS1 Positive Control
Expected Fusions None CCDC6 → RET, EML4 → ALK, SLC34A2 → ROS1
Input amount, ng 50 150
PreSeq Cq 25.9 22.5
Total Number of reads 452259 1946252
RNA Starts per Control GSP2 130 352
Pass QC? Yes Yes
Analysis software Archer Analysis v4.0.6 Archer Analysis v4.0.6

Libraries from the negative and positive samples described above were prepared using the FusionPlex ALK, RET, ROS1 v2 Kit, sequenced on an Illumina instrument, and analyzed in Archer Analysis v4.0.6. The adjacent figure is a screenshot of the resulting data as it appears in Archer Analysis.


FusionPlex Sarcoma Kit v1

The Archer FusionPlex Sarcoma Kit enriches for 26 genes associated with soft tissue cancers, including ALK and ROS1. The Archer SureShot Negative Control is an FFPE-treated cell line that is wild-type with respect to ALK and ROS1 rearrangement. The Archer SureShot ALK, RET, ROS1 Positive Control is an FFPE-treated cell line mixture containing physiologically relevant levels of EML4-ALK, CCDC6-RET, and SLC34A2-ROS1 fusions. Therefore, the FusionPlex Sarcoma Kit is expected to detect ALK and ROS1 fusions in the SureShot Positive Control.

Negative Control Positive Control
Sample Name AL21_S36_SARC_FP_NEG_R1_001.combined AL11_S26_SARC_FP_POS_L001_R1_001.combined
Sample source Archer SureShot Negative Control Archer SureShot ALK, RET, ROS1 Positive Control
Expected Fusions None EML4 → ALK, SLC34A2 → ROS1
Input amount, ng 50 50
PreSeq Cq 25.7 24.6
Total Number of reads 1001208 909315
RNA Starts per Control GSP2 73 90
Pass QC? Yes Yes
Analysis software Archer Analysis v4.0.7 Archer Analysis v4.0.7

Libraries from the negative and positive samples described above were prepared using the FusionPlex Sarcoma Kit, sequenced on an Illumina instrument, and analyzed in Archer Analysis v4.0.7. The adjacent figure is a screenshot of the resulting data as it appears in Archer Analysis.


FusionPlex Oncology Research Kit v1

The Archer FusionPlex Oncology Research Kit enriches for 75 genes most frequently associated with a variety of cancers, including ALK, RET and ROS1. As ALK, RET and ROS1 fusions do not occur in the normal lung, this tissue serves as a negative sample. The Archer SureShot ALK, RET, ROS1 Positive Control is an FFPE-treated cell line mixture containing physiologically relevant levels of EML4-ALK, CCDC6-RET, and SLC34A2-ROS1 fusions. Therefore, the FusionPlex Oncology Research Kit is expected to detect ALK, RET and ROS1 fusions in the SureShot Positive Control.

Negative Control Positive Control
Sample Name NM2123_S73_ORP_NEG_R1_001.combined AL57_S69_ORP_FP_POS_R1_001.combined
Sample source Fresh frozen RNA from normal lung Archer SureShot ALK, RET, ROS1 Positive Control
Expected Fusions None CCDC6 → RET, EML4 → ALK, SLC34A2 → ROS1
Input amount, ng 200 50
PreSeq Cq 20.7 25
Total Number of reads 2206748 950599
RNA Starts per Control GSP2 200 72
Pass QC? Yes Yes
Analysis software Archer Analysis v4.0.7 Archer Analysis v4.0.7

Libraries from the negative and positive samples described above were prepared using the FusionPlex Oncology Research Kit, sequenced on an Illumina instrument, and analyzed in Archer Analysis v4.0.7. The adjacent figure is a screenshot of the resulting data as it appears in Archer Analysis.


FusionPlex Solid Tumor Kit v1

The Archer FusionPlex Solid Tumor Kit enriches for over 50 genes associated with a variety of carcinomas, including ALK, RET and ROS1. The Archer SureShot Negative Control is an FFPE-treated cell line that is wild type with respect to ALK, RET and ROS1 rearrangement. The Archer SureShot ALK, RET, ROS1 Positive Control is an FFPE-treated cell line mixture containing physiologically relevant levels of EML4-ALK, CCDC6-RET, and SLC34A2-ROS1 fusions. Therefore, the FusionPlex Solid Tumor Kit is expected to detect ALK, RET and ROS1 fusions in the SureShot Positive Control.

Negative Control Positive Control
Sample Name AL41_S56_ST_FP_NEG_R1_001.combined AL31_S46_ST_FP_POS_R1_001.combined
Sample source Archer SureShot Negative Control Archer SureShot ALK, RET, ROS1 Positive Control
Expected Fusions None CCDC6 → RET, EML4 → ALK, SLC34A2 → ROS1
Input amount, ng 50 50
PreSeq Cq 25.5 25
Total Number of reads 919278 1311926
RNA Starts per Control GSP2 81 101
Pass QC? Yes Yes
Analysis software Archer Analysis v4.0.7 Archer Analysis v4.0.7

Libraries from the negative and positive samples described above were prepared using the FusionPlex Solid Tumor Kit, sequenced on an Illumina instrument, and analyzed in Archer Analysis v4.0.7. The adjacent figure is a screenshot of the resulting data as it appears in Archer Analysis.


FusionPlex CTL Kit v1

The Archer FusionPlex CTL Kit enriches for 34 genes associated with thyroid and lung cancers, including ALK, RET and ROS1. As ALK, RET and ROS1 fusions do not occur in the normal lung, this tissue serves as a negative sample. A clinical FFPE specimen known to harbor a ROS1 fusion serves as a positive sample for the FusionPlex CTL Kit.

Negative Control Positive Control
Sample Name NM2414_Normal_Lung_R1 NM2404_CD74-ROS1_R1
Sample source Fresh frozen RNA from normal lung Clinical FFPE harboring ROS1 fusion
Expected Fusions None CD74 → ROS1
Input amount, ng 200 200
PreSeq Cq 20.7 25.2
Total Number of reads 1587255 1821770
RNA Starts per Control GSP2 241 27
Pass QC? Yes Yes
Analysis software Archer Analysis v4.0.7 Archer Analysis v4.0.7

Libraries from the negative and positive samples described above were prepared using the FusionPlex CTL Kit, sequenced on an Illumina instrument, and analyzed in Archer Analysis v4.0.7. The adjacent figure is a screenshot of the resulting data as it appears in Archer Analysis.

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For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.