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Whether you are currently utilizing next-generation sequencing (NGS) or still considering it, the FDA-approved Oncomine Dx Express Test is designed to streamline your workflow, minimize quantity not sufficient (QNS), and enable you to connect more patients to precision oncology fast.
The Oncomine Dx Express Test indicated as a companion diagnostic (CDx) to identify non-small cell lung cancer (NSCLC) patients with EGFR exon 20 insertion mutations who may benefit from personalized treatment with ZEGFROVY™ (sunvozertinib), as listed in Table 1 in accordance with the approved therapeutic product labeling.
The test also detects tumor profiling biomarkers recommended by professional guidelines for multiple solid tumors (Table 2). This includes substitutions, insertions, and deletions in 42 genes, copy number variants in 10 genes, and fusions or splice variants in 18 genes relevant in NSCLC, colorectal cancer, cholangiocarcinoma, and melanoma, among others.
Table 1. Companion diagnostic indications
Tissue type |
Gene |
Variant |
Targeted therapy |
Non-small cell lung cancer (NSCLC) |
EGFR |
EGFR exon 20 insertions |
ZEGFROVY™ (sunvozertinib) |
Table 2. Oncomine Dx Express Test panel gene list
DNA |
RNA |
|||||||||
Substitutions, insertions, and deletions |
Copy number variants |
Fusions and splice variants |
||||||||
AKT1 AKT2 AKT3 ALK AR ARAF BRAF |
CDK4 CHEK2 CTNNB1 EGFR ERBB2 ERBB3 ERBB4 |
ESR1 FGFR1 FGFR2 FGFR3 FGFR4 FLT3 GNAS |
HRAS IDH1 IDH2 KEAP1 KIT KRAS MAP2K1 |
MAP2K2 MET NRAS NTRK1 NTRK2 NTRK3 PDGFRA |
PIK3CA PTEN RAF1 RET ROS1 STK11 TP53 |
AR EGFR ERBB2 ERBB3 FGFR1 |
FGFR2 FGFR3 KRAS MET PIK3CA |
ALK AR BRAF EGFR ESR1 FGFR1 |
FGFR2 FGFR3 MET NRG1 NTRK1 NTRK2 |
NTRK3 NUTM1 RET ROS1 RSPO2 RSPO3 |
The Genexus Dx System automates the NGS workflow from patient samples to reports with only two user touchpoints and as little as 20 minutes of hands-on time.
Pre-treated FFPE tissue sections are loaded onto the Genexus Dx Purification System and the instrument performs automated purification and quantification of DNA and RNA.
Library preparation, template preparation, sequencing, analysis, and reporting are performed by the Genexus Dx Integrated Sequencer. Throughout this procedure, sample and reagent information is recorded and tracked by one integrated software. This highly automated workflow helps reduce laboratory staff burden and the potential for human errors and alleviates the need for specialized bioinformatics expertise.
Oncomine Dx Express Test workflow
Unlike other NGS workflows, the Oncomine Dx Express Test delivers results in as little as 24 hours from pre-treated FFPE tissue sections to report*. Also, it uses a four-lane chip for flexible batching. This helps to reduce delays due to batching while maintaining operational efficiency to meet a wide range of testing demands.
* Timing varies by number of samples and type of run
Table 3. FFPE sample-to-report turnaround times
Lane |
Sample batch size |
Turnaround time |
1 |
2 samples |
18 hours |
2 |
6 samples |
26 hours 50 minutes |
4 |
12 samples |
38 hours 25 minutes |
The Genexus Dx Software directs the progress of the sample from creation of a run plan through automated sample preparation, library preparation, template preparation, sequencing, and analysis. The Genexus Dx Software generates the following results and reports for each sequenced sample and its associated controls.
Quality control specifications throughout the NGS workflow are automatically applied to streamline interpretation and help ensure reportable results are accurate. Positive calls are classified into 3 biomarker levels: Level 1: Companion Diagnostic (CDx) Biomarkers, Level 2: Cancer Mutations with Evidence of Clinical Significance, and Level 3: Cancer Mutations with Potential Clinical Significance.
The layout and contents of the report can be customized to facilitate a clear and concise report, providing clinicians with relevant information tailored to the patient.
Everything from instruments, software, reagents, and consumables, as well as service and ongoing support, comes from one supplier: Thermo Fisher Scientific, which aims to make your implementation, as well as day-to-day running of this workflow, as simple as possible.
Extensive performance studies were conducted to establish performance characteristics of the Oncomine Dx Express Test for FFPE tumor samples. A summary of selected studies is provided below. For complete studies and results, refer to the Oncomine Dx Express Test User Guide.
Table 4. Panel reproducibility positive call rate for tumor profiling variants by variant class
Variant type |
Fold LoD level |
Total calls |
Observed positive calls |
Observed negative calls |
Observed no calls |
Positive call rate (95% Cls)—no calls included |
Positive call rate (95% Cls)—no calls excluded |
SNV |
1–1.5x |
1368 |
1329 |
26 |
13 |
97.15% (96.13%, 97.91%) |
98.08% (97.20%, 98.69%) |
SNV |
2–3x |
576 |
575 |
0 |
1 |
99.83% (99.02%, 99.97%) |
100% (99.34%, 100%) |
Insertion |
1–1.5x |
504 |
503 |
0 |
1 |
99.80% (98.88%, 99.96%) |
100% (99.24%, 100%) |
Insertion |
2–3x |
144 |
144 |
0 |
0 |
100% (97.40%, 100%) |
100% (97.40%, 100%) |
Deletion |
1–1.5x |
576 |
561 |
9 |
6 |
97.40% (95.75%, 98.42%) |
98.42% (97.03%, 99.17%) |
Deletion |
2–3x |
216 |
216 |
0 |
0 |
100% (98.25%, 100%) |
100% (98.25%, 100%) |
CNV |
1–1.5x |
792 |
789 |
3 |
0 |
99.62% (98.89%, 99.87%) |
99.62% (98.89%, 99.87%) |
Fusion |
1–1.5x |
1584 |
1555 |
29 |
0 |
98.17% (97.38%, 98.72%) |
98.17% (97.38%, 98.72%) |
Fusion |
2–3x |
432 |
432 |
0 |
0 |
100% (99.12%, 100%) |
100% (99.12%, 100%) |
Fusion imbalance |
1–1.5x |
72 |
72 |
0 |
0 |
100% (94.93%, 100%) |
100% (94.93%, 100%) |
Splice variant |
1–1.5x |
288 |
287 |
1 |
0 |
99.65% (98.06%, 99.94%) |
99.65% (98.06%, 99.94%) |
Splice variant |
2–3x |
144 |
144 |
0 |
0 |
100% (97.40%, 100%) |
100% (97.40%, 100%) |
Table 5. Panel reproducibility negative call rate for tumor profiling variants by variant class
Variant type |
Fold LoD level |
Total calls |
Observed positive calls |
Observed negative calls |
Observed no calls |
Negative call rate (95% Cls)—no calls included |
Positive call rate (95% Cls)—no calls excluded |
SNV |
1–1.5x |
2964168 |
1319 |
2945554 |
17295 |
99.37% (99.36%, 99.38%) |
99.96% (99.95%, 99.96%) |
SNV |
2–3x |
1164456 |
455 |
1160937 |
3064 |
99.70% (99.69%, 99.71%) |
99.96% (99.95%, 99.96%) |
Insertion |
1–1.5x |
593064 |
1 |
589125 |
3938 |
99.34% (99.31%, 99.36%) |
100.00% (100.0%, 100%) |
Insertion |
2–3x |
233424 |
0 |
232810 |
614 |
99.74% (99.72%, 99.76%) |
100.00% (100.0%, 100%) |
Deletion |
1–1.5x |
783648 |
0 |
746619 |
37029 |
95.27% (95.23%, 95.32%) |
100.00% (100.0%, 100%) |
Deletion |
2–3x |
307872 |
0 |
300911 |
6961 |
97.74% (97.69%, 97.79%) |
100.00% (100.0%, 100%) |
CNV |
1–1.5x |
6408 |
0 |
6408 |
0 |
100% (99.94%, 100%) |
100% (99.94%, 100%) |
Fusion |
1–1.5x |
1825056 |
50 |
1821714 |
3292 |
99.82% (99.81%, 99.82%) |
100.00% (100.0%, 100%) |
Fusion |
2–3x |
564984 |
88 |
561681 |
3215 |
99.42% (99.40%, 99.43%) |
99.98% (99.98%, 99.99%) |
Fusion imbalance |
1–1.5x |
2880 |
0 |
1414 |
1466 |
49.10% (47.27%, 50.92%) |
100% (99.73%, 100%) |
Splice variant |
1–1.5x |
7200 |
101 |
7099 |
0 |
98.60% (98.30%, 98.84%) |
98.60% (98.30%, 98.84%) |
Splice variant |
2–3x |
2160 |
0 |
2160 |
0 |
100% (99.82%, 100%) |
100% (99.82%, 100%) |
The panel reproducibility study was conducted at three test sites to evaluate the repeatability and reproducibility of the Oncomine Dx Express Test for detection of EGFR exon 20 insertion variants in NSCLC starting from extracted nucleic acid.
Table 6. Agreement between Oncomine Dx Express Test and orthogonal method for EGFR exon 20 insertion detection
Parameter |
Agreed (N) |
Excluding ODxET unknowns [1] |
Including ODxET unknowns [1] |
||||
Total (N) |
Percent agreement |
95% CIs |
Total (N) |
Percent agreement |
95% CIs |
||
PPA |
84 |
84 |
100% |
(95.6%, 100%) |
84 |
100% |
(95.6%, 100%) |
NPA |
105 |
110 |
95.5% |
(89.8%, 98.0%) |
111 |
94.6% |
(88.7%, 97.5%) |
OPA |
189 |
194 |
97.4% |
(94.1%, 98.9%) |
195 |
96.9% |
(93.5%, 98.6%) |
[1] Unknowns are defined as values due to insufficient sample, or sample QC sequencing failure resulting in an invalid result or no call for the variant.
The variability across sites, operators, and instruments (reproducibility) and within-run precision performance (repeatability) was evaluated starting with the extracted nucleic acid. Three test sites, with two operators and four instruments per site, were used for the study.
Table 4. Panel reproducibility positive call rate for tumor profiling variants by variant class.
Variant type |
Fold LoD level |
Total calls |
Observed positive calls |
Observed negative calls |
Observed no calls |
Positive call rate (95% Cls)—no calls included |
Positive call rate (95% Cls)—no calls excluded |
SNV |
1–1.5x |
1368 |
1329 |
26 |
13 |
97.15% (96.13%, 97.91%) |
98.08% (97.20%, 98.69%) |
SNV |
2–3x |
576 |
575 |
0 |
1 |
99.83% (99.02%, 99.97%) |
100% (99.34%, 100%) |
Insertion |
1–1.5x |
504 |
503 |
0 |
1 |
99.80% (98.88%, 99.96%) |
100% (99.24%, 100%) |
Insertion |
2–3x |
144 |
144 |
0 |
0 |
100% (97.40%, 100%) |
100% (97.40%, 100%) |
Deletion |
1–1.5x |
576 |
561 |
9 |
6 |
97.40% (95.75%, 98.42%) |
98.42% (97.03%, 99.17%) |
Deletion |
2–3x |
216 |
216 |
0 |
0 |
100% (98.25%, 100%) |
100% (98.25%, 100%) |
CNV |
1–1.5x |
792 |
789 |
3 |
0 |
99.62% (98.89%, 99.87%) |
99.62% (98.89%, 99.87%) |
Fusion |
1–1.5x |
1584 |
1555 |
29 |
0 |
98.17% (97.38%, 98.72%) |
98.17% (97.38%, 98.72%) |
Fusion |
2–3x |
432 |
432 |
0 |
0 |
100% (99.12%, 100%) |
100% (99.12%, 100%) |
Fusion imbalance |
1–1.5x |
72 |
72 |
0 |
0 |
100% (94.93%, 100%) |
100% (94.93%, 100%) |
Splice variant |
1–1.5x |
288 |
287 |
1 |
0 |
99.65% (98.06%, 99.94%) |
99.65% (98.06%, 99.94%) |
Splice variant |
2–3x |
144 |
144 |
0 |
0 |
100% (97.40%, 100%) |
100% (97.40%, 100%) |
Table 5. Panel reproducibility negative call rate for tumor profiling variants by variant class.
Variant type |
Fold LoD level |
Total calls |
Observed positive calls |
Observed negative calls |
Observed no calls |
Negative call rate (95% Cls)—no calls included |
Positive call rate (95% Cls)—no calls excluded |
SNV |
1–1.5x |
2964168 |
1319 |
2945554 |
17295 |
99.37% (99.36%, 99.38%) |
99.96% (99.95%, 99.96%) |
SNV |
2–3x |
1164456 |
455 |
1160937 |
3064 |
99.70% (99.69%, 99.71%) |
99.96% (99.95%, 99.96%) |
Insertion |
1–1.5x |
593064 |
1 |
589125 |
3938 |
99.34% (99.31%, 99.36%) |
100.00% (100.0%, 100%) |
Insertion |
2–3x |
233424 |
0 |
232810 |
614 |
99.74% (99.72%, 99.76%) |
100.00% (100.0%, 100%) |
Deletion |
1–1.5x |
783648 |
0 |
746619 |
37029 |
95.27% (95.23%, 95.32%) |
100.00% (100.0%, 100%) |
Deletion |
2–3x |
307872 |
0 |
300911 |
6961 |
97.74% (97.69%, 97.79%) |
100.00% (100.0%, 100%) |
CNV |
1–1.5x |
6408 |
0 |
6408 |
0 |
100% (99.94%, 100%) |
100% (99.94%, 100%) |
Fusion |
1–1.5x |
1825056 |
50 |
1821714 |
3292 |
99.82% (99.81%, 99.82%) |
100.00% (100.0%, 100%) |
Fusion |
2–3x |
564984 |
88 |
561681 |
3215 |
99.42% (99.40%, 99.43%) |
99.98% (99.98%, 99.99%) |
Fusion imbalance |
1–1.5x |
2880 |
0 |
1414 |
1466 |
49.10% (47.27%, 50.92%) |
100% (99.73%, 100%) |
Splice variant |
1–1.5x |
7200 |
101 |
7099 |
0 |
98.60% (98.30%, 98.84%) |
98.60% (98.30%, 98.84%) |
Splice variant |
2–3x |
2160 |
0 |
2160 |
0 |
100% (99.82%, 100%) |
100% (99.82%, 100%) |
Repeatability—tumor profiling variants
A variance component analysis was performed for target variants tested near or above the LoD using the appropriate quantitative metric for each variant type (i.e., VAF for SNVs and indels, copy number for CNVs, and molecular counts for RNA variants). The results show a coefficient of variation (CV) of less than 10% between operators/instruments for all variants, except for one ALK, one ROS1 fusion, and one MET splice variants, which had CVs of 20.95%, 14.59%, and 11.65%, respectively. Reagent lot, within-run, and within-lab %CV varied by variant type, with the highest %CV observed for RNA variants.
The accuracy of the Oncomine Dx Express Test for detecting SNVs, indels, CNVs, fusions, and RNA splice variants was evaluated by comparing its results with those obtained from validated orthogonal methods across three separate studies.
The accuracy study I evaluated the accuracy of the Oncomine Dx Express Test in detecting various tumor profiling variants, including SNV/multi-nucleotide variants (MNVs), indels, CNVs, and RNA splice variants in FFPE clinical samples using a representative approach, comparing its results with the validated NGS orthogonal test. PPA and NPA estimates and the respective 95% confidence interval (CI) between Oncomine Dx Express Test and the orthogonal test were calculated using the orthogonal test result as reference and are summarized in Table 7.
Table 7. Agreement summary for SNVs, insertions, deletions, CNVs, and RNA tumor profiling variants
Variant type |
ODxET+, Orth+ |
ODxET+, Orth- |
ODxET-, Orth+ |
ODxET-, Orth- |
PPA (n/N) [95% CI] |
NPA (n/N) [95% CI] |
All variants |
586 |
112 |
11 |
800035 |
98.2% (586/597) [96.7%, 99.0%] |
100.0% (800035/800147) [100.0%, 100.0%] |
All SNVs |
397 |
47 |
2 |
387643 |
99.5% (397/399) [98.2%, 99.9%] |
100.0% (387643/387690) [100.0%, 100.0%] |
All insertions |
5 |
1 |
0 |
61874 |
100.0% (5/5) [56.6%, 100.0%] |
100.0% (61874/61875) [100.0%, 100.0%] |
All deletions |
23 |
2 |
0 |
78635 |
100.0% (23/23) [85.7%, 100.0%] |
100.0% (78635/78637) [100.0%, 100.0%] |
All CNV |
114 |
32 |
7 |
4294 |
94.2% (114/121) [88.5%, 97.2%] |
99.3% (4294/4326) [99.0%, 99.5%] |
All RNA |
47 |
30 |
2 |
261123 |
95.9% (47/49) [86.3%, 98.9%] |
100.0% (261123/261153) [100.0%, 100.0%] |
Abbreviations: ODxET, Oncomine Dx Express Test; Orth, orthogonal test
The accuracy study II evaluated the accuracy of the Oncomine Dx Express Test in detecting ERBB2 CNVs, ALK fusions, and RET fusions by comparing its results with validated orthogonal assays, as summarized in Table 8.
Table 8. Agreement summary for SNVs, insertions, deletions, CNVs, and RNA tumor profiling variants
Variant type / gene |
ODxET+, Orth+ |
ODxET+, Orth- |
ODxET-, Orth+ |
ODxET-, Orth- |
PPA (n/N) [95% CI] |
NPA (n/N) [95% CI] |
All variants |
72 |
6 |
0 |
112 |
100.0% (72/72) [94.9%, 100.0%] |
94.9% (112/118) [89.3%, 97.6%] |
Level 2 ERBB2 |
29 |
4 |
0 |
37 |
100.0% (29/29) [88.3%, 100.0%] |
90.2% (37/41) [77.5%, 96.1%] |
CNV |
|
|
|
|
||
All RNA variants |
43 |
2 |
0 |
75 |
100.0% (43/43) [91.8%, 100.0%] |
97.4% (75/77) [91.0%, 99. 3%] |
Level 2 ALK |
26 |
1 |
0 |
41 |
100.0% (26/26) [87.1%, 100.0%] |
97.6% (41/42) [87.7%, 99.6%] |
Level 2 RET |
17 |
1 |
0 |
34 |
100.0% (17/17) [81.6%, 100.0%] |
97.1% (34/35) [85.5%, 99.5%] |
The accuracy study III evaluated the accuracy of the Oncomine Dx Express Test in detecting EGFR T790M and EGFR L858R SNVs, and EGFR exon 19 deletions by comparing its results with an orthogonal PCR method, as summarized in Table 9.
Table 9. Agreement summary for SNVs, insertions, deletions, CNVs, and RNA tumor profiling variants
Variant type / gene |
ODxET+, Orth+ |
ODxET+, Orth- |
ODxET-, Orth+ |
ODxET-, Orth- |
PPA (n/N) [95% CI] |
NPA (n/N) [95% CI] |
All EGFR |
23 |
1 |
0 |
45 |
100.0% (23/23) [85.7%, 100.0%] |
97.8% (45/46) [88.7%, 99.6%] |
Level 2 EGFR |
23 |
1 |
0 |
45 |
100.0% (23/23) [85.7%, 100.0%] |
97.8% (45/46) [88.7%, 99.6%] |
SNV EGFR |
11 |
1 |
0 |
45 |
100.0% (11/11) [74.1%, 100.0%] |
97.8% (45/46) [88.7%, 99.6%] |
Deletion EGFR |
12 |
0 |
0 |
45 |
100.0% (12/12) [75.8%, 100.0%] |
100.0% (45/45) [92.1%, 100.0%] |
Abbreviations: ODxET, Oncomine Dx Express Test; Orth, orthogonal test
The ability of the Oncomine Dx Express Test to identify the EGFR exon 20 insertion biomarker in FFPE NSCLC tumor specimens was evaluated with specimens from patients enrolled in clinical trial WU-KONG1B (NCT03974022) and commercially sourced samples by comparing results from the Oncomine Dx Express Test to results obtained with the enrolling clinical trial assays (CTAs) used in the trial.
A clinical bridging study was conducted to establish reasonable assurance of safety and effectiveness of the Oncomine Dx Express Test for detection of EGFR exon 20 insertions in NSCLC FFPE tumor specimens to select patients for treatment with ZEGFROVY™ (sunvozertinib) in the United States. This included specimens from patients enrolled in the WU-KONG1B trial (NCT03974022) and commercially sourced biomarker-negative samples. The study evaluated the concordance between EGFR exon 20 insertions detected using clinical trial assays (CTAs) and the Oncomine Dx Express Test (ODxET) in the intent-to-test population and aimed to assess the clinical efficacy of the Oncomine Dx Express Test in identifying patients positive for EGFR exon 20 insertions who may benefit from treatment with ZEGFROVY™ (sunvozertinib).
The full analysis set consisted of 192 patients, including the primary efficacy population of 85 patients who received the 200 mg dose of sunvozertinib and 107 patients who received an unapproved dose. Overall response rates (ORRs) were evaluated by BIRC according to RECIST v1.1 for the primary efficacy population.
In the 200 mg cohort (N = 85), the ORR in the CTA-positive population was 46% (39/85), with 6% (5/85) of patients having a complete response (CR) and 40% (34/85) having a partial response (PR). Among these, 58 patients were both CTA-positive and tested positive for EGFR exon 20 insertions using the ODxET (ODxET+ | CTA+). In this subgroup (N = 58), the ORR was 41% (24/58), with 5% (3/58) patients having a CR and 36% (21/58) having a PR. These results, summarized in Table 10, demonstrate that the ORRs for the ODxET EGFR exon 20 insertion–positive population align with those observed in the CTA EGFR exon 20 insertion–positive population.
In the 200 mg cohort, the median duration of response (DoR) for the CTA-positive population was 11.1 months, with 72% of patients having a DoR ≥6 months and a median follow-up of 15.2 months. For the ODxET+ | CTA+ population, the median DoR was 9.8 months, with 63% of patients having a DoR ≥6 months and a median follow-up of 11.7 months. Additional details are provided in Table 10.
Table 10. Efficacy results of WU-KONG1B study
Efficacy parameter |
ZEGFROVY (N=85, CTA+) |
ODxET+ | CTA+ (N=58) |
Overall Response Rate (ORR), % (95% CIa) |
46 (35, 57) |
41 (29, 55) |
Complete Response, % |
6 |
5 |
Partial Response, % |
40 |
36 |
Duration of Response (DOR) |
N=39 |
N=24 |
Medianb, months (95% CI) |
11.1 (8.2, NE) |
9.8 (5.6, NE) |
Patients with DOR ≥6 months |
72% |
63% |
a. 95% CI for ORR was calculated based on Clopper-Pearson exact CI method. b. Kaplan-Meier estimate using confirmed responses
NE= Not estimable
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