Provide rapid results on clinically relevant biomarkers for multiple tumors cost effectively with a targeted panel

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

 

Table 2. Oncomine Dx Express Test panel gene list

 


NGS made easy—2 instruments, 1 software, and as little as 20 minutes of hands-on time

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


Expedite critical oncology treatment choices with as little as 24 hours turnaround time

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

 


Step into NGS with confidence thanks to automated informatics and reporting

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, key findings, and variant screens
  • Run report
  • Clinical test report
  • Clinical laboratory report

 

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.


One supplier for all your NGS needs

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.


Rely on the proven performance of an FDA-approved test

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.

  • Per-position false positive rate: 0% across 24 blank samples representing 10 tissue types for all variant categories, except for Level 3 single nucleotide variants (SNVs). For Level 3 SNVs, the per-position false positive rate was 0.00004% after masking certain Level 3 SNVs with variant allele frequencies below 5% to prevent false positives.
  • Per-sample false positive rate: 0% across the same 24 blank samples and 10 tissue types for all variant categories, except for Level 3 SNVs. For Level 3 SNVs, the per-sample false positive rate was 0.52% after masking certain Level 3 SNVs with variant allele frequencies below 5% to prevent false positives.

  • 3.24% to 4.38% allelic frequency for EGFR exon 20 insertion CDx variants with insertion lengths of 3, 6, 9, and 12 bp

  • 3.24% to 7.34% allelic frequency for SNVs
  • 2.98% to 5.24% allelic frequency for insertions
  • 3.08% to 4.67% allelic frequency for deletions
  • 4.56 to 5.78 copies for CNVs
  • 5.0 to 15.5 molecular counts for RNA fusion variants
  • 1.5 to 4.93 imbalance scores for RNA fusions by expression imbalance

 

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.

  • Reproducibility: the positive call rate was 100% for all EGFR exon 20 insertion variants, with no instances of no calls observed. The negative call rate was estimated using two wild-type (WT) NSCLC samples and was calculated for hotspots within the scope of the study. For WT samples, the negative call rate was 100.0%, excluding no calls.
  • Repeatability: the repeatability for the detection of EGFR exon 20 insertion variants was estimated with respect to positive variant locations for within-run, between system, between-operator, between-site, between-lot, and total variability. When including or excluding no calls, the within-run repeatability was 100%. For WT samples, the within-run repeatability was 100%, excluding no calls.

 

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.

 

 


Analytical accuracy—tumor profiling 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


Clinical studies

Clinical study for EGFR exon 20 insertions

 

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


Ready to speak to a Thermo Fisher Scientific representative?

We will be happy to answer your questions about bringing NGS to your laboratory.

For In Vitro Diagnostic Use.

CN: 63025