therascreen BRAF V600E RGQ PCR Kit

P190026 · QIAGEN GmbH · OWD · Apr 15, 2020 · Medical Genetics

Device Facts

• Record ID: P190026
• Device Name: therascreen BRAF V600E RGQ PCR Kit
• Applicant: QIAGEN GmbH
• Product Code: OWD · Medical Genetics
• Decision Date: Apr 15, 2020
• Decision: APPR
• Device Class: Class 3

Intended Use

The therascreen BRAF V600E RGQ PCR Kit is a real-time PCR test for the qualitative detection of V600E mutations in the BRAF gene using genomic DNA extracted from formalin-fixed paraffin-embedded (FFPE) human colorectal cancer (CRC) tumor tissue. The therascreen BRAF V600E RGQ PCR Kit is an in vitro diagnostic device intended to be used as an aid in selecting patients with metastatic colorectal cancer (mCRC) whose tumors carry the BRAF V600E mutation for treatment with BRAFTOVI (encorafenib) in combination with cetuximab. The therascreen BRAF V600E RGQ PCR Kit is for use on the Rotor-Gene Q MDx (US) instrument. The therascreen BRAF V600E RGQ PCR Kit is intended for in vitro diagnostic use.

Device Story

Device detects BRAF V600E mutation (T1799A) in FFPE colorectal cancer tissue; utilizes ARMS and Scorpion technology for selective amplification and detection. Input: genomic DNA extracted from FFPE sections using QIAamp DSP DNA FFPE Tissue Kit. Process: real-time PCR on Rotor-Gene Q MDx instrument; automated analysis via Rotor-Gene AssayManager (RGAM) software with Gamma MDx plug-in. Output: qualitative mutation status (Mutation Detected/No Mutation Detected) based on delta-Ct calculation. Used in clinical laboratories by trained personnel. Output informs physician selection of patients for BRAFTOVI (encorafenib) plus cetuximab therapy; identifies patients likely to benefit from targeted kinase/EGFR inhibition.

Clinical Evidence

PMA based on BEACON clinical trial (NCT01909453) and bridging study. Accuracy assessed against Sanger sequencing in 600 samples; 95.2% overall agreement. Clinical efficacy demonstrated in 665 randomized patients; BRAFTOVI + cetuximab showed statistically significant OS improvement (HR 0.60; 95% CI 0.45-0.79) and ORR (20.4% vs 1.9%) compared to control. CDx performance validated via concordance with CTA; hazard ratio for CDx+ subjects estimated at 0.493 (95% CI 0.344-0.659).

Technological Characteristics

Real-time PCR assay using ARMS and Scorpion technology. Components: Control Reaction Mix, V600E Mutation Reaction Mix, Taq polymerase, controls. Instrument: Rotor-Gene Q MDx (centrifugal rotary thermal cycling). Software: RGAM v2.1, Gamma MDx plug-in, Assay Profile v1.0.0. Connectivity: Standalone instrument. Sterilization: N/A (reagents).

Indications for Use

Indicated for patients with metastatic colorectal cancer (mCRC) to identify those with BRAF V600E mutations for treatment with BRAFTOVI (encorafenib) in combination with cetuximab. Requires FFPE tumor tissue with minimum 5% tumor content.

Regulatory Classification

Identification

The somatic gene mutation detection system is an in vitro diagnostic nucleic acid amplification and real-time detection system for the identification of genetic mutations in DNA extracted from human tumor tissues.

Submission Summary (Full Text)

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SUMMARY OF SAFETY AND EFFECTIVENESS DATA (SSED)

I. GENERAL INFORMATION

Device Generic Name: Real-time PCR Test
Device Trade Name: therascreen® BRAF V600E RGQ PCR Kit
Device Procode: OWD
Applicants Name and Address: QIAGEN GmbH
QIAGEN Strasse 1
Hilden 40724
Germany
Date(s) of Panel Recommendation: None
Premarket Approval Application: P190026
Date of FDA Notice of Approval: April 15, 2020

II. INDICATIONS FOR USE

The therascreen BRAF V600E RGQ PCR Kit is a real-time PCR test for the qualitative detection of V600E mutations in the BRAF gene using genomic DNA extracted from formalin-fixed paraffin-embedded (FFPE) human colorectal cancer (CRC) tumor tissue.

The therascreen BRAF V600E RGQ PCR Kit is an in vitro diagnostic device intended to be used as an aid in selecting patients with metastatic colorectal cancer (mCRC) whose tumors carry the BRAF V600E mutation for treatment with BRAFTOVI (encorafenib) in combination with cetuximab.

The therascreen BRAF V600E RGQ PCR Kit is for use on the Rotor-Gene Q MDx (US) instrument.

The therascreen BRAF V600E RGQ PCR Kit is intended for in vitro diagnostic use.

III. CONTRAINDICATIONS

None.

IV. WARNINGS AND PRECAUTIONS

The warnings and precautions can be found in the therascreen BRAF V600E RGQ PCR Kit labeling.

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V. DEVICE DESCRIPTION

The therascreen BRAF V600E RGQ PCR Kit is a real-time qualitative polymerase chain reaction (PCR) kit designed to detect the V600E mutation (T1799A) in exon 15 codon 600 of the BRAF gene. The therascreen BRAF V600E RGQ PCR System uses:

- QIAGEN QIAamp DSP DNA FFPE Tissue Kit.
- QIAGEN therascreen BRAF V600E RGQ PCR Kit.
- QIAGEN Rotor-Gene Q MDx Instrument (RGQ) MDx Instrument with Automated data analysis and results interpretation using Rotor-Gene AssayManager® (RGAM) software version 2.1, Gamma MDx plug-in and therascreen BRAF V600E FFPE Assay Profile.

The therascreen BRAF V600E RGQ PCR Kit is supplied in a 24-reaction package size (with scope of analyzing 24 clinical samples in 6 x 4 PCR runs (i.e., 6 samples + 2 run controls per PCR run x 4 PCR runs)) and each kit contains the following components are shown in Table 1.

Table 1. Kit Components
| Component | Purpose |
| --- | --- |
| Control Reaction Mix | To detect BRAF gene exon 3. It is used to determine the amount of amplifiable DNA present in the sample and is a factor used in the mutation analysis calculations. |
| V600E Mutation Reaction Mix: | Tor the identification of V600E on the BRAF gene exon 15* |
| BRAF Positive Control (PC): | PCR amplification control template |
| Nuclease and DNA free water | for No Template Control (NTC) |
| Nuclease and DNA free water for sample dilution | |
| Taq polymerase | |

* The BRAF Mutation Reaction mix will not distinguish between V600E and V600E Complex (V600Ec) mutations. V600Ec is a very rare somatic mutations in CRC. The assay is not analytically validated for V600Ec.

A. Specimen Preparation

The assay is validated for use with FFPE CRC specimens with a minimum of 5% tumor content. Initial preparation of specimens for use with the therascreen BRAF V600E RGQ PCR Kit follows standard pathology procedures. Tumor tissue is typically fixed in 10% neutral buffered formalin and then embedded in paraffin to form FFPE blocks. FFPE tissue blocks are cut into 4-5μm sections and mounted onto glass slides. A hematoxylin and eosin (H&E) stained slide is used to confirm that there is tumor present. Two non-stained tissue sections are scraped from the slide for Deoxyribonucleic Acid (DNA) extraction.

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DNA is manually extracted and purified using the QIAGEN QIAamp DSP DNA FFPE Tissue Kit following the standard extraction method with the following modifications:

- Two FFPE sections are used per extraction.
- Ethanol evaporation temperature is set at 35.0°C to 39.0°C for a minimum of 10 minutes.
- Proteinase K digestion is performed for 1 hour.
- The extracted DNA sample is eluted with two elution steps consisting of elution buffer (ATE) of 60 µl each, resulting in a final elution volume of 120 µl from each sample extraction run.

## B. Qualification of DNA Samples

Determination of DNA input for the assay is based on DNA qualification and is performed using the Control Reaction Mix to assess the amount of amplifiable DNA. Samples will be qualified for further Mutation Assessment if the amount of the amplifiable DNA (represented by the Ct value of the Control Reaction Mix) is determined to be within the pre-defined Control Working Range (CWR). The acceptable measurable range of the assay (Control CT 20.95–33.00).

## C. PCR Amplification and Detection

The therascreen BRAF V600E RGQ PCR Kit uses Amplification Refractory Mutation System (ARMS®) and Scorpion technology to selectively amplify and detect the BRAF V600E mutation. The ARMS technique is based on the use of mutation sequence-specific PCR primers that allow amplification of test DNA only when the 3′-end of the primer is hybridized to the target mutation sequence. In the presence of a wild-type sequence or other non-targeted BRAF mutations, the ARMS primer will not completely hybridize, and amplification will not occur.

The Scorpion contains both primer and probe elements. The probe element contains fluorophore and quencher. When target sequence is not available, the fluorophore and quencher are in a closed configuration, i.e., the fluorophore and quencher are in such close proximity that fluorescence is reduced through collisional quenching. During PCR, the Scorpion primer element and ARMS primer will amplify the target sequences, for which the scorpion probe will bind to during the annealing step. The binding leads to the fluorophore and quencher being physically separated (open configuration) and fluorescence increases. The open configuration is more thermodynamically stable than the closed configuration.

The Scorpion probes used in the therascreen BRAF V600E RGQ PCR Kit are labeled with carboxyfluorescein (FAM) or hexachloro-fluorescein (HEX) fluorescent reporter dyes each with a distinct absorption and emission profile. The FAM probe is used for target detection (both Wild Type and BRAF V600E

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mutant) and the HEX probe is used in the Internal Control Reaction (IC).

The therascreen BRAF V600E RGQ PCR Kit contains reagents that allow PCR amplification and qualitative detection of the mutation listed in Table 2.

Table 1: Mutation Targets of the therascreen BRAF V600E RGQ PCR Kit
| Mutation | Exon | Base change | COSMIC ID* |
| --- | --- | --- | --- |
| V600E | 15 | 1799T>A | 476 |

*COSMIC IDs taken from the Catalogue of Somatic Mutations in Cancer: https://cancer.sanger.ac.uk/cosmic

D. Test Controls

The therascreen BRAF V600E RGQ PCR Kit contains three controls: An Internal Control (IC), a Positive Control (PC) and a No Template Control (NTC), which have been designed to detect fault conditions. The Ct values obtained in the IC channel are checked to ensure the sample validity. If the RGAM fails to detect an in-range signal in the IC, the sample is reported as invalid and no BRAF V600E mutation status results for that sample are reported.

In addition to the IC, all samples must be tested with the Control Reaction mix to ensure that they give a Ct value within a specified range. This range is set to ensure that there is sufficient amplifiable DNA to proceed with analysis, but not so much as to overload the assay. The therascreen BRAF V600E RGQ PCR Kit has been verified to work within a specific working range (i.e. upper and lower Control Reaction Ct values, this is also known as Control Working Range, CWR) and any samples that do not give Ct values within this range are invalidated by the RGAM software, plug-in and associated assay profile.

If a run fails any of the validity criteria, the software displays the corresponding validity rule related to the failed control and does not provide test results for samples in the report. If all run validity criteria are correct, the software generates a report that confirms the respective controls validity and then displays sample results.

- Internal Control (IC): The BRAF V600E reaction mix contains reagents (ARMS primer, Scorpion probe and oligonucleotide template) for an IC reaction designed to detect failure of the reaction, e.g., due to PCR inhibition.
- No Template Control (NTC): An NTC tube contains nuclease-free water and is required in each RGQ run. The NTC serves as a control to assess potential contamination during assay set up.
- Positive Control (PC): A PC test is required in each RGQ run. The PC Tube contains long oligo sequence representing BRAF mutations. Detection of the BRAF V600E target within acceptable ranges confirms the proper functioning of each of the reaction mixes in the kit.

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For therascreen BRAF V600E RGQ PCR Kit test runs to be accepted as valid, the Ct values for PC, IC and NTC have to meet the following predefined criteria in Table 3.

Table 2: Run Validity Criteria for Controls

| Reaction Mix | Control | Channel | Acceptable Ct range (inclusive) |
| --- | --- | --- | --- |
| Control | PC | Green (FAM) | 27.82-33.85 |
| V600E | PC | Green (FAM) | 27.49-33.51 |
| All | NTC | Green (FAM) | No Amp (that is, not ≤ 40.00) |
| All | NTC | Yellow (HEX) - IC | 32.53-38.16 |

E. Instruments and Software

The therascreen BRAF V600E RGQ PCR Kit is designed to be used with the Rotor-Gene Q (RGQ) MDx instrument, which is a real-time PCR analyzer designed for rapid thermal cycling and real-time detection of PCR assays.

The RGQ incorporates a centrifugal rotary design for thermal cycling where a rotor, containing each tube, spins in a chamber of moving air, keeping all samples at a uniform temperature. Samples are heated and cooled in a low-mass-air oven according to a software-determined cycle that initiates the different phases of the PCR cycle. In the RGQ, fluorophores are excited from the bottom of the sample chamber by a light-emitting diode. Energy is transmitted through the thin wall at the bottom of each PCR tube. Emitted fluorescence passes through the emission filters on the side of the chamber and is detected by a photomultiplier tube. Detection is performed as each tube aligns with the detection optics; tubes pass the excitation / emission optics every 150 milliseconds. The fluorescence signals indicate the progress of the PCR reactions. The Rotor-Gene Q MDx has six channels (six excitation sources and six detection filters). Two of these channels; green and yellow, are used with the therascreen BRAF V600E RGQ PCR Kit. Cycling parameters, data analysis and results interpretation for the therascreen BRAF V600E RGQ PCR Kit are performed by:

- RGAM version 2.1 Software.
- Gamma MDx plug-in version 1.0.0.
- Mutation Assessment Assay Profile: therascreen BRAF V600E FFPE MA MDx Assay Profile v1.0.0.
- Sample Assessment Assay Profile: therascreen BRAF V600E FFPE SA MDx.

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The RGAM Software is a core software which provides general functionality including: PCR run set up, cycler control and management of experiment data, results, assay profiles and system configuration. The Gamma MDx plug-in extends the functionality of RGAM by providing cycle threshold (Ct) value calculation, data analysis and normalization features. Assay specific functionality, for example cycling conditions, thresholds and analysis cut-offs, and control ranges, is implemented by the therascreen BRAF V600E FFPE MA MDx Assay Profile. The RGAM software, plug-in and associated assay profile ensure that a user interface with restricted user options is displayed to the user and contains all the information required for automatic real-time PCR analysis including time and temperature profiles, data quality controls, and data analysis algorithms. The software suite also allows printing of test reports and creates result files in the software's file system.

In addition, the RGAM software, plug-in and associated assay profile perform a quality check using Automatic Data Scan (AUDAS) that focuses on parameters of the respective fluorescence curves from which Ct values will be determined. The AUDAS check is mainly intended to identify problems that occur during the real-time PCR amplification that potentially generate non-typical curve shapes due to saturation, noise, spikes, baseline dips, sloping curves related to the real-time PCR instrument parameters or due to a problem linked to the assay itself. The curves in such situations are automatically invalidated to avoid generating misleading results.

F. Interpretation of Results

The cycle threshold (Ct) at which the instrument distinguishes the amplification generated fluorescence as being above the background signal is within the range of 0 to 40. Ct values generated by the Control and Mutation Reaction Mixes indicate the quantity of assay specific input DNA. Low Ct values indicate higher input DNA levels and high Ct values indicate lower input DNA levels. Ct values generated by the Control and Mutation Reaction Mixes indicate the quantity of assay specific input DNA. Low Ct values indicate higher input DNA levels and high Ct values indicate lower input DNA levels.

If the Sample Validity Criteria are met, the sample is analyzed for the presence of the BRAF V600E mutation. The difference in Ct values (ΔCt) between the Control Reaction and the Mutation Reaction is a qualitative measure of BRAF V600E mutation status and is calculated as:

$$
\Delta \mathrm {C t} = [ \text {Mutation Reaction Ct value} ] - [ \text {Control Reaction Ct value} ]
$$

Samples are classed as mutation positive (reported as "Mutation Detected") if they give a ΔCt less than or equal to the assay cut-off ΔCt value of 7.0 (Table 4). Above this value, the sample will be reported as "No Mutation Detected". Additional BRAF V600E assay software flags will report on invalid samples.

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Table 4 Cycle Threshold (Ct)

| Result | Interpretation |
| --- | --- |
| ΔCt ≤7.0 | No Mutation Detected |
| ΔCt >7.0 | Mutation Detected |

## VI. ALTERNATIVE PRACTICES AND PROCEDURES

There are no other FDA cleared or approved alternatives for the testing of FFPE CRC tissue for BRAF V600E mutation status in the selection of patients who are eligible for a combined treatment with BRAFTOVI® (encorafenib) and ERBITUX®(cetuximab).

## VII. MARKETING HISTORY

The therascreen BRAF V600E RGQ PCR Kit has not been marketed in the United States or any foreign country.

## VIII. POTENTIAL ADVERSE EFFECTS OF THE DEVICE ON HEALTH

Failure of the device to perform appropriately, or failure to correctly interpret test results may lead to incorrect BRAF V600E mutation results, which could impact patient treatment decisions. A false positive test result may lead to inappropriate treatment and potentially any adverse effects associated with treatment with a targeted BRAF inhibitor rather than standard of care treatments. A false negative test may prevent a patient benefitting from a targeted therapy.

## IX. SUMMARY OF NON-CLINICAL STUDIES

### A. Laboratory Studies

The mutation status of samples was confirmed by an independent method. The percentage mutation or MAF was determined by a validated digital droplet PCR method.

#### 1. Correlation with the Reference Method

The analytical accuracy of the therascreen BRAF V600E RGQ PCR Kit was assessed by comparison of results an orthogonal method. A total of 606 CRC DNA samples collected and extracted from the BEACON clinical trial were tested by a validated Sanger Sequencing reference method. Samples were consecutively enrolled into the study based on the date of testing to minimize bias. Samples were also selected based on results obtained with the BRAF V600E clinical trial assay (CTA): 275 CTA positive, 275 CTA negative and 56 CTA indeterminate samples were selected. Of these, 600 samples returned Sanger testing results (including both valid and invalid/indeterminate). Of these samples, 79 samples (13%) were indeterminate with therascreen BRAF V600E RGQ PCR Kit and 136 were indeterminate by Sanger. A total of 417 were valid for both BRAF V600E

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and Sanger Sequencing. Agreement. was demonstrated by assessing the positive percent agreement (PPA), negative percent agreement (NPA) and overall percent agreement (OPA) from both of sets of results. Table 5 demonstrates an overall agreement of $95\%$ . Breakdown of the results including indeterminate and the results (both valid and indeterminate by both methods) are summarized in Table 6. The measures of agreement, with adjusting for the enrichment of CTA positives are shown in Table 7.

Table 5: Distribution of Results (Sanger sequencing versus BRAF V600E Kit)

| | Bi-Directional Sanger BRAF Result | | | | |
| --- | --- | --- | --- | --- | --- |
| | | Indeterminate | Mutation Detected | No Mutation Detected | Total |
| therascreen BRAF V600E Result | Indeterminate | 32 | 24 | 23 | 79 |
| | Mutation | 44 | 192 | 20 | 256 |
| | No Mutation | 60 | 0 | 205 | 265 |
| | Total | 136 | 216 | 248 | 600 |

Table 6. Agreement in Overall Mutation Status between therascreen BRAF V600E RGQ PCR Kit and Sanger Sequencing (as reference method), unadjusted analysis

| Measure of Agreement | N | Percent Agreement | Lower Two-sided 95% Confidence Limit* | Upper Two-sided 95% Confidence Limit* |
| --- | --- | --- | --- | --- |
| Overall Percent | 397/417 | 95.20 | 92.69 | 97.05 |
| Positive Percent | 192/192 | 100.00 | 98.10 | 100.00 |
| Negative Percent | 205/225 | 91.11 | 86.61 | 94.49 |

*Confidence intervals were calculated using Clopper-Pearson (Exact) Binomial.

Table 7: Agreement between therascreen BRAF V600E RGQ PCR Kit and Sanger Sequencing (as reference method), adjusted analysis

| Agreement Measure | Estimate | Lower Two-sided 95% Confidence Limit* | Upper Two-sided 95% Confidence Limit* |
| --- | --- | --- | --- |
| NPA | 94.24% | 91.83% | 96.50% |
| OPA | 96.23% | 94.57% | 97.76% |
| PPA | 100.00% | N/A** | N/A** |

* calculated using a non-parametric bootstrap method
** not calculated in cases where estimated value is 100.00%

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# 2. Analytical Sensitivity

## a) Analytical Sensitivity-Limit of Blank (LoB)

The LoB is defined as the highest measurement result that is likely to be observed for a blank sample. A total of 96 replicates were tested (water was used as test sample), no amplification was observed in either reaction (the Control and Mutation reactions). To assess performance of the therascreen BRAF V600E RGQ PCR Kit in the absence of mutant-positive template and to ensure that a blank sample does not generate an analytical signal that may indicate a low concentration of mutation, samples with no template were evaluated. The results demonstrated no detectable control or mutant CT value in any of the control or mutation reaction tubes. Therefore, the LoB for the therascreen BRAF V600E RGQ PCR Kit was set to Ct value of 40, the maximum PCR cycle number used for the Kit.

## b) Analytical Sensitivity -ΔCt Analytical Cut-off Determination

During assay development, the assay Cut-off was determined using 82 CRC FFPE samples including both positive and negative samples (characterized by highly sensitive orthogonal methods) for the BRAF V600E mutation. The analytical ΔCt cut-off value was determined based on false-positive rates and false-negative rates as shown in Table 8.

Table 8: False Positive rate and False Negative Rate for Chosen Assay Cut-off

| | False Negative | | False Positive | | Overall False Rate | |
| --- | --- | --- | --- | --- | --- | --- |
| Cut-Off | Fraction | Percentage | Fraction | Percentage | Fraction | Percentage |
| ΔCt 7 | 0 / 37 | 0.000 | 1 / 45 | 2.2% | 1 / 82 | 1.2% |

## c) Analytical Sensitivity-Limit of Detection (LoD)

The measurable range (CWR) for the therascreen BRAF V600E RGQ PCR Kit is based on the amount of amplifiable DNA in the specimen as determined by the Control reaction CT value. The stated measurable range for the assay is defined by the control CT pre-specified range of 20.95 to 33.00. The LoD is the minimum percentage of mutant DNA that can be detected in a background of wild-type DNA, when the total amplifiable DNA is within the stated input range and still below the threshold cutoff ΔCT value. The LoD is defined as the lowest amount of analyte in a sample that can be detected with at least a 95% probability as determined by a probit analysis. The LoD was determined using 10 clinical CRC samples representing high, medium and low DNA input levels. Samples were positive for the BRAF V600E mutation and the mutation allele frequency (MAF) was established using an independently validated

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ddPCR method.

A five or six-point MAF dilution series was made for each of the clinical samples by serially diluting mutant samples in a clinical wild type (WT) DNA background. These dilution series were then tested in multiple replicates using 2 lots of the therascreen BRAF V600E RGQ PCR Kit over a period of $\geq 3$ days with multiple instruments and operators. LoD values were determined using the results following a probit analysis. The LoD values are reported in Table 9.

Table 9: LoD Values for the therascreen BRAF V600E RGQ PCR Kit

| DNA Input Levels | Control Ct Range | LoD (MAF) |
| --- | --- | --- |
| High | ≥20.95–≤ 25.00 | 2% |
| Medium | >25.00 – ≤ 29.38 | 3.5% |
| Low | >29.38 – ≤ 33.00 | 7.8% |

The LoD values were further verified by an independent clinical sample set including seven Resection (RES) and Core Needle Biopsy (CNB) FFPE CRC samples.

# d) Analytical Sensitivity-Effect of DNA Input on $\Delta C t$

When samples at different total DNA levels contain the same proportion of mutant DNA, it is expected that the measured $\Delta \mathrm{CT}$ values will remain consistent. DNA extracted from 4 FFPE CRC samples (two wild-type and two mutant) were used to prepare pools of DNA with the lowest achievable control reaction CT and diluted across a minimum of six dilution levels that span the entirety of the CWR (measurable range of the assay).

For each sample tested, the linear, quadratic and cubic regression models were fitted to the data with $\Delta \mathrm{CT}$ (for positive samples) or Control CT values (for negative samples) as the response variable, and dilution number as the continuous explanatory variable. The regression model results were reported along with the corresponding standard errors, $95\%$ confidence limits and p-values. Linearity was demonstrated for all samples throughout the measurable range tested, there were no statistically significant differences in the regression models. Some quadratic and cubic effects were observed but the maximum difference predicted was within the precision limit (i.e., $< 2x$ standard deviation). Therefore, $\Delta \mathrm{Ct}$ values were consistent across the full DNA input range.

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## 3. Analytical Specificity

### a) Analytical Specificity-Primer and Probe Specificity

The purpose of this study was to demonstrate the theoretical specificity for the primers and probes used within the therascreen BRAF V600E RGQ PCR Kit. Multiple analyses were conducted to ensure that each oligonucleotide (Oligo) used in the therascreen BRAF V600E RGQ PCR Kit binds only to target sequence and not to sequences from other species or to non-target human genome sequences. Each primer and probe design were checked against the nucleotide (nr/nt) database using a blastn search and against the Human Genomic and Transcript (Human G+T) database using a blastn search. BLAST was also performed between each of the therascreen BRAF V600E RGQ PCR Kit primer and probe sequences to the IC template. Additional analysis was also performed to confirm that each oligo included in the therascreen BRAF V600E RGQ PCR Kit does not self-react or cross-react with each other to generate unspecific amplicons. This study concluded that the design of therascreen BRAF V600E RGQ PCR Kit does not produce non-specific amplifications against other species or human genome sequences.

### b) Analytical Specificity-Cross Reactivity

Cross-reactivity was evaluated by testing the therascreen BRAF V600E RGQ PCR Kit with non-targeted mutations on the BRAF V600 codon (V600Ec, V600D, V600K, V600R, V600M, and V600G) at high DNA input level and various MAF. Cell line gDNA samples were used in this study in order to obtain samples at challenging levels (i.e., high DNA input). Six replicates were assessed for each sample at each MAF level.

The assay showed no cross reactivity to V600K, V600R, V600M, V600G at all concentrations (up to 100% MAF) tested. Cross reactivity was observed for V600Ec and V600D using cell line gDNA. The design of therascreen BRAF V600E RGQ PCR Kit does not distinguish between V600E and V600Ec mutations. However, V600Ec was not able to be validated as a target because no clinical specimens were identified in the BEACON study.

The cross reactivity of BRAF V600D was confirmed using cell line DNA. No BRAF V600D positive clinical specimens were identified in the clinical study due to the low prevalence of BRAF V600D in the CRC population (0% reported in the COSMIC database at the time this summary report is written).

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c) Analytical Specificity-Cross Contamination

To evaluate the potential occurrence of cross contamination during the DNA extraction and subsequent therascreen BRAF V600E RGQ PCR Kit testing procedures (entire system), this study was performed using high DNA input level Positive BRAF V600E clinical samples (MT) and Wild-type clinical samples (WT to BRAF V600E). The assessment of cross contamination was carried out by extracting high positive MT samples and WT within the same DNA extraction runs and followed by testing these samples in a “checker board” pattern (contained both WT and MT samples) PCR runs and “WT only” runs. Any WT samples that produced false positive results would be used as evidence of “cross contamination”.

In total, 131 WT replicates were tested, and the observed percentage of correct mutation calls was 100%, demonstrating no cross contamination of the WT samples by high positive mutant samples sharing the same DNA extraction, RGQ and run set up procedure.

d) Analytical Specificity-Interfering Substances

The effect of potential interfering substances from both endogenous and exogenous substances was measured by comparison of correct call and ΔCt values between interferent spiked and control spiked extracts. Nine potential interfering substances were tested:

- Hemoglobin, a potential endogenous interfering substance that may be present in FFPE tissue samples.
- Potential exogenous interferents from the extraction procedure using the QIAamp DSP DNA FFPE Tissue Kit that may be introduced into the sample during the DNA extraction process:
- Paraffin Wax
- Ethanol
- Xylene
- Extraction Buffers (AW1, ATL, AW2 and AL)
- Proteinase K

Four (4) clinical FFPE CRC tissue samples (2 MT and 2 WT) were used in this study. The evaluation was performed by testing 9 replicates per interferent using the therascreen BRAF V600E RGQ PCR Kit. All results were as expected showing no statistically significant difference in Control Ct (WT samples) or Delta Ct (Mutant samples) (P values were > 0.05 for all interferent versus Interferent-free control). No false calls were observed for any test samples. In conclusion, none of the interferents tested had any impact on the therascreen BRAF V600E RGQ PCR Kit performance.

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e) Analytical Specificity-Interfering Substances

The presence of necrotic tissue in the range of 30–100% within CRC FFPE samples was evaluated in seven “high necrotic tissue” samples identified in the procured clinical CRC population (approximately 250 in total, only 7 contained necrotic tissue equal to or greater than 30%), no false BRAF V600E results were generated by the therascreen BRAF V600E RGQ PCR Kit (confirmed by Pyro-sequencing) and no association between % necrosis and Control Ct values was observed (following serial dilution of samples with necrotic tissue of ≥ 80%).

4. Precision of the Assay

a) Repeatability, Intermediate Precision and Lot Interchangeability

The objective of this study was to demonstrate the repeatability, intermediate precision and lot to lot variation of the therascreen BRAF V600E RGQ PCR Kit. The study used 9 FFPE clinical CRC samples. Each sample was normalized to the target DNA input level and percentage mutation as shown in Table 10. The positive samples % mutant allele were quantified by digital droplet PCR (ddPCR). Each test panel members were tested in a three-day period with 3 operators, 3 instrument and 3 kit lots included. In total 27 PCR runs were performed with 81 replicates per test panel member. The precision based on the proportion of correct calls is provided in Table 11 below. The variance component analysis output is provided in Table 12. The results demonstrated that the assays are reproducible across the range of allele frequencies

Table 3: Test Panel Members for the Precision Studies

| Panel Member | Mutant Status | Acquisition Method | DNA input level (Targeted Ct) | % Mutation Level* |
| --- | --- | --- | --- | --- |
| 1 | WT | RES | Low (Ct 31) | N/A |
| 2 | WT | RES | Medium (Ct 27.5) | N/A |
| 3 | Low Positive V600E (below LoD) | CNB | Low (Ct 31) | N/A |
| 4 | V600E | RES | High (Ct 23.5) | LoD (2.0%) |
| 5 | V600E | RES | Medium (Ct 27.5) | LoD (3.5%) |
| 6 | V600E | CNB | Low (Ct 31) | LoD (7.8%) |
| 7 | V600E | RES | Low (Ct 31) | LoD (7.8%) |
| 8 | V600E | RES | Low (Ct 31) | 2xLoD (15.6%) |
| 9 | V600E | RES | Medium (Ct 27.5) | 2xLoD (7.0%) |

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Table 11: Proportion of Correct Calls for Each Test Panel

| Grouping Variable(s) | | | Proportion | | Two-Sided 95% Confidence Limit | |
| --- | --- | --- | --- | --- | --- | --- |
| Sample | Acquisition Method | Mutation Level | Fraction | Percentage | Lower | Upper |
| Test Panel 1 | RES | WT | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 2 | RES | WT | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 3 | CNB | Low Positive (below LoD) | 78 / 81 | 96.30% | 89.56% | 99.23% |
| Test Panel 4 | RES | LOD | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 5 | RES | LOD | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 6 | CNB | LOD | 80 / 81 | 98.77% | 93.31% | 99.97% |
| Test Panel 7 | RES | LOD | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 8 | RES | 2 X LOD | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 9 | RES | 2 X LOD | 79 / 79 | 100.00% | 95.44% | 100.00% |

Table 12: Variance Components Analysis for Repeatability and Intermediate Precision Evaluation

| Alignment | Mutation Level | Number of Amplified | Number of | Mean | Between Run | Between Kit Lot (SD, % CV) | Between Operator (SD, % CV) | Between Instrument | Between Day (SD, % CV) | Between Template | Residual (SD, % CV) | #Total (SD, % CV) |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| Delta Ct | 2 X LOD | 160 | 0 | 3.57 | (0.0844, 2.36%) | (0.0647, 1.81%) | (0.0559, 1.56%) | (0.0000, 0.00%) | (0.0445, 1.25%) | (1.5281, 42.75%) | (0.4967, 13.90%) | (1.1981, 33.52%) |
| | LOD | 323 | 1 | 3.90 | (0.0653, 1.68%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (1.3368, 34.32%) | (0.4267, 10.95%) | (1.2365, 31.74%) |
| Green Ct (Control Assay) | 2 X LOD | 160 | 0 | 28.75 | (0.1349, 0.47%) | (0.0000, 0.00%) | (0.0926, 0.32%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (2.9368, 10.22%) | (0.2591, 0.90%) | (2.1049, 7.32%) |
| | LOD | 324 | 0 | 27.73 | (0.0913, 0.33%) | (0.0476, 0.17%) | (0.0361, 0.13%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (3.8626, 13.93%) | (0.1695, 0.61%) | (3.3562, 12.10%) |
| | WT | 243 | 0 | 29.91 | (0.0517, 0.17%) | (0.0314, 0.11%) | (0.0000, 0.00%) | (0.0063, 0.02%) | (0.0000, 0.00%) | (2.1832, 7.30%) | (0.2490, 0.83%) | (1.8045, 6.03%) |
| Green Ct (V600E Assay) | 2 X LOD | 160 | 0 | 32.32 | (0.0000, 0.00%) | (0.0934, 0.29%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (1.4071, 4.35%) | (0.4463, 1.38%) | (1.0955, 3.39%) |
| | LOD | 324 | 0 | 31.63 | (0.1527, 0.48%) | (0.0419, 0.13%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (2.9075, 9.19%) | (0.4400, 1.39%) | (2.5646, 8.11%) |

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The table above shows the standard deviation estimated for each of the investigational factors. The precision study met the prespecified acceptance criteria.

## b) Reproducibility Study

The purpose of this study was to assess the between-site precision (reproducibility) of the therascreen BRAF V600E RGQ PCR Kit at 3 clinical testing sites. The same "Test Panel Members" were used for both the Reproducibility (this study) and the Repeatability and Intermediate Precision Study (Section 6a). At each test site, three runs were performed (split between two operators, two RGQ instruments) over a three-day testing period. Each test panel was tested with 3 replicates in each PCR run, for a total of 27 replicates per test panel per site (81 reps across all three sites). The proportion of correct mutation calls for all test panels across three sites is provided in Table 13.

The proportion of correct mutation calls per site was provided for Test Panel 6 only in Table 14 (as Test Panel 6 was the only sample that produced one single incorrect call).

Table 13: Percentage Correct Mutation Call across 3 Sites for Reproducibility Study

| Grouping Variable(s) | | | Proportion | | Two-Sided 95% Confidence Limit | |
| --- | --- | --- | --- | --- | --- | --- |
| Sample | Acquisition Method | Mutation Level | Fraction | Percentage | Lower | Upper |
| Test Panel 1 | RES | WT | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 2 | RES | WT | 80 / 80 | 100.00% | 95.49% | 100.00% |
| Test Panel 3 | CNB | WT | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 4 | RES | LOD | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 5 | RES | LOD | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 6 | CNB | LOD | 80 / 81 | 98.77% | 93.31% | 99.97% |
| Test Panel 7 | RES | LOD | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 8 | RES | 2 X LOD | 81 / 81 | 100.00% | 95.55% | 100.00% |
| Test Panel 9 | RES | 2 X LOD | 81 / 81 | 100.00% | 95.55% | 100.00% |

Table 14: Proportion of Correct Mutation Calls Per Site (for Test Panel 6)

| Grouping Variable(s) | | | | Proportion | | Two-Sided 95% Confidence Limit | |
| --- | --- | --- | --- | --- | --- | --- | --- |
| Sample | Acquisition Method | Mutation Level | Site | Fraction | Percentage | Lower | Upper |
| Test Panel 6 | CNB | LOD | 1 | 26 / 27 | 96.30% | 81.03% | 99.91% |
| | | | 2 | 27 / 27 | 100.00% | 87.23% | 100.00% |

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| Grouping Variable(s) | | | | Proportion | | Two-Sided 95% Confidence Limit | |
| --- | --- | --- | --- | --- | --- | --- | --- |
| Sample | Acquisition Method | Mutation Level | Site | Fraction | Percentage | Lower | Upper |
| | | | 3 | 27 / 27 | 100.00% | 87.23% | 100.00% |

The summary statistics output for the Reproducibility study is provided in Table 15. The table shows the standard deviation estimated for each of the investigational factors. For example, the site-to-site observed variation (corresponding to the reproducibility of the assay) in $\Delta \mathrm{Ct}$ for 2xLOD samples is equal to $0.08\Delta \mathrm{Ct}$ .

Table 45: Summary Statistics Outputs for Reproducibility

| Analysis Variable | Mutation Level | Number of Amplified | Number of Non-Amplified | Mean | Between Site (SD, % CV) | Between Run Key Order (SD, % CV) | Between Template (SD, % CV) | Between Operator Within Site (SD, % CV) | Between Instrument (SD, % CV) | Between Day Within Site (SD, % CV) | Residual (SD, % CV) | #Total (SD, % CV) |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| Delta Ct | 2 X LOD | 162 | 0 | 3.64 | (0.0800, 2.20%) | (0.0587, 1.61%) | (1.4756, 40.50%) | (0.1004, 2.75%) | (0.0439, 1.21%) | (0.1006, 2.76%) | (0.4654, 12.77%) | (1.1570, 31.75%) |
| | LOD | 323 | 1 | 3.89 | (0.0460, 1.19%) | (0.0747, 1.92%) | (1.3340, 34.33%) | (0.0507, 1.31%) | (0.0000, 0.00%) | (0.0704, 1.81%) | (0.4486, 11.54%) | (1.2459, 32.07%) |
| Green Ct (Control Assay) | 2 X LOD | 162 | 0 | 28.61 | (0.1208, 0.42%) | (0.0803, 0.28%) | (2.9372, 10.27%) | (0.0830, 0.29%) | (0.0511, 0.18%) | (0.0000, 0.00%) | (0.1878, 0.66%) | (2.0976, 7.33%) |
| | LOD | 324 | 0 | 27.62 | (0.1260, 0.46%) | (0.0770, 0.28%) | (3.8494, 13.93%) | (0.0240, 0.09%) | (0.0624, 0.23%) | (0.0000, 0.00%) | (0.1518, 0.55%) | (3.3452, 12.11%) |
| | WT | 242 | 0 | 29.82 | (0.0821, 0.28%) | (0.0893, 0.30%) | (2.1804, 7.31%) | (0.0478, 0.16%) | (0.0279, 0.09%) | (0.0000, 0.00%) | (0.2150, 0.72%) | (1.7971, 6.03%) |
| Green Ct (V600 E Assay) | 2 X LOD | 162 | 0 | 32.25 | (0.2626, 0.81%) | (0.1537, 0.48%) | (1.4599, 4.53%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (0.0000, 0.00%) | (0.4617, 1.43%) | (1.1639, 3.61%) |
| | LOD | 323 | 1 | 31.50 | (0.1957, 0.62%) | (0.0849, 0.27%) | (2.9052, 9.22%) | (0.0780, 0.25%) | (0.0000, 0.00%) | (0.0810, 0.26%) | (0.4253, 1.35%) | (2.5652, 8.14%) |

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c) Lot Interchangeability

To demonstrate lot-to-lot interchangeability for the therascreen BRAF V600E RGQ PCR Kit, 3 kit lots were used to test 8 clinical CRC specimens including both confirmed MT and WT to BRAF V600E (The same test panel members as the Repeatability Study were used, except that Test panel 3 CNB WT was removed due to it being a low positive sample). The lowest proportion of correct calls was 96.30% for each therascreen BRAF V600E RGQ PCR Kit lot (Table 16) showing the reproducibility of the kit lots.

Table 16: Proportion of Correct Calls per Kit Lot
| Grouping Variable(s) | | | Proportion | | Two-Sided 95% Confidence Limit | |
| --- | --- | --- | --- | --- | --- | --- |
| Mutation Level | Method | Kit Lot | Fraction | Percentage | Lower | Upper |
| 2 X LOD | RES | 1 | 53 / 53 | 100.00% | 93.28% | 100.00% |
| | | 2 | 53 / 53 | 100.00% | 93.28% | 100.00% |
| | | 3 | 54 / 54 | 100.00% | 93.40% | 100.00% |
| LOD | RES | 1 | 81 / 81 | 100.00% | 95.55% | 100.00% |
| | | 2 | 81 / 81 | 100.00% | 95.55% | 100.00% |
| | | 3 | 81 / 81 | 100.00% | 95.55% | 100.00% |
| | CNB | 1 | 27 / 27 | 100.00% | 87.23% | 100.00% |
| | | 2 | 27 / 27 | 100.00% | 87.23% | 100.00% |
| | | 3 | 26 / 27 | 96.30% | 81.03% | 99.91% |
| WT | RES | 1 | 54 / 54 | 100.00% | 93.40% | 100.00% |
| | | 2 | 54 / 54 | 100.00% | 93.40% | 100.00% |
| | | 3 | 54 / 54 | 100.00% | 93.40% | 100.00% |

d) Sample Handling and Tumor Heterogeneity

A study was conducted to assess sample handling variability, including site variation, within the DNA extraction procedures.

This study focused on the DNA extraction of clinical FFPE samples to demonstrate that different laboratories produce the same results starting from the same clinical samples (different sections taken from the same FFPE block).

Eight FFPE CRC clinical specimens representing different DNA input levels and mutation levels were extracted at three different laboratories using three different lots of the QIAamp DSP DNA FFPE Tissue Kit. For each of the 8 FFPE specimens (4 WT and 4 MT), 36 sections were distributed evenly across three different sites.

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A total of 6 extractions per sample (two sections per extraction) were performed at each of the three different test sites using 3 extraction kit lots (18 extraction in total per RES sample). A total of 12 extractions per CNB sample (2 sections per extraction) were performed at a single test site using 3 extraction kit lots. The extracted DNA samples were tested at a single site using a single lot of the therascreen BRAF V600E RGQ PCR Kit. The percentage of correct mutation calls for MT and WT samples across 3 sites is provided in Table 17.

The results observed for extractions across multiple FFPE sections were highly concordant suggesting tumor heterogenicity would not impact on the therascreen BRAF V600E RGQ PCR Kit test results when neoplastic cells are confirmed to be present by a pathologist.

Table 5: Proportion of Correct Calls by Extraction Site

| Grouping Variable(s) | | | Proportion | | Two-Sided 95% Confidence Limit | |
| --- | --- | --- | --- | --- | --- | --- |
| Sample Level | Acquisition Method | Extraction Site | N Correct / N Total | Proportion | 95% Lower Confidence Limit | 95% Upper Confidence Limit |
| MT | RES | Site 1 | 24 / 24 | 100.00% | 85.75% | 100.00% |
| | RES | Site 2 | 24 / 24 | 100.00% | 85.75% | 100.00% |
| | RES | Site 3 | 24 / 24 | 100.00% | 85.75% | 100.00% |
| WT | CNB | Site 1 | 12 / 12 | 100.00% | 73.54% | 100.00% |
| | RES | Site 1 | 23 / 24 | 95.83% | 78.88% | 99.89% |
| | RES | Site 2 | 23 / 24 | 95.83% | 78.88% | 99.89% |
| | RES | Site 3 | 24 / 24 | 100.00% | 85.75% | 100.00% |

# 5. Tumor Cell Content

Different proportions of Tumor Content (TC%) were investigated to demonstrate that the therascreen BRAF V600E RGQ PCR Kit can detect BRAF V600E mutations across a range of sections with different amounts of tumor. Samples with no neoplastic cells were not qualified for inclusion in this test.

The TC% against BRAF V600E results were plotted using data obtained from the BEACON clinical trial (the sub-population selected for the Accuracy study). A total of 599 samples were included in the analysis. Within this population, 18 samples had TC% ≤ 5% (13 samples were negative, and 5 samples were positive with the therascreen BRAF V600E RGQ PCR Kit). Otherwise the results demonstrated that tumor content does not correlate with the CWR Ct values and that the assay works across the range of tumor content.

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# 6. Specimen Handling

The first objective of this study was to confirm that the therascreen BRAF V600E RGQ PCR Kit mutation status would remain unchanged when testing DNA samples extracted with and without macrodissection from specimens with low TC%. Sixty clinical CRC FFPE samples with TC% ranging from 5% to 50% were extracted with and without macrodissection and then tested with the therascreen BRAF V600E RGQ PCR kit. 58 samples produced valid results. The PPA, NPA and OPA between the macrodissected and non-macrodissected extraction procedures are reported in Table 18.

Table 16: Agreement Summary Table between Extraction Method with and without Macrodissection

| Measure of Agreement | Frequencies | Percent Agreement | Clopper-Pearson (Exact) Binomial Lower Two-sided 95% Confidence Limit | Clopper- Pearson (Exact) Binomial Upper Two- sided 95% Confidence Limit |
| --- | --- | --- | --- | --- |
| Overall Percent Agreement | 58/58 | 100.00 | 93.84 | 100.00 |
| Positive Percent Agreement | 18/18 | 100.00 | 81.47 | 100.00 |
| Negative Percent Agreement | 40/40 | 100.00 | 91.19 | 100.00 |

The second objective of this study was to verify that BRAF V600E mutation detection at close to LoD level would not have been impacted by samples extracted with and without macrodissection.

Positive clinical samples were extracted with and without macrodissection and tested at LoD level in multiple replicates. Both with and without macrodissection groups produced a positive rate $\geq 95\%$ meeting the study acceptance criterion for LOD samples (Table 19). A Fisher Exact test also demonstrated no statistically significant difference observed between the 2-extraction methods (Table 20).

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Table 17. Proportion of correct calls for Macro and Non-Macro Extraction Methods

| Grouping Variable(s) | Proportion | | Two-Sided 95% Confidence Limit | |
| --- | --- | --- | --- | --- |
| Sample Process | Fraction | Percentage | Lower | Upper |
| Macro | 28 / 28 | 100.00% | 87.66% | 100.00% |
| Non-Macro | 27 / 28 | 96.43% | 81.65% | 99.91% |

Table 20: Fishers Exact Test – Difference between Macro and Non-Macro Extraction Methods

| Obs | diff | Risk | Percentage Difference (%) | p-value |
| --- | --- | --- | --- | --- |
| 1 | Macro - Non-macro | 0.04 | 3.57 | 1.000 |

# 7. Guard Band Studies

For all Guard Band studies, two clinical CRC WT and two FFPE CRC MT at approximately 2x LoD were used.

# a) Volumetric Guard Band

The objective of this study was to verify the tolerance of the therascreen BRAF V600E RGQ PCR Kit to volumetric variations that can be introduced by the end user.

The volumetric tolerance was tested by varying the volume of each individual component while keeping the volume of the other components constant. Each component volume was varied by $\pm 6\%$ . This represents the total error that can be introduced by pipetting, calculated using accuracy and precision data for a standard pipette.

When the individual component volume was varied by $\pm 6\%$ the difference in means of Delta Ct (For MT sample) or Control Ct (For WT samples) between each pair (test vs nominal conditions) were assessed to be within $+/- 2 \times \mathrm{SD}$ (calculated in the Repeatability Study for the therascreen BRAF V600E RGQ PCR Kit). The variation observed due to the test conditions are therefore within the normal variation expected with the therascreen BRAF V600E RGQ PCR Kit. In addition, $100\%$ correct mutation calls were observed, for all tested samples, for all conditions.

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b) Thermal Cycling Guard Band

The objective of this study was to verify the tolerance of the BRAF Kit to temperature variations of the annealing step during routine PCR cycling. When the PCR annealing temperature was varied by ±1°C, the difference in means of ΔCt (For MT sample) or Control Ct (For WT samples) between each pair (test vs nominal conditions) were assessed to be within +/- 2×SD (calculated in the Repeatability Study for the therascreen BRAF V600E RGQ PCR Kit), except for one WT sample at 59°C condition. However, the proportion of correct calls across all samples, all test conditions was 100%.

c) Master Mix Guard Band

This study was designed to verify the robustness of the therascreen BRAF V600E RGQ PCR system during PCR setup, more specifically the master mix to a prolonged time on the bench prior to the addition of samples.

The effect of keeping Master mix at ambient temperature for up to 4 hours or in the fridge (2°C to 8°C) for up to 24 hours on the therascreen BRAF V600E RGQ PCR Kit mutation status was evaluated. The difference in means of Delta Ct (For MT sample) or Control Ct (For WT samples) between each pair (test vs nominal conditions) were assessed to be within +/- 2×SD (calculated in the Repeatability Study for the therascreen BRAF V600E RGQ PCR Kit). The proportion of correct mutation calls for all test samples was 100%.

d) Extraction Guard Band Study

The objective of this study was to confirm the extraction tolerance of the therascreen BRAF V600E RGQ PCR Kit to potential variation introduced during routine execution in the extraction protocol.

Eight clinical FFPE CRC specimens (4 WT and 4 MT) were used to assess different temperature and length (minutes) of proteinase K incubation and formalin de-crosslinking as shown in Table 21.

Table 81: Variations Introduced in to the Extraction Protocol

| Extraction Step | Low | Nominal | High |
| --- | --- | --- | --- |
| Proteinase K temp. | 53°C | 56°C | 59°C |
| Proteinase K time | 30 min | 60 min | 90 min |
| De-crosslinking temp. | 85°C | 90°C | 95°C |
| De-crosslinking time | 30 min | 60 min | 90 min |

Although some conditions did not meet the ±2xSD of the intermediate precision (calculated in the Repeatability Study for the therascreen BRAF V600E RGQ PCR Kit) acceptance criteria for WT samples, the frequency of correct calls

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observed for all test conditions was 100.00% (note: there were 2 false positive calls observed in the nominal condition for proteinase K).

## 8. Specimen Stability

### a) Stability of FFPE Sections and Extracted DNA

The stability of specimens was assessed for:

- FFPE section stability stored at room temperature (in dark).
- Extracted FFPE gDNA sample stability stored at -20°C (-35°C to -15°C).

The study tested 6 CRC samples (3 WT samples and 3 BRAF V600E MT samples) over a period of 25 months (N+1 month, to claim FFPE section and DNA stability for up to 24 months) at 9 different time points (including initial testing) with three replicates per sample tested per test point. FFPE Stability was assessed from T=0 through T=8 only. DNA stability was assessed at T=9, T=10, T=11, T=12 and T=13. The T=12 timepoint was performed to provide an n+1 timepoint, as 33 weeks will be claimed as maximum stability.

The frequency of correct call for all test samples was 100% for both FFPE sections and gDNA. FFPE section stability supported a stability claim of 24 months (N-1 timepoint). Extracted DNA data supported a stability claim of 33 months when stored under appropriate conditions.

### b) Kit Stability

The therascreen BRAF V600E RGQ PCR Kit stability testing included

- Real time storage (shelf-life)
- In-Use stability (including up to 6 freeze-thaw cycles and open vial, post-transport simulation).
- Transport simulation study (integrated in Real-Time and In-Use stability study).

For all Real-Time and In-Use stability Test Timepoints (TTP), the same batch of pooled extracted DNA clinical samples (BRAF V600E WT and MT samples at approximately 2xLoD) were used. Transport Simulation and In-Use stability were assessed using three therascreen BRAF V600E RGQ PCR Kits. Real-Time stability was assessed using three therascreen BRAF V600E RGQ PCR Kit lots. A minimum of 12 WT and MT replicates were tested at each TTP for the Real-Time stability study. A minimum of 6 WT and MT replicates were tested at each TTP for In-Use stability.

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# Real Time Stability Testing

Real-Time stability testing was performed at 4 testing time points up to 10 months (TTP0, TTP4, TTP7 and TTP10) generated from WT and BRAF V600E MT (2xLoD) samples. The Real-Time timepoints for WT and MT samples showed $100\%$ correct calls. The Real-time stability study supported stability of the BRAF V600E Kit at 10 months of storage at the defined temperature conditions. The Real-time stability claim is for 10 months at $-30$ to $-15^{\circ}\mathrm{C}$ . Real-Time stability (closed bottle, post-transport simulation) planned for up to 25 months.

# In-Use Stability Testing

In-use stability testing was performed at 3 testing time points up to 7 months (TTP0, TTP4 and TTP7). For all In-use time points tested, the percentage of correct mutation status was $100\%$ . The In-use stability claim is for 6-freeze/thaw cycles (N-1) for the first 7 months of storage at $-20^{\circ}\mathrm{C}$ .

# Transport Simulation Study

Study kits were exposed to conditions designed to simulate the extremes of environmental factors that may be experienced during the distribution from the manufacturing site to the customer. To ensure the worst-case scenario was simulated, 3 cycles of transport conditions were applied. The first and second cycle were proposed to simulate the transportation to the warehouses and subsequent interim storage; the third cycle represented transport to the customer. Kits subjected to transport conditions were also used for Real-time and In-use studies. For the Real-time stability study 1 kit lot was subjected to simulated transport cycles in the final packaging after time point 0. For the In-use study, all kit lots were subjected to transport conditions before time point zero to reflect the customer use. The time points and conditions are shown in Table 22 below. The transport simulation study was integrated into the Real-time study. The transport simulation claim is 9 months at $-20^{\circ}\mathrm{C}$ .

Table 22:Transport Simulation Conditions

| Cycle | Duration | Place | Temperature |
| --- | --- | --- | --- |
| 1 | 5 days ± 2 hours | On dry ice | n/a |
| | 2 days ± 2 hours | Freezer | -30°C to -15°C |
| 2 | 5 days ± 2 hours | On dry ice | n/a |
| | 2 days ± 2 hours | Freezer | -30°C to -15°C |
| 3 | 5 days ± 2 hours | On dry ice | n/a |
| | 2 days ± 2 hours | Freezer | -30°C to -15°C |
| | Storage until testing is required | Freezer | -30°C to -15°C |

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X. SUMMARY OF PRIMARY CLINICAL STUDIES

Array BioPharma Inc (Array) is the developer of encorafenib for the treatment of metastatic colorectal (mCRC) patients with a BRAF V600E mutation. BRAF V600 mutations lead to constitutive activation of BRAF kinase and sustained RAS/RAF/MEK/ERK pathway signaling, resulting in increased cell proliferation and survival. Encorafenib is a BRAF kinase inhibitor and cetuximab is an EGFR inhibitor.

Array was the sponsor of the BEACON study (Clinical trial number ARRAY-818-302; NCT01909453). Eligible patients were required to have BRAF V600E mutation-positive metastatic colorectal cancer (CRC), as detected using an investigational QIAGEN therascreen BRAF V600E RGQ polymerase chain reaction (PCR) Kit clinical trial assay (CTA). Clinical studies of the device were initiated on September 28, 2016 and were conducted under an approved investigational device exemption. Patients were enrolled into the BEACON study between October 9, 2016 and January 31, 2019 with data cutoff date of February 11, 2019. The database for this PMA included test results from 1688 patients (11 patients were removed due to no patient information available in the database).

The BEACON study used results from local BRAF V600E local laboratory testing (LDT) to identify patients for enrollment. The QIAGEN CTA Assay was used as central laboratory confirmation of each enrolled subject's BRAF mutation status or to determine BRAF V600E mutation status for patients without a local LDT result. The validated CDx assay contains software design changes to the CTA assay used in the BEACON study and therefore upon completion of the BEACON study, a Bridging Study was conducted; both to demonstrate concordance between the LDTs and CDx assay and between the CTA and CDx assays and to assess the impact of the use of LDT's on mutation prevalence and efficacy reporting.

The efficacy and safety of the combination of encorafenib and cetuximab was evaluated in Array's BEACON study. The BEACON study and the bridging study between the Clinical Trial Assay (CTA) and the therascreen BRAF V600E RGQ PCR Kit were the clinical basis for providing evidence of clinical performance. The therascreen BRAF V600E RGQ PCR Kit has been validated by QIAGEN as a companion diagnostic device (CDx) for a combination of BRAFTOVI® (encorafenib) and cetuximab, for the treatment of BRAF V600E mutant mCRC.

This device SSED comprises a summary of the device clinical performance studies using the BEACON clinical study results to support the assurance of safety and effectiveness of the therascreen BRAF V600E RGQ PCR Kit when used in accordance with its intended use.

The study analyses conducted and summarized in this SSED are as follows:
- Efficacy of the drug combination based on the CTA results.
- Efficacy of the drug combination using the CDx results, including adjustment for the use of LDTs during patient pre-screening (i.e., prior to BRAF CTA test).

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The major efficacy outcome measure was overall survival (OS). The results demonstrated that BRAFTOVI in combination with cetuximab demonstrated a statistically significant improvement in OS for mCRC patients whose tumors have BRAF V600E mutations detected by the QIAGEN therascreen BRAF V600E RGQ PCR Kit

## A. Study Design – BEACON Clinical Trial

The BEACON CRC Study (ARRAY-818-302; NCT01909453), was a Phase 3 multicenter, randomized, open-label, 3-arm study designed to evaluate the efficacy and safety of encorafenib + cetuximab + binimetinib (referred to as the Triplet arm) and encorafenib + cetuximab (referred to as the Doublet arm) versus Investigator’s choice of either irinotecan/cetuximab or FOLFIRI/cetuximab (Control arm) in patients with BRAF V600E mCRC whose disease had progressed after 1 or 2 prior regimens in the metastatic setting. Randomization was stratified by Eastern Cooperative Oncology Group (ECOG) performance status (0 versus 1), prior use of irinotecan (yes versus no), and cetuximab product used (US-licensed versus EU-approved). The primary endpoints of the BEACON study were OS (Triplet arm vs. Control arm) and confirmed ORR by Blinded independent central review (BICR) per Response Evaluation Criteria in Solid Tumors (RECIST) v1.1 (Triplet arm vs. Control arm). The secondary endpoints of the BEACON study were OS and ORR by BICR per RECIST v1.1 of the Doublet Arm compared against the Control Arm.

This SSED presents analysis from the Doublet Arm against the Control Arm, in order to align with NDA labelling. Two committees were involved in the conduct of the BEACON study: a Steering Committee (SC) and a Data Monitoring Committee (DMC). The SC was appointed to oversee the study conduct. A detailed description of the SC responsibilities, membership and procedures were outlined in the SC Charter.

A detailed description of the DMC responsibilities, membership and operations were outlined in the DMC Charter. The control group was treated with a legally marketed alternative with similar indications for use.

## 1. Inclusion and Exclusion Criteria for Molecular Screening

Enrollment in the BEACON study occurred two ways.

- Population 1: Patients who satisfied the Screening eligibility criteria, were enrolled based on local BRAF test result (LDT), and were retrospectively confirmed to have the BRAF V600E mutation status with the central CTA, or
- Population 2: Patients were tested prospectively to determine BRAF V600E mutation status with the CTA..

## a) Molecular Pre-screening Inclusion Criteria

All of the following inclusion criteria had to be met for a patient to be eligible to undergo molecular tumor pre-screening:

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- Provide a signed and dated Prescreening informed consent document
- Age ≥ 18 years at time of informed consent
- Histologically- or cytologically-confirmed CRC that is metastatic
- Eligible to receive cetuximab per locally approved label with regard to tumor RAS status
- Able to provide a sufficient amount of representative tumor specimen (primary or metastatic, archival or newly obtained) for central laboratory testing of BRAF and KRAS mutation status (minimum of 6 slides; optimally up to 15 slides).

## b) Molecular Pre-screening Exclusion Criteria

Patients meeting any of the following criteria at Prescreening were not eligible to undergo molecular tumor prescreen:

- Leptomeningeal disease
- History or current evidence of RVO or current risk factors for RVO (e.g., uncontrolled glaucoma or ocular hypertension, history of hyperviscosity or hypercoagulability syndromes)
- Known history of acute or chronic pancreatitis
- History of chronic inflammatory bowel disease or Crohn's disease requiring medical intervention (immunomodulatory or immunosuppressive medications or surgery) ≤ 12 months prior to randomization
- Concurrent neuromuscular disorder that is associated with the potential of elevated CK (e.g., inflammatory myopathies, muscular dystrophy, amyotrophic lateral sclerosis, spinal muscular atrophy)
- Known history of human immunodeficiency virus (HIV) infection
- Known history of Gilbert's syndrome or is known to have any of the following genotypes: UGT1A1*6/*6, UGT1A1*28/*28, or UGT1A1*6/*28
- Known contraindication to receive cetuximab or irinotecan at the planned doses; refer to the most recent cetuximab and irinotecan summary of product characteristics (SPC) or local label as applicable
- Prior anti-EGFR treatment
- More than 2 prior regimens in the metastatic setting
- Disease relapse during treatment or within 6 months following adjuvant therapy will be considered metastatic disease.
- Maintenance therapy given in the metastatic setting will not be considered a separate regimen.

## 2. Clinical Inclusion and Exclusion Criteria for Patient Enrollment

In the event of a positive CTA mutation result, a patient was confirmed eligible and enrolled if they also satisfied the remaining eligibility criteria. Otherwise, the patient was excluded.

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a) Enrollment Inclusion Criteria (abridged list)

All of the following inclusion criteria had to be met for a patient to be eligible to be included in this study:

- Provide a signed and dated Screening informed consent document
- Age ≥ 18 years at time of informed consent
- Histologically- or cytologically-confirmed CRC that is metastatic
- Presence of BRAF V600E in tumor tissue as previously determined by a local assay at any time prior to Screening or by the central laboratory. Notes:

- Only PCR and NGS-based local assays results will be acceptable
- If at any time in the Phase 3 portion of the study there is lack of BRAF V600E confirmation by the central laboratory (for any reason including discordance and inadequate available tissue) in 37 total patients or discordance (a valid result of “no BRAF V600E mutation” as determined by the central laboratory) between the local assay and the central laboratory in 18 patients, all subsequent patients will be required to have BRAF V600E determined by the central laboratory prior to enrollment.
- Central testing cannot be repeated to resolve discordances with a local result once the central laboratory delivers a definitive result (positive or negative).
- If the result from the central laboratory is indeterminate or the sample is deemed as inadequate for testing, additional samples may be submitted.
- Results from local laboratories with more than 1 discordant result leading to patient enrollment will not be accepted for further patient enrollment.
- Sites with more than 2 randomized patients having indeterminate results after initiation of protocol version 6 will be required to enroll all subsequent patients based only on central laboratory assay results.

- Able to provide a sufficient amount of representative tumor specimen (primary or metastatic, archival or newly obtained) for confirmatory central laboratory testing of BRAF and KRAS mutation status (minimum of 6 slides; optimally up to 15 slides).
- Eligible to receive cetuximab per locally approved label with regard to tumor RAS status
- Progression of disease after 1 or 2 prior regimens in the metastatic setting. Notes:

- Disease relapse during treatment or within 6 months following adjuvant therapy will be considered metastatic disease.
- Patients who have received 2 prior regimens (i.e., those entering the study in the 3rd line setting), must have received or have been offered and refused prior oxaliplatin unless it was contraindicated due to underlying conditions.
- Maintenance therapy given in the metastatic setting will not be considered a separate regimen.

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- In the Phase 3 portion of study, the number of patients having received 2 prior regimens will be limited to 215 (35% of the total randomized). Patients with 2 prior regimens who have entered Screening at the time that the limit has been reached will be permitted to continue into the study if they are otherwise determined to be eligible.
- Evidence of measurable or evaluable non-measurable disease per RECIST, v1.1
- ECOG PS of 0 or 1

## b) Enrollment Exclusion Criteria (abridged list)

Patients meeting any of the following criteria at screening were not included in the study:

- Prior treatment with any RAF inhibitor, MEK inhibitor, cetuximab, panitumumab or other EGFR inhibitors
- Prior irinotecan hypersensitivity or toxicity that would suggest an inability to tolerate irinotecan 180 mg/m² every 2 weeks
- Symptomatic brain metastasis Notes: Patients previously treated or untreated for this condition who are asymptomatic in the absence of corticosteroid and antiepileptic therapy are allowed. Brain metastases must be stable for ≥ 4 weeks, with imaging (e.g., magnetic resonance imaging [MRI] or computed tomography [CT]) demonstrating no current evidence of progressive brain metastases at screening.
- Leptomeningeal disease
- History or current evidence of RVO or current risk factors for RVO (e.g., uncontrolled glaucoma or ocular hypertension, history of hyperviscosity or hypercoagulability syndromes)
- Use of any herbal medications/supplements or any medications or foods that are strong inhibitors or inducers of cytochrome P450 (CYP) 3A4/5 ≤ 1 week prior to the start of study treatment
- Known history of acute or chronic pancreatitis
- History of chronic inflammatory bowel disease or Crohn's disease requiring medical intervention (immunomodulatory or immunosuppressive medications or surgery) ≤ 12 months prior to randomization
- Impaired cardiovascular function or clinically significant cardiovascular diseases, including any of the following:

- History of acute myocardial infarction, acute coronary syndromes (including unstable angina, coronary artery bypass graft [CABG], coronary angioplasty or stenting) ≤ 6 months prior to start of study treatment;
- Symptomatic congestive heart failure (i.e., Grade 2 or higher), history or current evidence of clinically significant cardiac arrhythmia and/or conduction abnormality ≤ 6 months prior to start of study treatment, except atrial fibrillation and paroxysmal supraventricular tachycardia.

- Uncontrolled hypertension defined as persistent elevation of systolic blood pressure ≥ 150 mmHg or diastolic blood pressure ≥ 100 mmHg despite current therapy
- Impaired hepatic function, defined as Child-Pugh class B or C

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- Impaired GI function or disease that may significantly alter the absorption of encorafenib or binimetinib (e.g., ulcerative diseases, uncontrolled vomiting, malabsorption syndrome, small bowel resection with decreased intestinal absorption)
- Concurrent or previous other malignancy within 5 years of study entry, except cured basal or squamous cell skin cancer, superficial bladder cancer, prostate intraepithelial neoplasm, carcinoma in-situ of the cervix, or other noninvasive or indolent malignancy without Sponsor approval
- History of thromboembolic or cerebrovascular events ≤ 6 months prior to starting study treatment, including transient ischemic attacks, cerebrovascular accidents, deep vein thrombosis or pulmonary emboli
- Concurrent neuromuscular disorder that is associated with the potential of elevated CK (e.g., inflammatory myopathies, muscular dystrophy, amyotrophic lateral sclerosis, spinal muscular atrophy)
- Treatment with any of the following:
- Cyclical chemotherapy within a period of time that was shorter than the cycle length used for that treatment (e.g., 6 weeks for nitrosourea, mitomycin-C) prior to starting study treatment
- Biologic therapy (e.g., antibodies) except bevacizumab or aflibercept, continuous or intermittent small molecule therapeutics, or any other investigational agents within a period of time that is ≤ 5 half-lives (t1/2) or ≤ 4 weeks (whichever is shorter) prior to starting study treatment
- Bevacizumab or aflibercept therapy ≤ 3 weeks prior to starting study treatment
- Radiation therapy that included > 30% of the bone marrow
- Residual CTCAE ≥ Grade 2 toxicity from any prior anticancer therapy, with the exception of Grade 2 alopecia or Grade 2 neuropathy
- Known history of HIV infection
- Active hepatitis B or hepatitis C infection
- Known history of Gilbert's syndrome or is known to have any of the following genotypes: UGT1A1*6/*6, UGT1A1*28/*28, or UGT1A1*6/*28
- Known contraindication to receive cetuximab or irinotecan at the planned doses; refer to the most recent cetuximab and irinotecan SPC or local label as applicable

## 3. Follow-up Schedule

All patients were scheduled to return for follow-up examinations every 6 weeks (± 7 days) from the date of for the first 24 weeks of treatment, then every 12 weeks (± 7 days) thereafter until disease progression, withdrawal of consent, initiation of subsequent anticancer therapy, patient was lost to follow-up, death or defined end of study. Following discontinuation of the treatment period, patients were followed for survival every 3 months until withdrawal of consent, lost to follow-up, death or defined end of study.

## 4. Clinical Endpoints

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This SSED presents analysis from the Doublet Arm against the Control Arm (which was the secondary endpoint), in conjunction with the corresponding NDA (210496) (See Section D. Safety and Effectiveness Results).

The Endpoints were the following:

- OS, defined as the time from randomization to death due to any cause, of Doublet Arm vs. Control Arm
- Confirmed ORR (by BICR) per RECIST, v1.1 of Doublet Arm vs. Control Arm

# B. Accountability of PMA Cohort

A total of 1677 patients were screened for participation in the BEACON study, including both the SLI/JSLI cohorts and the randomized Phase 3. Of these, 975 patients $(58.1\%)$ discontinued either the pre-screening or screening phase and were not enrolled. A total of 665 patients were randomized. The majority of patients who were not enrolled or randomized due to inclusion/exclusion criteria not met did not have the required BRAF V600E mutation $(56.9\%)$ , followed by patients who did not meet other inclusion/exclusion criteria $(30.7\%)$ and patients for whom no further informed consent was obtained $(12.3\%)$ .

Of the 665 enrolled patients, 220 were included in the Doublet arm and 221 enrolled in the Control arm.

To conduct the Bridging study analysis, in total, 1934 test results, representing 1688 patients (patient ID) were included in the "QIAGEN Merged database". 11 patient IDs had no associated patient information available. This accounts for the lower total patient number screened for the BEACON study (1677), compared to patient IDs in the Bridging Study (1688). Of the 1677 patients screened, 1488 patient samples provided CTA results.

189 patients were excluded from analyses in the Bridging study because either they provided no CTA result (161) or they presented with no neoplastic cells (28). A further cohort of 39 patients from a safety lead in a Japanese subset were removed, which left 1449 patients included in bridging analyses. In the population screened with LDT a prevalence of close to $100\%$ is expected. The non-screened population presents the most representative estimate of prevalence.

Table 93: Bridging Study Population Prevalence

| BEACON Population | CTA Prevalence | CDx Prevalence |
| --- | --- | --- |
| Population 1 with LDT screening | 97.8% (544 / 556) | 97.2% (520 / 535) |
| Population 2 without LDT screening | 38.3% (285 / 745) | 37.0% (280 / 756) |
| Overall | 63.7% (829 / 1301) | 62.0% (800 / 1291) |

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# C. Study Population Demographics and Baseline Parameters

The CTA evaluable and CTA non-evaluable populations were consistent in terms of key demographic, specimen and sample handling characteristics (Table 24) and therefore the CTA evaluable population is representative of the wider study population.

Region, tumor content $(\%)$ , MSI status, presence of liver metastases at baseline and number of organs involved based on target and non-target lesion assessment were statistically significantly different (at the $5\%$ significance level) between the CTA evaluable and CTA non-evaluable patients.

Table 4: Demographic, Disease and Specimen Characteristics Data Comparing CTA Evaluable and CTA Non-Evaluable Patients (Population: Population 1 and 2)

| | CTA Evaluable | CTA Unevaluable | pValue |
| --- | --- | --- | --- |
| Total | 1301 | 182 | |
| Age (yrs) | | | |
| Mean | 59.4 | 57.9 | 0.144 |
| Std | 12 | 12.5 | |
| Min | 18 | 24 | |
| Median | 61 | 59 | |
| Max | 91 | 86 | |
| N | 1301 | 182 | |
| | | | |
| Gender [N (%)] | | | |
| Female | 633 (48.7) | 83 (46.1) | 0.51 |
| Male | 666 (51.3) | 97 (53.9) | |
| MISSING | 2 | 2 | |
| | | | |
| Region [N (%)] | | | |
| Europe | 685 (52.7) | 64 (35.2) | <.001 # |
| North America | 115 (8.8) | 4 (2.2) | |
| Rest of World | 501 (38.5) | 114 (62.6) | |
| | | | |
| ECOG Status [N (%)] | | | |
| 0 | 314 (50.3) | 17 (63.0) | 0.198 |
| 1 | 310 (49.7) | 10 (37.0) | |
| MISSING | 677 | 155 | |
| | | | |
| Prior use of Irinotecan [N (%)] | | | |
| N | 309 (49.5) | 11 (40.7) | 0.372 |
| Y | 315 (50.5) | 16 (59.3) | |
| MISSING | 677 | 155 | |

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| | CTA Evaluable | CTA Unevaluable | pValue |
| --- | --- | --- | --- |
| Cetuximab Source [N (%)] | | | |
| EU-approved | 573 (86.8) | 27 (93.1) | 0.568 # |
| US-licensed | 87 (13.2) | 2 (6.9) | |
| MISSING | 641 | 153 | |
| | | | |
| Sample type [N (%)] | | | |
| CNB | 137 (10.6) | 19 (10.4) | 1.000 # |
| FNA | 7 (0.5) | 1 (0.5) | |
| RES | 1148 (88.9) | 162 (89.0) | |
| MISSING | 9 | 0 | |
| | | | |
| Tumor Content (%) | | | |
| Mean | 46.2 | 42.2 | 0.038 |
| Std | 22.8 | 24.7 | |
| Min | 0 | 0 | |
| Median | 45 | 41 | |
| Max | 100 | 100 | |
| N | 1300 | 182 | |
| MISSING | 1 | 0 | |
| | | | |
| Necrotic Tissue (%) | | | |
| Mean | 2.9 | 2.2 | 0.291 |
| Std | 8.4 | 8.2 | |
| Min | 0 | 0 | |
| Median | 0 | 0 | |
| Max | 77 | 85 | |
| N | 1129 | 169 | |
| <1 | 26 | 2 | |
| MISSING | 146 | 11 | |
| | | | |
| | | | |
| MSI Status [N (%)] | | | |
| Abnormal High | 53 (9.4) | 0 (0.0) | <.001 # |
| Abnormal Low | 2 (0.4) | 0 (0.0) | |
| Normal | 481 (85.6) | 8 (33.3) | |
| Not Evaluable | 26 (4.6) | 16 (66.7) | |
| MISSING | 739 | 158 | |
| | | | |
| Presence of liver metastases at baseline [N (%)] | | | |
| No | 1300 | 182 | |
| Yes | 1300 | 182 | |

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| | CTA Evaluable | CTA Unevaluable | pValue |
| --- | --- | --- | --- |
| N | 907 (69.7) | 156 (85.7) | <.001 |
| Y | 394 (30.3) | 26 (14.3) | |
| | | | |
| Removal status of primary tumor [N (%)] | | | |
| Completely Resected | 384 (76.3) | 9 (100.0) | 0.126 # |
| Partially Resected | 119 (23.7) | 0 (0.0) | |
| MISSING | 798 | 173 | |
| C-reactive protein (CRP) baseline level | 0 | 0 | |
| Mean | 0 | 0 | 0.177 |
| Std | 0 | 0 | |
| Min | 0 | 0 | |
| Median | 0.5 | 0.1 | |
| Max | 647 | 29 | |
| N | 654 | 153 | |
| MISSING | | | |
| | | | |
| Side of Tumor [N (%)] | 35 (5.3) | 3 (10.3) | |
| Both Sides | 229 (34.7) | 10 (34.5) | 0.304 # |
| Left Colon | 357 (54.1) | 13 (44.8) | |
| Right Colon | 39 (5.9) | 3 (10.3) | |
| Unknown Colon | 641 | 153 | |
| MISSING | | | |
| | | | |
| Number of organs involved based on Target and Non-target lesion assessment [N (%)] | 311 (23.9) | 16 (8.8) | |
| 3+ | 990 (76.1) | 166 (91.2) | <.001 |
| <=2 | | | |

## D. Safety and Efficacy Results

### 1. Safety Results

The safety with respect to treatment with BRAFTOVI™ and cetuximab will not be addressed in detail in this SSE. Refer to United States product insert for safety information on these treatments. No Adverse Device Effects occurred in the PMA clinical study.

The safety of the therascreen BRAF V600E RGQ PCR device is related to its accuracy, as false results may lead to inappropriate treatment decisions. A false negative result would prevent a patient from receiving a potentially beneficial treatment. A false positive result

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would potentially expose the patient to an ineffective treatment with possible adverse effects associated with the therapeutic.

The accuracy of the BRAF V600E kit relative to the validated reference method of Sanger Sequencing, was determined using specimens from the BEACON study. The estimated OPA, PPA, and NPA between the BRAF V600E Kit and Sanger Sequencing (with Sanger as the reference method) were 95.20%, 100.00% and 91.11% respectively, demonstrating that the BRAF V600E Kit has high accuracy when compared to the reference method and that the possibility of false results is very low. Additionally, the use of the BRAF V600E kit poses minimum safety hazard to patients, as biopsy specimens are routinely used in diagnosis and staging of mCRC.

## 2. Effectiveness Results-Based on Mutation Detection with CTA

The analysis of effectiveness was based on the Secondary Efficacy endpoints of OS and ORR for Doublet Arm vs Control Arm in 665 mCRC patients with BRAF V600E mutation positive assessed by a clinical trial assay (CTA). The Secondary endpoints were used (rather than Primary endpoints) in order to align with amended NDA labelling.

## Overall Survival

The study demonstrated statistically and clinically significant superiority in OS for the Doublet arm vs. the Control arm as summarized in Table 25 and Figure 1. The analysis of OS found 40% reduction in risk of death was observed for the Doublet arm compared to the Control arm (HR 0.60, 95% CI: 0.45, 0.79). The median OS in the Doublet arm was 2.99 months longer than that in the Control arm, with median OS estimates using Kaplan-Meier methodology of 8.41 months (95% CI: 7.46, 11.04) in the Doublet arm and 5.42 months (95% CI: 4.76, 6.57) in the Control arm (p = 0.0002, stratified log-rank test).

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Table 25: Efficacy Results from BEACON CRC

| | BRAFTOVI with cetuximab
N = 220 | Irinotecan with cetuximab or FOLFIRI with cetuximab
N = 221 |
| --- | --- | --- |
| Overall Survival | | |
| Number of Events (%) | 93 (42) | 114 (52) |
| Median OS, months (95% CI) | 8.4 (7.5, 11.0) | 5.4 (4.8, 6.6) |
| HR (95% CI)^{a,b} | 0.60 (0.45, 0.79) | |
| P-value^{a,c} | 0.0003 | |
| Overall Response Rate (per BICR) | | |
| ORR (95% CI)^{d} | 20% (13%, 29%) | 2% (0%, 7%) |
| CR | 5% | 0% |
| PR | 15% | 2% |
| P-value^{a,e} | <0.0001 | |
| Median DoR, months (95% CI) | 6.1 (4.1, 8.3) | NR (2.6, NR) |

CI = Confidence interval; CR = Complete…