AmoyDx EGFR 29 Mutations Detection Kit

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1 AmoyDx EGFR 29 Mutations Detection Kit Detection of 29 mutations in exons Instruction for Use Instruction Version: B1.1 Revision Date: August 2013 Store at -20±2

2 Background Due to its association with malignancies, epidermal growth factor receptor (EGFR) has become the target of an expanding class of anti-cancer therapies, such as gefitinib (Iressa) and erlotinib (Tarceva), which are tyrosine kinase inhibitors (TKIs). These drugs work best on patients whose cancer is driven by abnormal EGFR signaling. Lung cancer patients who experienced rapid, durable, complete or partial responses to TKIs therapy have been found to harbor somatic mutations in the EGFR gene. Cancer patients with somatic EGFR mutations have shown an impressive 60% response rate, much higher than that for conventional chemotherapy. Therefore, detection of the EGFR mutation status in tumor tissue is key to offering tailored, personalized treatment to cancer patients. Resistance to therapy, either in the primary tumor or acquired after TKI treatment, is also associated with somatic mutations. The AmoyDx EGFR 29 Mutations Detection Kit is highly selective and sensitive, detecting 29 of the most common somatic mutations (both activating and resistance-related) in the EGFR gene. The procedure is easily adapted for use in high-throughput sample processing. The purpose of the kit is to aid physicians and clinical researchers in identifying non-small cell lung cancer patients whose tumors harbor EGFR mutations. Intended Use AmoyDx EGFR 29 Mutations Detection Kit is a highly sensitive real-time PCR-based test designed to accurately identify 29 EGFR mutations in exons (Table 1). The used DNA is extracted from fresh, frozen or formalin-fixed paraffin-embedded (FFPE) tissue. If tumor tissues are unavailable, peripheral blood (plasma or serum) can also be used for detection of EGFR mutations. It is demonstrated that there is cell-free DNA of the apoptotic and necrotic tumor cell existing in peripheral blood. The authoritative clinical trials indicated the concordance rate of EGFR mutations between tumor tissue samples and matched peripheral blood (plasma and serum) was 52.7%. The AmoyDx EGFR 29 Mutations Detection Kit is China FDA (CFDA) approved for clinical use in China and CE marked for IVD use in Europe. Table 1 Details of 29 somatic mutations in EGFR gene Detection Name Mutation Exon Base Change Cosmic ID Limit Ex18-mutant-1 G719A G>C % Ex18-mutant-2 G719S G>A % Ex18-mutant-3 G719C G>T % Ex19-mutant-1 E746_A750del (1) _2249del % Ex19-mutant-2 E746_A750del (2) _2250del % Ex19-mutant-3 L747_P753>S _2257del % Ex19-mutant-4 E746_T751>I _2252>AAT(complex) % Ex19-mutant-5 E746_T751del _2253del % Ex19-mutant-6 E746_T751>A _2251del % Ex19-mutant-7 E746_S752>A _2254del % Ex19-mutant-8 E746_S752>V _2255>T(complex) % Ex19-mutant-9 E746_S752>D _2255del % Ex19-mutant-10 L747_A750>P _2248>GC(complex) % Ex19-mutant-11 L747_T751>Q _2252>GCA(complex) % Ex19-mutant-12 L747_E749del _2247del % 1 /7

3 Ex19-mutant-13 L747_T751del _2253del % Ex19-mutant-14 L747_S752del _2256del % Ex19-mutant-15 L747_A750>P _2248TTAAGAGAAG>C(complex) % Ex19-mutant-16 L747_P753>Q _2258>CA(complex) % Ex19-mutant-17 L747_T751>S _2251del % Ex19-mutant-18 L747_T751del _2254del % Ex19-mutant-19 L747_T751>P _2251>C(complex) % Ex20-mutant-1 T790M C>T % Ex20-mutant-2 S768I G>T % Ex20-mutant-3 H773_V774insH _2320insCAC % Ex20-mutant-4 D770_N771insG _2311insGGT % Ex20-mutant-5 V769_D770insASV _2308insGCCAGCGTG % Ex21-mutant-1 L858R T>G % Ex21-mutant-2 L861Q T>A % Kit Contents This kit contains sufficient reagents to carry out 24 tests (Table 2), and additional EGFR Mixed Standard DNA for positive control reactions. The EGFR Taq Mix contains the Taq DNA polymerase for PCR amplification and uracil-n-glycosylase which works at room temperature to prevent PCR products carryover contamination. The 19-Del Reaction Mix can detect the presence of any of 19 deletions in exon 19. The Insertions Reaction Mix can detect the presence of any of 3 insertions in exon 20. The Reaction Mix in tube 1-8 contains the reagents for the detection of EGFR mutation and internal control, the EGFR mutation is indicated by FAM signal, and the internal control is indicated by HEX signal. The Reaction Mix in tube 9 is external control, it s used to assess the DNA quality and indicated by FAM signal. Table 2 Kit Contents Tube No. Reagents Supplied Volume (μl) 1 19-Del Reaction Mix L858R Reaction Mix T790M Reaction Mix Insertions Reaction Mix G719A and G719C Reaction Mix G719S Reaction Mix S768I Reaction Mix L861Q Reaction Mix External Control Reaction Mix EGFR Mixed Standard 2 (Positive Control) EGFR Taq Mix 80 Equipment and Reagents Not Supplied With Kit 1. Compatible PCR instruments are Rotor-Gene 6000 (72 wells) and Rotor-Gene Q (72 wells). 2. Sterile, nuclease-free tubes. 3. Dedicated pipette and filter pipette tips for handling DNA. 2 /7

4 4. Sterile, nuclease-free H 2 O. Shipping and Storage The kit requires cold-chain-transportation. All contents of the kit should be stored immediately upon receipt at -20±2 in the dark in a constant temperature freezer. Avoid unnecessary freezing and thawing of the kit contents. Do not use the reagent after five freeze-thaw cycles. Once opened, this reagent is stable at -20±2 until the expiry. Stability The shelf-life of the kit is six months when stored under the recommended conditions and in the original packaging. Do not use the kit after the stated expiry date. Specimen Material Human genomic DNA must be extracted from fresh, frozen or formalin-fixed paraffin-embedded (FFPE) tissue or peripheral blood (plasma or serum), and stored at -20 or -70 prior to use. High quality DNA is essential and we recommend use of DNA extraction kit (AmoyDx FFPE DNA Kit, Cat No. ADx-FF01, for paraffin embedded specimens; AmoyDx Tissue DNA Kit, Cat No. ADx-TI01, for tissue and pleural effusion specimens; AmoyDx Serum/Plasma Cell-free DNA kit, Cat No.ADx-BL02, for peripheral blood). The OD value of DNA samples should be measured using a spectrophotometer after extraction. The Thermo Fisher NanoDrop 1000/2000 spectrophotometer is recommended. Make sure A 260 /A 280 value is between 1.8 and 2.0. Note: a) For fresh tissue samples, it is very important to make sure that there are at least 1% tumor cells in the samples. b) For pathological sections and FFPE samples, it s very important to make sure that there are tumor cells existing in the samples. It s recommended to use 3~8 sections of FFPE samples, each with a thickness of 5µm. It should be avoided to use the FFPE samples with more than 3 years storage time. c) For plasma, do not use heparin as anticoagulant. The DNA in plasma and serum should be isolated within 2 hours, and stored at -20. The recommended volume of plasma and serum is no less than 1 ml. Technological Principles The kit uses novel, patented primers and probes to detect mutations in a real-time PCR assay. The mutant DNA is amplified accurately by the specific primers, and detected by the novel probes. Protocol 1. The reaction mix contains the reaction buffer, dntps, specific oligos and probes. 2. The mutation reaction mix includes a mutation detection system and an internal control system. The mutation detection system is used to detect the mutation status of EGFR gene (positive or negative). The internal control system is designed to detect the presence of inhibitors, which may lead to false negative results. The external control reaction mix is used to assess the DNA quality, that is, to detect the presence of inhibitors, which may lead to false negative results. 3. The threshold at which the signal is detected above background fluorescence is called the Cycle threshold (Ct). The Ct values used to determine if a sample is positive or negative are based on extensive validation. If the Ct value falls within the appointed range (see below), the sample is classed as mutation positive. If the Ct value is outside the appointed range, the sample is classed as negative or below the detection limit of the kit. 4. The EGFR Mixed Standard contains a recombinant EGFR gene with the 29 mutations, and normal human genomic DNA. 3 /7

5 5. The 9 reactions for each sample must be analyzed within the same PCR run to avoid run-to-run variations in threshold settings. It is recommended that the EGFR Mixed Standard should be analyzed during each PCR run, along with no-template controls. 6. The amount of sample DNA used for each sample PCR reaction depends on the sample type. (1) For non-paraffin embedded samples, the recommended DNA amount in each test tube is 3~6 ng. a) Non-paraffin embedded specimens include fresh tissue, frozen pathological sections, non-heparin anticoagulant blood plasma, blood serum and non-heparin anticoagulant blood. (2) For paraffin embedded samples with less than 3 years storage, we recommend use of 6 ng template DNA. (3) For paraffin embedded samples with more than 3 years storage, we recommend use of 9 ng template DNA. (4) The volume of DNA added to the reaction tube is 3 µl. Experimental Procedure 1. Thaw the Reaction Mix and EGFR Mixed Standard 2 at room temperature. 2. Centrifuge the Reaction Mix, EGFR Taq Mix and EGFR Mixed Standard 2 prior to use. 3. According to the ratio in Table 3, transfer the appropriate amount of Reaction Mix and EGFR Taq Mix into a sterile tube.. Note: The volumes given for each reaction mix have been optimized and validated. Changing volumes of any reagent may result in a loss of performance. Do not store user-prepared mixes, use immediately. Since Taq DNA polymerase is viscous, please pay attention to the centrifugation and pipetting process. Minimize the contact interface between the pipette tip and Taq DNA polymerase to avoid adding excess enzyme. 4. Mix the solution thoroughly by gently pipetting it up and down. Note: avoid vortexing solutions with EGFR Taq Mix. 5. Centrifuge briefly. 6. Transfer 22 μl of the mixed solution into the appropriate PCR tubes. 7. Add 3 μl sample DNA (3~9 ng per reaction, see above), 3 μl EGFR Mixed Standard or 3 μl ddh 2 O (no-template control, NTC) to the appropriate PCR tubes. 8. Seal the PCR tubes. 9. Place the PCR tubes into the real-time PCR instrument. 10. Carry out the real-time PCR using the cycling conditions described in Table 4. Note 1: prior to the operation, please set up the PCR program according to the following steps: 1select Gain Optimisation, the Auto Gain Optimisation Setup window will open; 2Click Perform Calibration Before 1st Acquisition and Optimise Acquiring. 3Click OK, then click Close to continue. Please see the following Figure 1, 2 and 3 for more details. Note 2: make sure the total volume of solution in each well is 25 µl (22 µl reagent plus 3 µl DNA). 4 /7

6 Table 3 Test Reaction Set-up (volumes given below are for one reaction) Master Mix Assay Reaction Mix (μl) Taq (μl) 19-Del L858R T790M Insertions G719A and G719C G719S S768I L861Q External Control For: ADx-EG07-RG72 Table 4 Cycling Parameters Figure 1 Temperature Time Cycles Stage min 1 Stage s 64 10s 72 8s 15 Stage s 60 15s Data collection of FAM and HEX 72 8s 31 Figure 2 Figure 3 5 /7

7 Sample Data Analysis 1. The FAM signals of the mutation detection system indicate the mutation status of the sample. The HEX signals indicate the internal control status. The internal control amplifies and detects a region of genomic DNA that has no known mutations or SNPs. 2. Check the FAM signal from the external control assay: (1) The Ct value should be between 10~19. (2) If the requirements of item (1) are satisfied, further analysis should be carried out. However, if the external control Ct <10, the DNA is overloaded, the procedure should be repeated with reduced DNA. If all the results of eight tubes (1-8) are negative, the sample is classified as negative. (3) If the external control Ct >19, it shows that the DNA template contains PCR inhibitors or the DNA amount is insufficient, indicating that the DNA needs to be re-extracted or increase the DNA amount. If the result in any of the eight tubes (1-8) is positive, the sample is classified as positive. 3. The HEX signal in the internal control is also used as control. If the HEX signal assay fails but the FAM signal works well, continue with the analysis. If both the HEX and FAM signals fail, the obtained data must be discarded and the experiment should be repeated. 4. Analyze one sample at a time. It s necessary to choose the reaction wells for positive control, no-template control and sample simultaneously. Then users can adjust the threshold of FAM amplification curve, and obtain the Ct value of mutant group. 5. The EGFR Mixed Standard 2 FAM Ct value should be less than 21, but variation may occur due to different threshold settings on different instruments. 6. Analysis of mutation assay results (see Table 5): (1) The calculation of Ct: Ct = mutant FAM Ct value external control FAM Ct value. The mutant Ct value indicates the Ct value of the sample mutant FAM signal; the external control Ct value indicates the Ct value of external control FAM signal of that sample. (2) If the FAM Ct value is in the Positive range, the Ct of the reaction tube is calculated to confirm the result. If the Ct value is less than or equal to the corresponding Cut-off value of Ct, the sample is confirmed as positive. If the Ct value is greater than the Cut-off Ct value, the sample is classified as negative or below the limits of the kit. (3) If the sample FAM Ct value is greater than or equal to the critical negative value shown in the Negative row in Table 5, the sample is classified as negative or below the detection limit of the kit. Table 5 Result Determination Mutation Name 19-Del L858R T790M Insertions G719A/G719C G719S S768I L861Q Mutant Ct Positive Value Ct <29 Ct <29 Ct <28 Ct <29 Ct <29 Ct <28 Ct <29 Ct <29 Ct Cut-off value Negative Mutant Ct Value Ct 29 Ct 29 Ct 28 Ct 29 Ct 29 Ct 28 Ct 29 Ct 29 Warnings and Precautions 1. Please read the instruction carefully and become familiar with all components of the kit prior to use. 2. The product specified above does not contain any virus, reagent by-product of the same or metabolic by-product of Hepatitis A, B, C, D or HIV. 6 /7

8 3. Do not exchange and mix up the kit contents with different batches. 4. The kit and its contents cannot be resold or modified for resale without the written approval of manufacturer. 5. Using other sources of reagents is not recommended. Strictly distinguish the reagents from mixed standard to avoid contamination. Otherwise, false positive may be produced. 6. Do the experiments with attention to prevent exogenous DNA contamination to reagents. It is recommended that, use separate, dedicated pipette and filter pipette tips to add DNA template during the preparation of reagents. 7. To optimize the activity and performance, mixtures should always be protected from light to avoid photo bleaching. 8. All the chemicals are potential hazard, only trained professionals can use this kit. Please wear suitable lab coat and disposable gloves. The used kit should be disposed of properly. Notes 1. Symbol for "AUTHORISED REPRESENTATIVE IN THE EUROPEAN COMMUNITY". 2. Symbol for "IN VITRO DIAGNOSTIC MEDICAL DEVICE". 3. Symbol for "KEEP DRY". 4. Symbol for "THIS WAY UP". 5. Symbol for FRAGILE, HANDLE WITH CARE. Information of European Authorised Representative Wellkang Ltd t/a Wellkang Tech Consulting Suite B, 29 Harley Street, London W1G 9QR United Kingdom References 1. Shama SV, Bell DW, Settleman J, et al; Epidermal growth factor receptor muataions in lung cancer. Nat Rev Cancer, 2007,7(3): Ressel R, Moran T, Queralt C, et al; Screening for epidermal growth factor receptor mutations in lung cancer. N Engl J Med, 2009,361(10): Mork Ts, Wu YL, Thongprasert S, et al; Gefitinib or carboplatin-paclitaxel in pulmonary ademocarcinoma. N Engl J Med, 2009,361(10): Gazdar AF; Personalized medicine and inhibition of EGFR singnaling in lung cancer. N Engl J Med, 2009, 361(10): Dancey JE; Epidermal growth factor receptor inhibitors in non-small cell lung cancer. Drugs, 2007, 67(8): Kobayashi S, Boggon TJ, Dayaram T, et al; EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. N Engl J Med, 2005, 352(8): Yasuda H., S kobayshi, Costa, D. B, et al. EGFR exon 20 insertion mutations in non-small-cell lung cancer: preclinical data and clinical implications. Lancet Oncol,2012, 13(1): e Kimura H, Suminoe M, Kasahara K, et al; Evaluation of epidermal growth factor receptor mutation status in serum DNA as a predictor of response to gefitinib (IRESSA). Br J Cancer, 2007, 97(6): Huang Z, Wang ZJ, Bai H, et al; The detection of EGFR mutation status in plasma is reproducible and can dynamically predict the efficacy of EGFR-TKI. Thoracic Cancer, 2012, 3(4): /7

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