SuperARMS EGFR Mutation Detection Kit

Transcription

1 SuperARMS EGFR Mutation Detection Kit Detection of 41 mutations in exons Instruction for Use Instruction Version: P1.0 Revision Date: July 2016 Store at -20±5

2 Background For: ADx-EG14 Due to its association with malignancies, epidermal growth factor receptor (EGFR) has become the target of an expanding class of anticancer 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. Currently, tumor tissue is the most frequent material for EGFR mutation testing, however, for the advanced non-small cell lung cancer (NSCLC) patients, tumor tissue is always difficult to obtain. Peripheral blood of cancer patients frequently contains circulating tumor DNA (ctdna) derived from tumor cells, which has been used to detect tumor-specific alterations. Moreover, blood sampling is minimally invasive, readily accessible, and relatively repeatable. Thus, using blood for EGFR mutation identification and follow-up shows promise. The SuperARMS EGFR Mutation Detection Kit is highly selective and sensitive, detecting 41 of the most common somatic mutations (both activating and resistance-related) in the EGFR gene. Our company s patented technology allows detection of 0.2% - 0.8% mutant DNA in a background of 99.8% % normal DNA, while ensuring that false negatives are minimized. 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 The SuperARMS EGFR Mutation Detection Kit is a highly sensitive real-time PCR-based test designed to accurately identify 41 EGFR mutations in exons The used DNA is extracted from peripheral blood (plasma or serum). Kit Contents This kit contains sufficient reagents to carry out 12 tests (Table 1). Table 1 Kit Contents Contents Amount P-EGFR Reaction Strips 8 strips P-EGFR Reaction Mix µl*16 P-EGFR Enzyme Mix 40 µl P-EGFR Positive Control 400 µl One 8-tube strip is employed for 2 tests (Table 2). The 19-Del reaction mix can detect the presence of any of 29 deletions in exon 19. The 20-Ins reaction mix can detect the presence of any of 6 insertions in exon 20. The G719X reaction mix can detect the presence of G719A and G719C. Table 2 Mutation Information for Each Strip Tube No. Reagent Supplied Volume (μl) Mutation detected FAM HEX ROX CY Del / L858R Del IC L858R / 1/7

3 2 T790M 10 T790M IC / / 3 G719X / L861Q / S768I 10 G719X IC L861Q S768I 4 20-Ins Ins IC / / 5 19-Del / L858R Del IC L858R / 6 T790M 10 T790M IC / / 7 G719X / L861Q / S768I 10 G719X IC L861Q S768I 8 20-Ins Ins IC / / * IC: Internal Control The reagents are pre-loaded into strips that are compatible with Stratagene Mx3000P /Mx3005P, ABI7500, SLAN-96S instruments. For the transparent strip, the number is marked on the side of each tube. For the milky white strip, one pinhole will lay in the corner of the tab beside tube No.1, and the other pinhole will lay in the middle of the tab beside tube No.8. Equipment and Reagents Not Supplied With Kit 1. Compatible PCR instruments: Stratagene Mx3000P /Mx3005P, ABI7500, SLAN-96S (1) For Stratagene Mx3000P /Mx3005P, if there s low net fluorescence signal (dr) but high background signal (R), please reduce the signal gain setting of instrument properly. (2) For ABI instruments please set up as follows: Reporter Dye: FAM, VIC, ROX, CY5; Quencher Dye: TAMRA; Passive Reference: NONE. (3) For SLAN-96S, please set up as follows: Probe mode: FAM, VIC, ROX, CY5. During the result analysis, open the Preference window and select Absolute Fluorescence Value Normalization in Amplification Curve section. (4) We recommend that all PCR instruments in use should be conducted fluorescence calibration once a year. 2. Sterile, nuclease-free tubes and pipette tips. 3. Dedicated pipettes and filtered pipette tips for handling DNA template. 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±5 in the dark in a constant temperature freezer. Avoid unnecessary freezing and thawing of the contents of the kit. Do not use the reagent after five freeze-thaw cycles. Once opened, this reagent is stable at -20±5 until the expiry. Stability The shelf-life of the kit is eight 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 peripheral blood (plasma or serum). Selection of high quality DNA extraction reagents is essential for the kit. We recommend use AmoyDx Circulating DNA kit, Cat No. ADx-BL03. Note: a) The kit requires 10 ml whole blood and the recommended volume of plasma is no less than 4 ml. 2/7

4 b) The plasma should be separated from whole blood within 2 hours, If not, please store the blood sample at 2~8 for no more than 4 hours. We recommend use AmoyDx Cell-free DNA Protection Vacuum Tube (Cat No. ADx-VT01-R) for blood collection. (The collected blood samples are stable for 5~7 days at 4~25 for storage and transportation). c) EDTA is recommended for anticoagulation, avoid using heparin anticoagulant. d) The DNA should be extracted from plasma within 2 hours, if not, please store the plasma at -20±5 for no more than 2 years. e) If the extracted DNA is not used immediately, it should be stored at -20±5 for no more than 3 months. Technological Principles The kit adopts ARMS (Amplification Refractory Mutation System) and real-time PCR technology, which uses novel, proprietary primers and probes in a real-time PCR assay to detect EGFR mutations in human plasma cfdna samples. The mutant EGFR gene DNA is amplified by the specific primers, and detected by the novel probes. A highly validated procedure based on EGFR Taq DNA polymerase contributes to outstanding assay sensitivity and selectivity. Protocol 1. The reaction buffer, dntps, specific oligos and novel probes are pre-loaded in the PCR tubes. 2. The contents in P-EGFR Reaction strip and P-EGFR Reaction Mix formed 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 and monitor the accuracy of experimental operation. 3. The P-EGFR Positive Control contains a recombinant gene with EGFR mutations, and normal human genomic DNA. Experimental Procedure 1. Thaw the P-EGFR Positive Control and P-EGFR Reaction Mix at room temperature. When the reagents are completely thawed, mix the reagents by inverting the tube 10 times and centrifuge briefly to collect the contents at the bottom of the tube. 2. Briefly centrifuge P-EGFR Enzyme Mix prior to use. 3. Add 67.5 µl DNA sample, and 2.16 µl P-EGFR Enzyme Mix into µl P-EGFR Reaction Mix. 4. Add 67.5 µl no-template controls (sterile water, NTC), and 2.16 µl P-EGFR Enzyme Mix into µl P-EGFR Reaction Mix. 5. Add 67.5 µl P-EGFR Positive Control, and 2.16 µl P-EGFR Enzyme Mix into µl P-EGFR Reaction Mix. 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. 6. Mix each solution thoroughly by gently pipetting up and down more than 10 times. Note: avoid vortexing solutions with Taq DNA Polymerase. 3/7

5 7. Centrifuge briefly. 8. Take out the P-EGFR Reaction Strips and centrifuge the strips if there are any reagent droplets in the caps of the PCR tubes. Then briefly uncover the caps prior to use. 9. Transfer 70 µl of above mixed solution to the appropriate PCR tube of the P-EGFR Reaction Strips. Add the solution to the inside of the tube wall above the reagents in the tube. 10. Seal the strips. 11. Spin down the PCR tubes gently or centrifuge them briefly to collect the reagents at the bottom of tubes. Note: this spin or centrifuge step is essential for proper mixing of the reagents. 12. Place the PCR tubes into the real-time PCR instrument. A recommended plate layout is shown in Table 3. Table 3 Suggested PCR Plate Layout Well layout A Sample 1 Sample 3 Sample 5 NTC B Sample 1 Sample 3 Sample 5 NTC C Sample 1 Sample 3 Sample 5 NTC D Sample 1 Sample 3 Sample 5 NTC E Sample 2 Sample 4 Sample 6 PC F Sample 2 Sample 4 Sample 6 PC G Sample 2 Sample 4 Sample 6 PC H Sample 2 Sample 4 Sample 6 PC 13. Carry out real-time PCR using the cycling conditions described in Table 4. Note: The reaction volume is 80 μl per well. Please pack the post-pcr tubes with two disposable gloves and discard properly. Do NOT open the post-pcr tubes to avoid contamination. Table 4 Cycling Parameters Stage Temperature Time Cycles min s s 72 30s 93 40s 60 45s Data collection of FAM, HEX/VIC, ROX, CY s Sample Data Analysis 1. The FAM/ROX/CY5 signals of the mutation detection system indicate the mutation status of the sample. The HEX/VIC signals indicate the internal control status. The internal control amplifies and detects a region of genomic DNA that has no known mutations or SNPs. 4/7

6 2. Ensure the passive reference is unselected, and select single mutation detection for each tube accordingly. It is necessary to choose the reaction wells for positive control, no-template control and sample simultaneously. Then users could adjust the threshold of each amplification curve, and obtain the Ct value of mutant group. 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. 4. Assess each NTC Ct value of FAM/ROX/CY5 signals to ensure that there is no positive amplification, if the NTC has positive amplification, the data must be discarded as there is contamination. If the HEX/VIC signal occasionally rises, further analysis could be carried out. 5. In general, the Ct values of FAM/ROX/CY5 signals for P-EGFR Positive Control will be less than 20, but variation may occur due to different threshold settings on different instruments. 6. The Ct value for HEX/VIC signal should be less than 19, otherwise, the DNA sample may contains PCR inhibitors or the DNA amount is insufficient, indicating that the DNA needs to be re-extracted or increase the DNA amount. 7. If the Ct value is less than the corresponding Cut-off value of Ct, the sample is confirmed as positive. Otherwise, the sample is classified as negative or below the detection limit of the kit. (See Table 5) a) The calculation of Ct: Ct = mutant Ct value (FAM/ROX/CY5) internal control Ct value (HEX/VIC). The mutant Ct value indicates the Ct value of the mutant signal from a sample. The internal control FAM Ct value indicates the Ct value of the internal control signal of the sample. Table 5 Result Determination Tube No. FAM ROX CY / Ct Cut-off value 2 8 / / Performance Characteristics 4 11 / / The performance characteristics of this kit were validated on Stratagene Mx3000P /Mx3005P, ABI7500, and SLAN-96S 1. Sensitivity: The kit allows detect % mutant DNA in a background of % normal DNA (Table 6). Table 6 LOD for each EGFR mutation Exon Mutation Base Change Cosmic ID Name % LOD Exon 18 Exon 19 G719A 2156G>C 6239 E-18-M1 0.20% G719C 2155G>T 6253 E-18-M3 0.40% E746_A750del (1) 2235_2249del E-19-M1 0.20% E746_A750del (2) 2236_2250del E-19-M2 0.20% L747_P753>S 2240_2257del E-19-M3 0.60% E746_T751>I 2235_2252>AAT(complex) E-19-M4 0.40% E746_T751del 2236_2253del E-19-M5 0.40% E746_T751>A 2237_2251del E-19-M6 0.20% E746_S752>A 2237_2254del E-19-M7 0.20% E746_S752>V 2237_2255>T(complex) E-19-M8 0.20% E746_S752>D 2238_2255del E-19-M9 0.40% 5/7

7 L747_A750>P 2238_2248>GC(complex) E-19-M % L747_T751>Q 2238_2252>GCA(complex) E-19-M % L747_E749del 2239_2247del E-19-M % L747_T751del 2239_2253del E-19-M % L747_S752del 2239_2256del E-19-M % L747_A750>P 2239_2248TTAAGAGAAG>C(complex) E-19-M % L747_P753>Q 2239_2258>CA(complex) E-19-M % L747_T751>S 2240_2251del E-19-M % Exon 19 Exon 20 Exon 21 L747_T751del 2240_2254del E-19-M % L747_T751>P 2239_2251>C(complex) E-19-M % L747_T751del 2238_2252del E-19-M % L747_S752>Q 2239_2256>CAA E-19-M % E746_T751>V 2237_2252>T E-19-M % E746_T751>T 2236_2253> ACG / E-19-M % L747_A750>P 2239_2250>CCC / E-19-M % L747_K754>QL 2239_2261>CAATT / E-19-M % E746_K754>EQHL 2238_2261>GCAACATCT / E-19-M % E746_S752>EQ 2238_2256>GCAA / E-19-M % E746_A750>QP 2236_2248>CAAC E-19-M % E746_T751>Q 2236_2253>CAA E-19-M % T790M 2369C>T 6240 E-20-M1 0.20% S768I 2303G>T 6241 E-20-M2 0.20% H773_V774insH 2319_2320insCAC E-20-M3 0.40% D770_N771insG 2310_2311insGGT E-20-M4 0.60% V769_D770insASV 2307_2308insgccagcgtg E-20-M5 0.60% D770_N771insSVD 2311_2312insGCGTGGACA E-20-M8 0.40% D770ASVD 2309_2310AC>CCAGCGTGGAT E-20-M9 0.40% H773_V774insNPH 2319_2320insAACCCCCAC E-20-M % L858R 2573T>G 6224 E-21-M1 0.20% L861Q 2582T>A 6213 E-21-M2 0.20% 2. Productivity: The kit can be used to analysis 12 samples maximum. (see Table 7) Table 7 Sample Qty detected with the Kit PCR Run(s) Control Qty Total samples can be detected 2 runs 4 (2 controls/run * 2) 12 4 runs 8 (2 controls/run * 4) 8 3. Accuracy: Accuracy of the kit was established by testing 7 mutant positive reference controls and 8 negative reference controls, the detection concordance rate is 100%. 4. Precision: Precision of the kit was established by performing a certain mutant positive reference control for 10 repeats; all the controls can be detected. 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 users have separate, dedicated pipettes and filtered 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 could 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