Instruction manual for product # PNAC Version 1.2

Transcription

1 PNAClamp BRAF Mutation Detection Kit For in vitro diagnostic use Instruction manual for product # PNAC-2001 Version 1.2 Store at -20 C. Instruction Version: Ver. 1.2 Date of Revision: 2012 February 1 / 15 PNG-PCBUM001

2 Table of Contents Intended Use... 3 Background Information... 4 Principles and Overview... 5 Contact Information... 6 Additional Equipment and Reagents Required... 6 Warnings and Precautions... 7 Components of the PNAClamp BRAF Mutation Detection Kit... 7 Procedures DNA Preparation Preparation of the Real-Time PCR Mixture Real-Time PCR reaction Assessment Examples of Analysis References Explanation of Symbols Endnotes / 15 PNG-PCBUM001

3 Product Name Product Name: PNAClamp Mutation Detection Kit Brand Name: PNAClamp BRAF Mutation Detection Kit PNAClamp BRAF Mutation Detection Kit PNAClamp BRAF Mutation Detection Kit Please read the instructions carefully prior to use. The PNAClamp BRAF Mutation Detection Kit is a CE marked diagnostic device in accordance with the European Union in vitro Diagnostic Medical Device Directive 98/79/EC. INTENDED USE The PNAClamp BRAF Mutation Detection Kit detects the V600E somatic mutation in Valine 600 position of human in BRAF oncogene (Table 1). The PNAClamp BRAF Mutation Detection Kit is to be used by trained laboratory professionals, within a laboratory environment, using (for example) DNA extracted from formalin-fixed paraffinembedded samples of colorectal tissue, thyroid cancer biopsies, and thyroid fine-needle aspiration biopsy (FNAB). The kit is for in vitro diagnostic use. Table 1. BRAF mutations detected by the kit No. Reagent Exon Amino Acid Change Nucleotide change Cosmic No. 1 BRAF PNA mix #2 15 p.v600e c.1799t>a 476 Cosmic No. is taken from the Catalogue of Somatic Mutations in Cancer. ( 3 / 15 PNG-PCBUM001

4 BACKGROUND INFORMATION The B-type Raf Kinase (BRAF) protein is a serine/threonine kinase that has important roles in cellular proliferation, differentiation, and programmed cell death. A BRAF mutation is commonly found in many human cancers including melanoma, colorectal cancer, lung cancer, and papillary thyroid carcinoma. V600E mutation (thymidine to adenosine change in position 1799 in DNA level) is the most prominent mutation, occurring in 90% of these cancers. Therefore, BRAF V600E mutation may serve as a biomarker for diagnosis, prognosis, and treatment options for cancer patients. 4 / 15 PNG-PCBUM001

5 PRINCIPLES AND OVERVIEW The PNAClamp BRAF Mutation Detection Kit is based on peptide nucleic acid (PNA)-mediated real-time PCR clamping technology. PNA is a synthetic DNA analog in which the phosphodiester backbone is replaced by a peptide-like repeat formed by (2-aminoethyl)-glycine units. Since PNA contains no charged phosphate groups, the binding between PNA/DNA is stronger than between DNA/DNA due to the lack of electrostatic repulsion. In addition, PNA is resistant to DNases and proteases, and is stable at wide range of ph. PNA-mediated real-time PCR clamping relies on the following two unique properties of PNA probes. First, PNA will hybridize to its complementary DNA target sequence only if the sequence is in complete match. Since PNA/DNA duplexes are more thermodynamically stable than the corresponding DNA-DNA duplexes, even with a single mismatch, PNA will not bind to complementary DNA strand, unlike DNA. Second, PNA oligomers are not recognized by DNA polymerases and will not be utilized as primers in subsequence real-time PCR. Instead, it serves as a sequence-selective clamp that prevents amplification during subsequent PCR. When there is a mutation in target gene and therefore a mismatch is present, the DNA/PNA duplex is destabilized, allowing strand elongation from a bound DNA oligomer which serves as a PCR primer. The outcome is the positive reaction in real-time PCR from the samples harboring mutant allele, while amplification of the wild-type gene is suppressed. Figure 1. Principle of the PNAClamp BRAF Mutation Detection Kit 5 / 15 PNG-PCBUM001

6 The PNAClamp BRAF Mutation Detection Kit can rapidly detect BRAF mutation (within 2 h) with high sensitivity even with a small amount of DNA (10~25 ng). The detection limit of the kit, when the mutated gene is mixed with wild-type background, is less than 1%. CONTACT INFORMATION The PNAClamp BRAF Mutation Detection Kit should be kept frozen on arrival. For any questions including technical support or concerns, please contact the distributors or the manufacturer. Manufacturer Manufacturer: PANAGENE Inc. 816 Tamnip-dong, Yuseong-gu, Daejeon, , Korea [email protected] EC Representative: PentaGen, s.r.o Ke Klinku 143, Horni Bezdekov, Czech Republic [email protected] ADDITIONAL EQUIPMENT AND REAGENTS REQUIRED Reagents and equipment for DNA extraction 0.2 ml DNase-free PCR tubes or plates Pipettes A real-time PCR instrument fitted with a detector enabling evaluation of SYBRGreen dye Table 2. List of real time PCR machines that have been tested Company Model Bio-Rad * CFX 96 Roche Light cycler 480 II ABI ABI 7500 ABI ABI 7900 * Current protocol has been optimized with Bio-Rad CFX 96. For other instruments, minor optimization might be necessary. 6 / 15 PNG-PCBUM001

7 WARNINGS AND PRECAUTIONS PNAClamp BRAF Mutation Detection Kit All experiments should be performed under proper sterile conditions with aseptic techniques. Always wear powder-free gloves when you handle the kit. To avoid repeated freezing and thawing, aliquot all reagents into appropriate volumes and store frozen until use. Thaw appropriate volumes of reagents before each experiment. All experimental procedures should be performed at room temperature. However, exposing BRAF PNA 2X premix at room temperature should be minimized for the optimal amplification. Dissolve reagents completely and mix them thoroughly by vortexing. The BRAF PNA 2X premix solution contains SYBRGreen dye and should be kept dark. If DNA has been extracted from a paraffin block, additional purification steps may be required. PCR tubes should be centrifuged briefly before use. Use extreme caution to prevent contamination of PCR reactions with synthetic control material. Components of the PNAClamp BRAF Mutation Detection Kit No. Name of component Description Volume 1 Non PNA mix #1 Primers only 180 l 2 BRAF PNA mix #2 V600 PNA and primers 180 l 3 BRAF PNA 2X premix PCR reaction premix 1,250 l 4 Clamping control Wild-type DNA 400 l *Each kit contains enough material to test 50 DNA samples for all mutations. 7 / 15 PNG-PCBUM001

8 PROCEDURES Figure 2. Flow of the PNAClamp BRAF Mutation Detection Kit 1. DNA preparation Specimen collection and DNA extraction reagents are not included in the kit and should be provided by the user. 1) Specimens that can be analyzed using the PNAClamp BRAF Mutation Detection Kit are paraffin embedded tissues, biopsy tissues or thyroid fine-needle aspiration biopsy (FNAB). 2) We strongly recommend using High Pure PCR Template Preparation Kit (Roche Diagnostics, catalog number ) for DNA extraction, especially for paraffin embedded tissues. 3) Specimen transport: Use standard pathology methodology to ensure specimen quality. 4) Extracted DNA can be stored at 4ºC for up to 24 hours, or at -20ºC for long term storage. 8 / 15 PNG-PCBUM001

9 2. Preparation of the Real-Time PCR Mixture Table 3. Set up reaction mix per one reaction Components Volume BRAF PNA 2X Premix (#3) 10 µl Each PNA mix (#1~#2) 3 µl Extracted DNA (10~25 ng total) or Clamping Control (#4) 7 µl Total volume 20 µl 1) Prepare 2 PCR tubes for one set of DNA samples to be tested. Label them as S1 and S2. Prepare another set of 2 tubes for Clamping Control (wild-type DNA) and label them as C1 and C2. 2) Add 10 µl of BRAF PNA 2X Premix (#3 from the kit) to each tube. 3) For each PCR tube, add 3 µl of corresponding PNA mix from #1~2 from the kit. For example, S1 and C1 tubes will have #1 Non PNA mix #1, S2 and C2 tubes will have #2 BRAF PNA mix #2. 4) For S1~S2 PCR tubes, add 7 µl of prepared DNA sample (10~25 ng total) to each tube to yield 20 l final volume. 5) For C1~C2 PCR tubes, add 7 µl of Clamping Control (#4 from the kit). 6) If you have more than one DNA samples to be tested, prepare one set of clamping control for the entire experiment. In such case, it is recommended to prepare a master mix containing 2X Premix and each PNA mix for all the samples and to aliquot 13 µl to each PCR tube. 9 / 15 PNG-PCBUM001

10 3. Real-Time PCR reaction 1) Perform real-time PCR using the cycling conditions described below: ONE CYCLE Pre-denaturation 94ºC 5 min FOUR-STEP CYCLING (40 CYCLES) Denaturation 94ºC 30 sec PNA clamping 70ºC 20 sec Annealing 63ºC 30 sec Extension* 72ºC 30 sec 2) Set up the detection for reading SYBRGreen at 72ºC. 4. Assessment A. Clamping Control (wild-type DNA control) 1) Determine Ct value from each PCR reaction. The cycle number at which a signal is detected above background fluorescence is termed as the cycle threshold (Ct). 2) The Ct values of the wild-type DNA control (tube C1~C2) should fall in the range given in Table 4. The assay should be repeated if the values are not in recommended range. Table 4. The acceptable Ct ranges of Clamping Control Assay Acceptable Ct range 1 Non PNA mix #1 (C1) 30 2 BRAF PNA mix #2 (C2) >33 B. DNA samples 1) Determine Ct values of each sample (S1 and S2). i. Ct value of Non PNA mix (S1) should be 22~35. ii. Ct value of Non PNA mix (S1) can serve as an internal to indicate the purity and the concentration of sample DNA. Thus, the validity of the test can be decided by the Ct value of Non PNA mix (S1) as shown in Table / 15 PNG-PCBUM001

11 iii. If the Ct value of Non PNA mix (S1) is greater than 35, target gene was not successfully amplified and therefore the result is not reliable. Check DNA amount and purity. New DNA prep might be required. iv. If the Ct value of Non PNA mix (S1) is less than 22, the result may be false positive. Repeat the PCR reaction with lower amount of DNA. v. If the Ct value of Non PNA mix (S1) is between 30 and 35 (30 Ct <35), the target gene was amplified with low efficiency. For more reliable result, it is suggested to repeat PCR reaction with a higher amount of DNA. Table 5. The acceptability of the test Acceptability Ct value of S1 Descriptions and recommendations Optimal 22< Ct <30 The amplification and the amount of DNA sample are optimal. Acceptable 30 Ct <35 Invalid Ct Ct The target gene was amplified with low efficiency. For more reliable result, it is suggested that repeat PCR reaction with a higher amount of DNA. Possibility of false positive is high. Repeat the PCR reaction with a lower amount of DNA. The amplification was failed. Check DNA amount and purity. New DNA prep might be required. 2) Calculate the ΔCt-1 values by subtracting the sample Ct values from the Standard Ct values. If the Ct of DNA samples is displayed as NA (not applicable), then set Ct value as 38 for further calculation. *ΔCt-1 = [Standard Ct] [Sample Ct (S2)] where Standard Ct = 35 3) Calculate ΔCt-2 [Ct value of sample subtracted by Ct value of Non PNA mix]. **ΔCt-2 = [Sample Ct (S2)] - [Non PNA mix Ct (S1)] 4) Assess the result along with the values of ΔCt-1 and ΔCt-2 as given in Table 6. Table 6. Assessment of the result ΔCt-1 ΔCt-2 Assessment 2 ΔCt-1 All value BRAF V600E mutant ΔCt-2 3 BRAF V600E mutant 0 ΔCt-1 <2 3< ΔCt-2 Wild-type ΔCt-1 <0 All value Wild-type 11 / 15 PNG-PCBUM001

12 EXAMPLES OF ANALYSIS 1) Profile of Clamping Control and DNA sample 1 ; Sample Non PNA mix #1 2 ; Sample BRAF PNA mix #2 3 ; Clamping control Non PNA mix #1 4 ; Clamping control BRAF PNA mix #2 Table 7. Example of sample Ct values Assay Sample No. Sample 1 Ct Sample 2 Ct Standard Ct **ΔCt-2 *ΔCt-1 1 Non PNA mix #1 (S1) BRAF PNA mix #2 (S2) (5) *ΔC t-1 = [Standard Ct] [Sample Ct] **ΔC t-2 = [Sample Ct] - [Non PNA mix Ct (S1)] Table 8. Analysis of data Assay Sample No. Sample 1 Sample 2 ΔCt-2 ΔCt-1 ΔCt-2 ΔCt-1 2 BRAF PNA mix # Results BRAF V600E mutant Wild-type 1. When ΔCt-1 is equal to or greater than 2, the sample is assessed to be mutated ( ). 2. If ΔCt-1 is equal to or greater than 0 and less than 2 ( ), then ΔCt-2 needs to be determined. 3. If ΔCt-2 is less than 3, the sample is assessed to be mutated ( ). 12 / 15 PNG-PCBUM001

13 REFERENCES 1. Choi et al., Frequency of KRAS, BRAF, and PIK3CA mutations in advanced colorectal cancers: Comparison of peptide nucleic acid-mediated PCR and direct sequencing in formalin-fixed, paraffin-embedded tissue. Pathol Res Pract 207(12):762-8, Shin et al., National Cancer Center, Korea Annual Report of the Korea Central Cancer Registry based on registered data from 139 hospitals. Cancer Res Treat. 36(2):103-14, Ezzat et al., Thyroid incidentalomas. Prevalence by palpation and ultrasonography. Arch Intern Med. 154(16): , Meier et al., Thyroid nodules: pathogenesis, diagnosis, and treatment. Baillieres Best Pract Res Clin Endocrinol Metab. 14(4): , Kang et al., Prevalence, clinical and ultrasonographic characteristics of thyroid incidentalomas. Thyroid. 14(1):29-33, Rapp et al., Structure and biological activity of v-raf, a unique oncogene transduced by a retrovirus. Proc Natl Acad Sci USA 80(14): , / 15 PNG-PCBUM001

14 EXPLANATION OF SYMBOLS Do not reuse Caution Batch Code Use by Manufacturer EC Representative In Vitro Diagnostic Medical Device Catalogue number Temperature Limitation PANAGENE Inc. 816 Tamnip-dong, Yuseong-gu, Daejeon, , Korea PentaGen, s.r.o Ke Klinku 143, Horni Bezdekov, Czech Republic 14 / 15 PNG-PCBUM001

15 ENDNOTES Information in this document is subject to change. Panagene assumes no responsibility for any errors that may appear in this document. No other warranties of any kind, express or implied, including without limitation, implied warranties of merchantability or fitness for a particular purpose, are provided by Panagene. Panagene shall have no liability for any direct, indirect, consequential, or incidental damages arising out of the use, the results of use, or the inability to use this product. PANAGENE Inc. 816 Tamnip-dong, Yuseong-gu, Daejeon, , Korea Tel: / 15 PNG-PCBUM001