Group A Streptococcus (GAS) Real Time PCR Kit User Manual For
Contents
1. Liferiver Revision No ZJO003 Issue Date Jul 1 2012 Group A Streptococcus GAS Real Time PCR Kit User Manual C For In Vitro Diagnostic Use Only 20 C 3s RD 0180 01 aal Shanghai ZJ Bio Tech Co Ltd For use with LightCycler1 0 2 0 Instrument www liferiver com cn Tel 86 21 34680596 Eo rer Obelis S A trade liferiver com cn Fax 86 21 34680595 Boulevard G n ral Wahis 53 2 floor No 15 Building No 188 Xinjunhuan road 1030 Brussels BELGIUM Tel 32 2 732 59 54 PuJiang Hi tech Park Shanghai China Fax 32 2 732 60 03 E Mail mail obelis net 1 Intended Use Group A Streptococcus real time PCR kit is used for the detection of group A streptococcus in samples like serum plasma nasal and pharyngeal secretions skin exudate C S F sputum blood and etc 2 Principle of Real Time PCR The principle of the real time detection is based on the fluorogenic 5 nuclease assay During the PCR reaction the DNA polymerase cleaves the probe at the 5 end and separates the reporter dye from the quencher dye only when the probe hybridizes to the target DNA This cleavage results in the fluorescent signal generated by the cleaved reporter dye which is monitored real time by the PCR detection system The PCR cycle at which an increase in the fluorescence signal is detected initially Ct is proportional to the amount of the specific PCR product Monitoring the fluorescence intensities during Real Time all2. Take 1ml sample in a tube centrifuge the tube at 13000rpm for 2min and remove the supernatant and keep the pellet 2 Add 50u DNA extraction buffer to the pellet close the tube then vortex for 10 seconds Spin down briefly in a table centrifuge 3 Incubate the tube for 10 minutes at 100 C 4 Centrifuge the tube at 13000rpm for 10 minutes The supernatant contains the DNA extracted and can be used for PCR template 9 1 3 Serum or plasma samples 1 Take 50ul serum or plasma add 50ul DNA extraction buffer close the tube then suspend the pellet with vortex vigorously Spin down briefly in a table centrifuge 2 Incubate the tube for 10 minutes at 100 C 3 Centrifuge the tube at 13000rpm for 10 minutes The supernatant contains the DNA extracted and can be used for PCR template Attention A During the incubation make sure the tube is not open Since the vapor will volatilize into the air and may cause contamination if the sample is positive B The extraction sample should be used in 3 hours or stored at 20 C for one month C DNA extraction kits are available from various manufacturers You may use your own extraction systems or the commercial kit based on the yield For the DNA extraction please comply with the manufacturer s instructions 9 2 Internal Control It is necessary to add internal control IC in the reaction mix Internal Control IC allows the user to determine and control the possibility of PCR inhibition A
3. Water Positive Contolqualitaive asa 35 Joo QS quantitative detection 13 Data Analysis and Interpretation The following sample results are possible Crossing point value Result Anal Doom T sam OO otam OO 25 35 Below the detection limit or negative Positive and the software displays the quantitative value 25 Target Nucleic Acid 40cycles 1 38 40 Re test If it is still 38 40 report as 1 PCR Inhibition No diagnosis can be concluded For further questions or problems please contact our technical support at trade liferiver com cn
4. cedure 9 1 DNA Extraction DNA extraction buffer is supplied in the kit please thaw the buffer thoroughly and spin down briefly in the centrifuge before use It s better to use commercial kits for nucleic acid extraction 9 1 1 Sputum sample 1 Trypsin digestive Solution preparation e Tube racks Add 10g trypsin to 200ml sterile purified water and mix thoroughly Adjust the PH value to 8 0 with 2 NaOH solution Add 2mL 25mmol L CaCl mix thoroughly and store at 4 C Please incubate at 37 C for 10 minutes before use 2 Estimate the volume of the sputum and add partes aequales of the trypsin digestive solution then vortex vigorously Set at room temperature for 30 minutes Transfer 0 5ml mixture to a new tube Centrifuge the tube at 13000rpm for 5 minutes carefully remove and discard supernatant from the tube without disturbing the pellet 3 Add 1 0ml normal saline Resuspend the pellet with vortex vigorously Centrifuge at 13000rpm for 5 minutes Carefully remove and discard supernatant from the tube without disturbing the pellet 4 Repeat step 3 5 Add 50ul DNA extraction buffer closed the tube then resuspend the pellet with vortex vigorously Spin down briefly in a table centrifuge 6 Incubate the tube for 10 minutes at 100 C 7 Centrifuge the tube at 13000rpm for 10 minutes The supernatant contains the DNA extracted and can be used for PCR template 9 1 2 Nasal and pharyngeal secretions skin exudate or C S F samples 1
5. dd the internal control IC lul rxn and the result will be shown in the 560nm Channel 9 3Quantitation The kit can be used for quantitative or qualitative real time PCR For performance of quantitative real time PCR standard dilutions must be prepared first as follows Molecular Grade Water is used for dilution Dilution is not needed for performance of qualitative real time PCR detection Take positive control 1x10 copies ml as the starting high standard in the first tube Respectively pipette 36ul of Molecular Grade Water into next three tubes Do three dilutions as the following figures Dilution of Standards Aul Aul Aul To generate a standard curve on the real time oo Mi er pe system all four dilution standards should be used and defined as standard with specification of the corresponding concentrations y y y y Attention A Mix thoroughly before next transfer 1X107 1X10 1X10 1X104copiesmi B The positive control 1x10 copies ml contains high concentration of the target DNA Therefore be careful during the dilution in order to avoid contamination 9 4 PCR Protocol 17 ul 0 4 14l The Master Mix volume for each reaction Reaction Mix Enyzme Mix Memel Conio should be pipetted as follows T ae l XPCR system without 560nm channel may be treated 18 4 pl l with 1ul Molecular Grade Water instead of 1ul IC Master Mix 1 The volumes of Reaction Mix and the Enzyme Mix per reaction multiply with 2ul 18 pl the number of
6. nal positive control 1x10 copies ml contained allows the determination of the gene load For further information please refer to section 9 3 Quantitation 4 Kit Contents DNA Extraction Buffer 2 vials 1 5ml GAS Reaction Mix 1 vial 450u1 1 vial 12ul 1 vial 400u1 Internal Control IC 1 vial 30ul GAS Positive Control 1x10 copies ml 1 vial 30u1 Analysis sensitivity 5 X 10 copies ml LOQ 1X 10 1X 10 copies ml Note Analysis sensitivity depends on the sample volume elution volume nucleic acid extraction methods and other factors If you use the DNA extraction buffer in the kit the analysis sensitivity is the same as it declares However when the sample volume is dozens or even hundreds of times greater than elution volume by some concentrating method it can be much higher 5 Storage e All reagents should be stored at 20 C Storage at 4 C is not recommended e All reagents can be used until the expiration date indicated on the kit label e Repeated thawing and freezing gt 3x should be avoided as this may reduce the sensitivity of the assay e Cool all reagents during the working steps e Reaction Mix should be stored in the dark 6 Additionally Required Materials and Devices e Biological cabinet e Trypsin digestive Solution e Real time PCR reaction tubes plates e Pipets 0 5 ul 1000 ul PCR Enzyme Mix Molecular Grade Water e Real time PCR system e Vortex mixer e Cryo container e Sterile filter tips fo
7. ows the detection of the accumulating product without having to re open the reaction tube after the amplification 3 Product Description The group A streptococcus bacterium Streptococcus pyogenes or GAS is a form of B hemolytic Streptococcus bacteria responsible for most cases of streptococcal illness Other types B C D and G may also cause infection Several virulence factors contribute to the pathogenesis of GAS such as M protein hemolysins and extracellular enzymes Acute rheumatic fever ARF is a complication of respiratory infections caused by GAS Post streptococcal glomerulonephritis PSGN is an uncommon complication of either a strep throat or a streptococcal skin infection It is classified as a type III hypersensitivity reaction Group A streptococcus real time PCR kit contains a specific ready to use system for the detection of Group A streptococcus by polymerase chain reaction PCR in the real time PCR system The master contains reagents and enzymes for the specific amplification of the Group A streptococcus DNA Fluorescence is emitted and measured by the real time systems optical unit during PCR The detection of amplified Group A streptococcus DNA fragment is performed in fluorimeter channel 530nm with the fluorescent quencher BHQ1 DNA extraction buffer is available in the kit In addition the kit contains a system to identify possible PCR inhibition by measuring the 560nm fluorescence of the internal control IC An exter
8. r micro pipets e Sterile microtubes e Disposable gloves powderless e Biohazard waste container e Refrigerator and Freezer e Desktop microcentrifuge for eppendorf type tubes RCF max 16 000 x g 7 Warnings and Precaution Carefully read this instruction before starting the procedure e For in vitro diagnostic use only e This assay needs to be carried out by skilled personnel e Clinical samples should be regarded as potentially infectious materials and should be prepared in a laminar flow hood e This assay needs to be run according to Good Laboratory Practice e Do not use the kit after its expiration date e Avoid repeated thawing and freezing of the reagents this may reduce the sensitivity of the test e Once the reagents have been thawed vortex and centrifuge briefly the tubes before use e Prepare quickly the Reaction mix on ice or in the cooling block e Set up two separate working areas 1 Isolation of the RNA DNA and 2 Amplification detection of amplification products e Pipets vials and other working materials should not circulate among working units e Use always sterile pipette tips with filters e Wear separate coats and gloves in each area e Avoid aerosols 8 Sample Collection Storage and transport e Collect samples in sterile tubes e Specimens can be extracted immediately or frozen at 20 C to 80 C e Transportation of clinical specimens must comply with local regulations for the transport of etiologic agents 9 Pro
9. samples which includes Extraction DNA Master Mix the number of controls standards and Bie ae a sample prepared Molecular Grade Water Reaction is used as the negative control For Plate Tube reasons of unprecise pipetting always add an extra virtual sample Mix completely then spin down briefly in a PCR Instrument centrifuge 2 Pipet 18ul Master Mix with micropipets of sterile filter tips to each Real time PCR reaction plate tubes Separately add 2ul DNA sample positive and negative controls to different reaction plate tubes Immediately close the plate tubes to avoid contamination 3 Spin down briefly in order to collect the Master Mix in the bottom of the reaction tubes 4 Perform the following protocol in the instrument 37 C for 2min Icycle Selection of fluorescence channels 94 C for 2min Icycle 93 C for 5sec 60 C for 30sec Fluorescence measured at 60 C 10 Threshold setting Choose Arithmetic as back ground and none as Noise Band method then adjust the Noise band just above the maximum level of molecular grade water and adjust the threshold just under the minimum of the positive control 11 Calibration for quantitative detection Input each concentration of standard controls at the end of run and a standard curve will be automatically formed 12 Quality control Negative control positive control internal control and QS curve must be performed correctly otherwise the sample results is invalid Molecular Grade
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