qualitative detection and differentiation of types 6 and 11 papiloma

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  • 8/10/2019 Qualitative Detection and Differentiation of Types 6 and 11 Papiloma

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    For Professional Use Only

    GUIDELINES

    toAmpliSens HPV6/11-FRTPCR kit

    for qualitative detection and differentiation of types 6 and 11

    ofhuman papillomavirus (HPV)DNA in clinical material by the

    polymerase chain reaction (PCR) with real-time hybridization-

    fluorescence detection

    Ecoli s.r.o., Studenohorska12841 03 Bratislava 47

    Slovak RepublicTel.: +421 2 6478 9336Fax: +421 2 6478 9040

    Federal Budget Institute ofScience Central ResearchInstitute for Epidemiology

    3A Novogireevskaya StreetMoscow 111123 Russia

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    TABLE OF CONTENTSINTENDED USE .................................................................................................................. 3AMPLIFICATION AND DATA ANALYSIS WITH Rotor-Gene 3000/6000 (CorbettResearch, Australia) INSTRUMENTS ................................................................................. 3AMPLIFICATION AND DATA ANALYSIS WITH iCycler iQ5 (Bio-Rad, USA)INSTRUMENTS ................................................................................................................. 11

    AMPLIFICATION AND DATA ANALYSIS WITH Mx3000P (Stratagene, USA)INSTRUMENT ................................................................................................................... 16

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    INTENDED USE

    Guidelines describe the procedure of the use of AmpliSens

    HPV 6/11-FRTPCR kitfor

    qualitative detection and differentiation of types 6 and 11 ofhuman papillomavirus (HPV)

    DNA by means of real-time hybridization-fluorescence detection with the following real-time PCR instruments:

    Rotor-Gene 3000, Rotor-Gene 6000 (Corbett Research, Australia),

    iCycler iQ5 (Bio-Rad, USA),

    Mx3000P (Stratagene, USA).

    AMPLIFICATION AND DATA ANALYSIS WITH Rotor-Gene 3000/6000 (Corbett

    Research, Australia) INSTRUMENTS

    Carry out sample pretreatment and reaction mixture preparation stages according to the

    instruction manual. Transparent no domed 0.2-mlPCR tubes (detection through the

    bottom of a tube) or 0.1-ml tubes are recommended for use.

    Hereinafter, all terms corresponding to different instruments and software are

    indicated in the following order: for Rotor-Gene 3000/for Rotor-Gene 6000.

    Whenworking with Rotor-Gene 3000 instrument use the program Rotor-Gene version 6.

    When working with Rotor-Gene 6000 instrument use the program Rotor-Gene 6000

    versions 1.7 (build 67) or higher.

    Programming the instrument

    1. Turn the instrument on and start Rotor-Gene program.

    2. Place the tubes in the rotor so that the first tube is in No. 1 well, insert the rotor in the

    reaction module, and secure the cover (the rotor cells are numbered and these

    numbers are used for sample order programming).

    Balance the rotor if it is not loaded entirely. Fill unused wells with empty tubes. Do

    not use tubes from previous runs.No.1 well should be loaded with a test tube from the current experiment (notempty).

    3. Program the instrument to run amplification and detection:

    In the opened window select Advancedmode. Activate the Newbutton.

    Select 36-Well Roto r (or 72-Well Roto r) and No Domed Tubes/Lock ing r ing

    attached. Click Next.

    In the opened window define the operator and set the reaction volume: React ion

    vo lumeis 25 l. Tick off the 15loi l layer vo lum eoption.

    set amplification program.

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    Table 1

    DNAHPVtypes 6 and 11 amplification program for

    Rotor-Gene 3000/6000 (Corbett Research, Australia)

    Stage emperature, TimeFluorescence

    detection

    Cycle

    repeatsHold 95 15 min 1

    Cycling

    95 15 s

    4560 35 s

    FAM/Green,JOE/Yellow,ROX/Orange

    This program can be applied for both AmpliSensHPV6/11-FRTandAmpliSensHPV16/18-FRTPCR kits.

    Following amplification programs can be used as well:AmpliSens-1 RG (see

    Table 2) and amplification program for HPVHCR DNA types 16, 18, 31,33, 35, 39, 45, 51, 52, 56, 58, 59 (see Table 3) (this program is applied forAmpliSensHPVHCR screen-titre-FRT PCR kit). AmpliSens-1 RGamplification program is a universal program and it can be used for runningdifferent tests within one run (for example tests for detection of STIs). Fordetection of DNA ofHCRHPV and HPVDNA types 6, 11 within one runAmpliSens FRT HR HPVScreenRG4x Program can be applied.

    Using amplification program for HPVHCR DNA types 16, 18, 31, 33, 35,39, 45, 51, 52, 56, 58, 59 (from AmpliSensHPVHCR screen-titre-FRT PCRkit) does not affect analytical performances of this PCR kit.

    Table 2

    AmpliSens-1 RG amplification program

    Step Temperature, TimeFluorescence

    detection

    Cycle

    repeats

    Hold 95 15 min 1

    Cycling 1

    95 5 s

    560 20 s

    72 15 s

    Cycling 2

    95 5 s

    4060 20 s

    FAM/Green,

    JOE/Yellow,ROX/Orange,

    Cy5/Red

    72 15 s

    Cy5/Red detection channel should be enabled for running multiplex tests (ifrequired).

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    Table 3

    Amplification program for HPVHCR DNA types16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59

    Step Temperature, TimeFluorescence

    detectionCycle repeats

    Hold 95 15 min 1Hold 2 65 2 min 1

    Cycling

    95 20 s

    564

    Touchdown:1 deg. per cycle

    25 s

    65 55 s

    Cycling 2

    95 15 s

    40

    60 25 s

    65 25 s

    FAM/Green,JOE/Yellow,

    ROX/Orange,Cy5/Red

    The file AmpliSens FRT HR HPVScreen RG4x Program.proenclosed toAmpliSensHPVHCR screen-titre-FRT PCR kit can be used for programming.

    Click the Calibrate/Gain Opt imis at ionbutton in the New Run Wizardwindow.

    a) for detection in FAM/Green, JOE/Yellow, ROX/Orange, and Cy5/Redchannels

    select Calibrate Acq uir ing /Opt imis e Acq uir ing;

    b) click Perform Calibrat ion Before 1st Acquis i t ion/Perform Opt imisat ion

    Before 1stAcquis i t ion.

    c) click the Edit button in the Auto ga in ca l ib rat ion ch annel set tings window

    and set Min Reading as4andMax Reading as8for all channels.

    4. Select the Start runbutton for amplification to run. Name the experiment and save it to

    the disk (results of the run will be automatically saved in this file).

    5. Enter data in the table of samples (opens by default when the run begins). Define

    names/numbers of clinical samples in the Namecolumn. Define the Negative Control

    of amplification as NCA andthe Positive Control of amplification as C+. Enter the

    Unknown type for all clinical and control samples. Indicate the None type for empty

    wells.

    The sample will not be analyzed if its type is defined as None.

    Due to the fact that the PCR kit applies a multiplex control including several DNA matrixes

    (HPVtype 6, HPVtype 11 and human DNA) several pages should be created in protocol.

    To do this, indicate HPV 6(FAM/Green channel) in the Pagearea of the Name field. Click

    New. A new page for information about samples will appear. It contains the same names

    of samples as in previous page. Indicate HPV 11(JOE/Yellow channel) in thePagearea

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    TROUBLESHOOTING

    Review this section before running the experiment

    Problem Cause How to identify Ways to eliminateNegative samples areanalyzed as positive

    samples by Rotor-Gene program

    Incorrectmathematical

    processing ofnegative samples inthe presence of dropof fluorescence atthe initial cycles(Fig. 2a)

    A normal positivesample has a S-

    shaped curve offluorescenceaccumulation (Fig. 1,3-5). The negativesamples processedincorrectly appear asquite straight bottom-up lines (Fig. 7)

    Use the Ignore Firstoption: select

    5 cycles. If it does nothelp, increase thisvalue by 1-5

    The threshold linecrosses descendingfluorescence curvesat the initial cycles

    (Fig. 6)

    The red threshold linecrosses (or touches)fluorescence curvesat the left (initial

    cycles) on the chart ofprocessedfluorescence curves(Fig. 6)

    Use the Eliminatecycles beforeoption: select 5(crossing the

    threshold withfluorescence curve isignored for the first 5cycles)

    Drop of sensitivity dueto contamination ofinstrument lenses

    Lensescontamination leadsto reduction ofeffectiveness offluorescenceexcitation anddetection. Primarilythis has an impact

    on the samplescontaining smallquantity of specificDNA which showlow fluorescencegrowth

    Low backgroundsignal in all fourdetection channels(

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    increase can appearafter cleansing theinstrument lensesfrom severcontamination

    Desensitization due to

    decrease ofpolymerase (TaqF)activity

    Incorrect storage or

    contamination causeenzymedeterioration

    It appears as a fail of

    the positive control orif a boundary Ct valueof the positive controlis greater than thethreshold of weaksamples

    Use the reagent

    stored under requiredcondition (see partStability and Storagein the InstructionManual) or use a newreagent

    Note! A report on all parameters specified as well as a report on auto-calibration isavailable if the Sett ings button is activated. In particular, the Messages tab, theAutoca l ib ra tion Log Messages option.

    Problem Feature Ways to eliminateContamination of a specificDNA

    Detection of a signal of thenegative control in anychannel

    Repeat the experiment. Takemeasures to detect andeliminate the source ofcontamination

    The volume of a DNA sampleadded to a reaction tube isless than required/DNAsamples is not added

    Background signal of asample is much stronger thanthe others (see raw curves,Fig. 2b). The sample isnegative

    Repeat PCR for this sample

    The volume of the reactionmixture added to a reaction

    tube is less thanrequired/reaction mixture isnot added/the volume of aDNA sample added to areaction tube is greater thanrequired

    Background signal of asample is much lower than the

    others (see raw curves, Fig.2b).

    If the sample is negative,repeat the test

    The autocalibration parameterf rom 4Fl to 8Flis not set or itis a failure of the first tube inthe rotor (the No.1 well isempty; a volume of DNAsample or reaction mixture

    added to the tube is incorrect)

    Most of the fluorescencebackground signals are lessthan 1 or greater than 20

    Set the parameter in the nextrun. In case of off-scalereading or if the signals aretoo weak (no positive signalsafter processing; abackground is less than 0.5)

    the experiment should berepeated beginning with PCR

    Polymerase (TaqF) was notadded to a reaction mixture

    Positive signals are absent forall samples including apositive control

    Repeat the experimentbeginning with PCR. Ensureappropriate preparation ofreaction mixtures

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    Unprocessed data (raw channel)

    Fig. 1. Raw curves are normalFig. 2. Raw curves have a bend (drop offluorescence at the initial cycles)

    Fig. 2b. Level of background signal points on thepossible error:DNA sample was not added to the tube 1;double volume of DNA sample was added to the

    tube 2

    Processed data (Quantitation analysis)

    ) processed curves are normal (S-shaped, threshold line crosses curves at the area of

    growth of fluorescence)

    Fig. 3. FAM channelFig. 4. JOE channel

    2

    1

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    Fig. 5. ROX channelinternal control(-globin gene)

    b) curves are processed incorrectly

    Fig. 6. Threshold line crosses fluorescencecurves twice

    Fig. 7. Incorrect processing of the curves withbend (from Fig. 2)

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    AMPLIFICATION AND DATA ANALYSIS WITH iCycler iQ5 (Bio-Rad, USA)

    INSTRUMENTS

    Carry out sample pretreatment and reaction mixture preparation stages according to the

    instruction manual. Transparent domed 0.2-mlPCR tubes (detection through the cap of

    the tube) are recommended for use.

    1. Switch on the instrument and the power supply of the optical module.

    The lamp should be warmed up for at least 15 min before the experiment starts.

    2. Open the iQ5 program.

    Table 4

    DNAHPVtypes 6 and 11 amplification programfor iCycler iQ, iQ5 (Bio-Rad, USA)

    Step Temperature, TimeFluorescence

    detection

    Cycle

    repeats

    1 95 15 min 1

    295 20 s

    4560 1 min FAM, HEX, ROX

    This program can be applied for both AmpliSens

    HPV6/11-FRTandAmpliSensHPV16/18-FRTPCR kits.

    Following amplification programs can be used as well:AmpliSens-1 iQ (seeTable 5) and amplification program for HPVHCR DNA types 16, 18, 31,33, 35, 39, 45, 51, 52, 56, 58, 59 (see Table 6) (this program is applied forAmpliSensHPVHCR screen-titre-FRT PCR kit). AmpliSens-1 iQ amplificationprogram is universal program and it can be used for running different testswithin one run (for example tests for detection of STIs). For detection of DNAof HCR HPV and HPV DNA types 6, 11 within one run AmpliSens FRT HRHPV ScreenRG4x Program can be applied.

    Using amplification program for HPVHCR DNA types 16, 18, 31, 33, 35,

    39, 45, 51, 52, 56, 58, 59 (from AmpliSens

    HPVHCR screen-titre-FRT PCRkit) does not affect analytical performances of this PCR kit

    Table 5

    AmpliSens-1 iQ amplification program

    Step Temperature, TimeFluorescence

    detection

    Cycle

    repeats

    1 95 15 min 1

    2

    95 5 s

    560 20 s

    72 15 s

    3

    95 5 s

    4060 30 s FAM, HEX, ROX, Cy5

    72 15 s

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    Cy5/Red detection channel should be enabled for running multiplex tests (ifrequired).

    Table 6

    Amplification program for HPVHCR DNA types

    16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59

    Step Temperature, TimeFluorescence

    detection

    Cycle

    repeats

    Cycle 1 95 15 min 1

    Cycle 3

    95 15 s

    665

    Touchdown:1 deg. per cycle

    55 s

    65 25 s

    Cycle 4

    95 15 s

    4160 55 s Real-time

    65 25 s

    The AmpliSens FRT HR HPV Screen iQ5.tmo file enclosed to AmpliSensHPVHCR screen-titre-FRTPCR kitcan be used for programming.

    Create a new plate setup in the Edit Plate Setup tab. Indicate samples as Unknown.

    Proceed to the Select fluoro forestab and set fluorescence detection for all tubes in the

    FAM, HEX and ROX channels. Go back to the Samp les: Whole plate loadingand click

    the Per Dye Layerbutton.

    Click Run. Select Well factor (both well factor by experiment tubes and fixed well factor

    are acceptable for use but the latter is recommended). Run the experiment.

    Data analysis

    1. Proceed to thePCR Quant i f icat iontab in theData Analysismode.

    2. Review data in one channel at a time.

    3. Ensure that the threshold line was set correctly for each channel. If it is required,

    activate User Def ined, 2 through 10 cycles parameter. Normally threshold line

    should cross s-shaped curves of signal accumulation of positive samples and controls

    and not cross the base line. Otherwise, raise the threshold line up to the level where it

    crosses positive samples only.

    4. Activate the Resultsbutton (below the fluorofore buttons).

    5. Proceed to the PCR Standard Curv etab, review parameters of the reaction, copy the

    results.

    6. Click on the results grid using the mouse right button. Select Export to Excelfrom the

    drop-down menu. Agree to save the file. If Microsoft Excel program is loaded on the

    computer it will open automatically (Microsoft Excel program is required for further

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    data analysis). Results in the FAM, HEX, ROX, and then Cy5 channels follow

    consistently.

    TROUBLESHOOTING

    Problem Cause How to identify Ways to eliminate

    Drop of sensitivity dueto deterioration ofprobes

    Incorrect storage orutilizing kitcomponents (hightemperature,multiple openingreagent tubes, foulworking conditions)can cause destroy ofoligonucleotides

    Probe destruction canbe find out as a resultof comparison ofexperimental dataobtained at the firstuse of the reagentsand after a period oftime or in comparisonwith the reagents ofthe same lot storedproperly. It isappeared as an

    increase ofbackgroundfluorescence(fluorescence isassessed in theBackground

    subtractedmode atthe beginning of theexperiment) twice asmuch in differentexperiments (in casethe same instrument

    is used). Note!Effectof f luorescenceincrease can appearin case the lamp waschanged, opticalsystem was cleaned,or calibration wasdone)

    Use mixtures storedunder statedconditions untillabeled expire date(see part Stabilityand Storage in theInstruction Manual)

    Drop of sensitivity dueto decrease of activityof polymerase (TaqF)

    Incorrect storage orcontamination causeenzyme

    deterioration

    It appears as a fail ofthe positive control orif a boundary Ct value

    of the positive controlis much greater thanthe normal one

    Use the reagentstored under requiredcondition (see part

    Stability and Storagein the InstructionManual) or use a newreagent

    Problem Feature Ways to eliminate

    Contamination of a specificDNA

    Detection of a signal for anegative control in anychannel

    Repeat the experiment. Takemeasures to detect andeliminate the source ofcontamination

    The volume of a DNA sampleadded to a reaction tube is

    less than required/DNAsamples is not added

    Background signal of thesample is much stronger than

    the others (see raw curvesBackground subtractedmode). The sample isnegative

    Repeat PCR for this sample

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    The volume of a reactionmixture added to a reactiontube is less thanrequired/reaction mixture isnot addedorthe volume of aDNA sample added to a

    reaction tube is greater thanrequired

    Background signal of thesample is much lower than theothers (see raw curves-Background subtractedmode)

    If the sample is negative,repeat the test

    Incorrect adjustment of thethreshold level

    Threshold line is located alongwith negative samples orabove some or all positivecurves (S-shaped)

    Set the threshold line so that itcrosses only sigmoid curvesof f luorescence accumulationor at the level of betweenfinal values of negative andpositive samples

    Drops were not removed fromthe tube walls beforeexperiment started

    Curves of f luorescenceaccumulation have negativeor positive steps (Fig. 2)

    Select the BaseLineThresholdwindow (the rightmouse button on the graph offluorescence) and indicate

    that base line is to becalculated beginning with thefirst cycle after the step

    Polymerase (TaqF) was notadded to a reaction mixture

    Positive signals are absent forall samples including apositive control

    Repeat the experimentbeginning with PCR. Ensureappropriate preparation ofreaction mixtures

    Unprocessed (raw) data (Background su bt racted mode).

    Fig. 1 Raw curves are normal (FAM) Fig. 2. Baseline has a step:drops werenot removed from the tube walls before theexperiment in the sample indicated as Err

    Err

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    Processed data

    Processed curves are normal; S-shaped; thresholds are located correctly (PCR Base Line

    Subtracted Curv e Fit mode)

    Fig. 3. FAM channel Fig.4. HEX channel

    Fig 5. ROX channelinternal control(-globin gene)

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    AMPLIFICATION AND DATA ANALYSIS WITH Mx3000P (Stratagene, USA)

    INSTRUMENT

    Carry out sample pretreatment and reaction mixture preparation stages according to the

    instruction manual. Transparent domed 0.2-mlPCR tubes (detection through the cap of

    the tube) are recommended for use.

    1. Switch on the instrument and open the Mx3000P program.

    2. In the New Experiment Option swindow select Quantitative PCR (Multiple Standards )

    and selectTurn lamp on for warm-up.

    The lamp should be warmed up for at least 15 min before the experiment starts.

    3. Place the tubes in the instrument, secure the locking tool and close the lid.4. Select Opt ics Conf igura tion in the Opt ions menu. In the Dye Assignm ent tab

    indicate JOE next to the HEX/JOE fi lter s et option; indicate FAM next to the FAM

    filter setoption.

    5. In theInst rumentmenu of the Mx3000P program select the Filter Set Gain Sett ings

    option. In the opened window set the following parameters of multiplication factors:

    Cy5 x4

    ROX x1

    HEX/JOE x4

    FAM x4

    Prior to analysis, remove drops from tube walls, because drops falling duringamplification cause signal errors and complicate data analysis. Do not turnstrip/plate over when loading into the PCR instrument.

    6. Define parameters of fluorescence acquiring in the Plate Setupmenu. To do this:

    a) hold Ctrland use the mouse to select all cells in which test tubes are inserted.

    b) define all selected cells as Unknown in the Well type window. In the Collect

    f luorescenc e data option select FAM, JOE, ROX, and Cy5. Double click each

    cell and enter a sample name (Well Inform at ionwindow). Indicate the positive

    control as +, the negative control as . Sample names can be entered during or

    after the amplification run in the Plate Setupmenu.

    7. Proceed to the Thermal Prof i le Setup tab and set the amplification program (see

    Table 7):

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    Table 7

    DNA HPVtypes 6 and 11 amplification program

    for Mx3000P, Mx3005P (Stratagene, USA)

    Step Temperature, Time Fluorescencedetection Cyclerepeats

    1 95 15 min 1

    295 20 s

    4560 1 min FAM, HEX/JOE, ROX

    This program can be applied for both AmpliSensHPV6/11-FRTandAmpliSensHPV16/18-FRTPCR kits.

    Following amplification programs can be used as well:AmpliSens-1 Mx (seeTable 2) and amplification program for HPV HCRDNA types 16, 18, 31,

    33, 35, 39, 45, 51, 52, 56, 58, 59 (see Table 9) (this program is applied forAmpliSensHPVHCR screen-titre-FRT PCR kit). AmpliSens-1 Mxamplification program is universal program and it can be used for runningdifferent tests within one run (for example tests for detection of STIs). Fordetection of DNA of HPVHCR and HPV DNA types 6, 11 within one runAmpliSens FRT HR HPVScreenRG4x Program can be applied.

    Using amplification program for HPV HCR DNA types 16, 18, 31, 33, 35,39, 45, 51, 52, 56, 58, 59 (from AmpliSensHPVHCR screen-titre-FRT PCRkit) does not affect analytical performances of this PCR kit

    Table 8

    AmpliSens-1 Mx amplification program

    Step Temperature, TimeFluorescence

    detection

    Cycle

    repeats

    Segment 1 95 15 min 1

    Segment 2(Cycling)

    95 5 s

    560 20 s

    72 15 s

    Segment 3

    (Cycling)

    95 5 s

    4060 30 sFAM, HEX/JOE, ROX,

    Cy572 15 s

    Cy5/Red detection channel should be enabled for running multiplex tests (ifrequired).

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    Table 9Amplification program for HPV HCRDNA types

    16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59

    Step Temperature, TimeFluorescence

    detection

    Cycle

    repeats

    Segment 1 95 15 min 1Segment 2 65 2 min 1

    Segment 3(Cycling)

    95 20 s

    564

    Touchdown:1 deg. per cycle

    25 s

    65 55 s

    Segment 4(Cycling)

    95 20 s

    4060 25 s

    65 55 sCy5, FAM,

    HEX/JOE, ROX

    The AmpliSens FRT HR HPV Screen Mx.mxp file enclosed to AmpliSensHPVHCR screen-titre-FRTPCR kitcan be used for programming.

    8. In the Plate Setup tab of the Setupmode indicate names of the samples. Define all

    samples as Unknown. Select FAM, JOE/HEX, ROX dyes for all samples.

    9. Run the program.

    10. Proceed to the analysis of results after the end of the run.

    Data analysis

    1. Proceed to the Analys is item by clicking the button on the toolbar in the Mx300P

    program.

    2. Ensure that all test samples are enabled (the cells are tinted) in the opened Analys is

    Selection/Setuptab. Otherwise, hold Ctrland select all test samples with the mouse.

    3. Proceed to the Results tab.

    4. On the Dyes shown toolbar activate displaying FAM channel and deactivate

    displaying all others channels. Set 150in the Thresho ld f luorescencefield for FAM

    channel. One at a time activate next channel and deactivate the previous one and

    enter threshold values according to the table:

    Cy5 150

    ROX 150

    HEX/JOE 150

    FAM 150

    5. Activate displaying all channels (FAM, HEX and ROX buttons should be selected in

    the Dyes Show n field at the bottom of the program window).

    6. Ensure that the JOE, FAM and ROX fluorescence channels are ticked off in the

    Thresho ld f luorescencefield.

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    7. Ensure that the threshold line is set correctly. Normally, a threshold line should cross

    S-shaped curves of signal accumulation of positive samples and controls and should

    not cross the base line. Otherwise, the threshold should be raised.

    8. Select Text Report option in the Area to analyzefield. Review the results and export

    data for further analysis (for example export to Excel:Fi le>Export Instrument

    Data>Export Instrum ent Data to Excel).

    TROUBLESHOOTING

    Problem Cause How to identify Ways to eliminateDrop of sensitivity dueto deterioration ofprobes

    Incorrect storage orutilizing kitcomponents (hightemperature,multiple opening

    reagent tubes, foulworking conditions)can cause destroy ofoligonucleotides

    Probe destruction canbe find out as a resultof comparison ofexperimental dataobtained at the first

    use of the reagentsand after a period oftime or in comparisonwith the reagents ofthe same lot storedproperly. It isappeared as anincrease ofbackgroundfluorescence(fluorescence isassessed in the Rmode at thebeginning of theexperiment) twice asmuch in differentexperiments (in casethe same instrumentis used). Note!Effectof f luorescenceincrease can appearafter cleansing theoptical system

    Use mixtures storedunder statedconditions untillabeled expire date(see part Stability

    and Storage in theInstruction Manual)

    Drop of sensitivity dueto decrease ofpolymerase (TaqF)activity

    Incorrect storage orcontamination causeenzymedeterioration

    It appears as a fail ofthe positive control orif a boundary Ct valueof the positive controlis greater than thethreshold of weaksamples

    Use the reagentstored under requiredcondition (see partStability and Storagein the InstructionManual) or use a newreagent

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    REF R-V11(RG,iQ,Mx)-CE / VER 17.02.12-02.04.14 / Page 20 of 22

    Problem Feature Ways to eliminate

    Contamination of a specificDNA

    Detection of a signal for anegative control in anychannel

    Repeat the experiment. Takemeasures to detect andeliminate the source ofcontamination

    The volume of a DNA sampleadded to a reaction tube isless than required/DNAsamples is not added

    Background signal of asample is much stronger thanthe others (see raw curvesR-mult icompon ent viewmode) The sample is negative

    Repeat PCR for this sample

    The volume of a reactionmixture added to a reactiontube is less thanrequired/reaction mixture isnot addedorthe volume of aDNA sample added to areaction tube is greater than

    required

    Background signal of asample is much lower than theothers (see raw curves-R-mul t icompo nent v iewmode)

    If the sample is negative,repeat the test

    Incorrect adjustment of thethreshold level

    Threshold line is located alongwith negative samples orabove some or all positivecurves (S-shaped)

    Set the threshold line so that itcrosses only sigmoid curvesof f luorescence accumulationor at the level of betweenfinal values of negative andpositive samples

    Polymerase (TaqF) was notadded to a reaction mixture

    Positive signals are absent forall samples including apositive control

    Repeat the experimentbeginning with PCR. Ensureappropriate preparation ofreaction mixtures

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    REF R-V11(RG,iQ,Mx)-CE / VER 17.02.12-02.04.14 / Page 21 of 22

    Unprocessed data(R mode)

    Fig. 1. Raw curves are normal Fig. 2. Level of background signal pointon a possible problem: DNA samplewas not added to the Err tube

    Processed data

    Normal curves that were processed, dRmode (S-shaped)

    Fig. 3. FAM channel

    Fig. 4. HEX channel

    Fig. 5. ROX channelinternal control

    (-globin gene)

    Err

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    List of Changes Made in the Instruction Manual

    VERLocation of

    changesEssence of changes

    02.04.14

    SA

    Cover page

    Footer

    Address of European representative was added

    REF R-V11(RG,iQ,Mx)--B was deleted