mentype amlplex qs...primer for each transcript is fluorescence-labelled with 6-fam, btg, bty. the...

Mentype® AMLplexQS AMLGAv3en

Mentype® AMLplexQS Manual

Novel detection of chromosomal aberrations in acute myeloid leukemia

In-Vitro-Diagnostics

AMLGAv3en

45-31220-0xxx*

Batch Code

Biotype Diagnostic GmbH Moritzburger Weg 67 D-01109 Dresden Germany

*xxx defines the packaging size

Made in Germany

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Biotype Diagnostic GmbH develops, produces and markets their PCR-based rapid Mentype® Detection Kits. Our products provide customers with fast and reliable testing methods for professional medical diagnostics.

Our Mentype® Test Kits guarantee highest quality standards for clinical research and diagnostics.

For information and enquiries about the Mentype® AMLplexQS

PCR Amplification Kit, please do not hesitate to get in touch or visit www.biotype.de

http://www.biotype.de/en/home.html

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Product description

The verification of specific chromosomal aberrations has high prognostic value in nearly all types of acute leukemia. Molecular biological evidence of chromosomal aberrations (translocations) represents an important diagnostic completion. Detecting specific translocations enables subtype-classification of leukemic diseases and provides essential information for the risk-directed therapy of patients. Mentype® AMLplexQS facilitates detection of the most common chromosomal aberrations yet observed in acute myeloid leukemia (AML) and represents a simple-to-use, routine-fit and reliable screening tool. Mentype® AMLplexQS contains optimised reagents for high resolution detection of 11 fusion gene transcripts (AML1-ETO, BCR-ABL, CALM-AF10, CBFB-MYH11, DEK-CAN, MLL-AF6, MLL-AF9, MLL-ELL, MLL-PTD, NPM1-MLF1 and PML-RARA) with 34 transcript variants in total (Table1). The test is performed by fragment analysis using capillary gel electrophoresis. One primer for each transcript is fluorescence-labelled with 6-FAM, BTG, BTY. The test kit includes an internal PCR-Control (Quality Sensor “QS-Control”) and a “cDNA Control” (ABL-Control) providing helpful information about PCR efficiency, quality of applied cDNA templates, and presence of PCR-inhibitors. Mentype® AMLplexQS was validated and evaluated for GeneAmp® 9700 Silver Thermocycler, Eppendorf Mastercycler ep-S, Biometra T1, ABI PRISM® 310, ABI PRISM® 3130 and 3500 Genetic Analyzer running POP-4™ and POP-7™. The development, manufacture and distribution of Biotype® products are certified according to DIN EN ISO 13485.

Mentype® AMLplexQS PCR Amplification Kit

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Content 1. Description of the Mentype® AMLplexQS ..................................................... 6 2. PCR amplification ..................................................................................... 10

2.1 Master mix preparation .......................................................................... 10 2.2 PCR amplification parameter .................................................................. 11

3. Electrophoresis using the ABI PRISM® 310 Genetic Analyzer ................ 12 3.1 Matrix generation .................................................................................. 12 3.2 Sample preparation ............................................................................... 16 3.3 Setting up the Data Collection Software .................................................. 16

4. Electrophoresis using the ABI PRISM® 3100-Avant/ 3100 Genetic Analyzer ............................................................................. 17

4.1 Spectral calibration / matrix generation ................................................... 17 4.2 Sample preparation ............................................................................... 19 4.3 Setting up the Data Collection Software .................................................. 20

5. Electrophoresis using the ABI PRISM® 3130/ 3130xl Genetic Analyzer .......................................................................... 22

5.1 Spectral calibration / matrix generation ................................................... 22 5.2 Sample preparation ............................................................................... 25 5.3 Setting up the Data Collection Software .................................................. 26

6. Electrophoresis using the ABI PRISM® 3500/ 3500xL Genetic Analyzer.......................................................................... 28

6.1 Spectral calibration / matrix generation ................................................... 28 6.2 Sample preparation ............................................................................... 31 6.3 Setting up a run .................................................................................... 32

7. Analysis .................................................................................................... 35 7.1 Analysis parameters / analysis method ................................................... 35 7.2 Biotype® template files .......................................................................... 36 7.3 Controls ................................................................................................ 37 7.4 Fragment lengths and aberration variants ............................................... 37

8. Interpretation of results ........................................................................... 41 9. References ................................................................................................ 42 10. Explanation of Symbols ......................................................................... 43

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A Analytical Validation ................................................................................ 44 A a) Determination of the Standard Reaction and Batch specific Tolerance ...... 44 A b) Accuracy of the Measurement ............................................................... 44 A c) Analytical Specificity.............................................................................. 45 A c) a) Analytical Specificity of negatively pre-typed cDNA ........................ 45 A c) b) Analytical Specificity of positively pre-typed cDNA .......................... 45

A d) Analytical Sensitivity .............................................................................. 46 A e) Assay Performance with Different PCR-Thermocyclers ............................ 46 A f) PCR Annealing Temperatures ................................................................ 46 A g) Fluctuations of PCR buffer Batches ........................................................ 47 A h) In-use stability ...................................................................................... 47

B Clinical Performance Data ....................................................................... 48 B a) Study Design, ethics and regulatory aspects ........................................... 48 B b) Reference Methods ............................................................................... 48 B c) DNA-Extraction and Purification ............................................................. 48 B d) Results ................................................................................................. 48 B e) References: .......................................................................................... 50

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1. Description of the Mentype® AMLplexQS

Table 1. Detected Chromosomal Aberrations and Variants

Gene-Fusions Chromosomal Aberration Variants AML1-ETO t(8;21) (q22;q22) - BCR-ABL t(9;22) (q34;q11) e1a3

e1a2

b3a2

b3a3

b2a2

b2a3 CALM-AF10 t(10;11) (p13;q14) AF10_240-CALM_1987

AF10_240-CALM_2092 CBFB-MYH11 inv(16) (p13;q22) Type A

Type B Type C

Type D Type E

Type F Type G

Type H Type I

Type J DEK-CAN t(6;9) (p23;q34) -

MLL-AF6 t(6;11) (q27;q23) -

MLL-AF9 t(9;11) (p22;q23) 6A_(THP-1)

7A_(10A) 8A_(MM6)

6B_(9B) MLL-ELL t(11;19) (q23;p13.1) e10e2

e10e3 MLL-PTD Partial Tandem Duplication e9e3

e10e3 e11e3

NPM1-MLF1 t(3;5) (q25.1;q34) - PML-RARA t(15;17) (q22;q21) bcr1 (PR-L)

bcr2 (PR-V) bcr3 (PR-S)

Table 2. Quality Sensors of the Mentype® AMLplexQS

Quality Sensors Meaning Internal PCR-Control (QS-Control) Reflects quality of PCR performance cDNA-Control (ABL-Control) Reflects quality of cDNA templates

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Kit content Mentype® AMLplexQS PCR Amplification Kit (100 Reactions) Nuclease-free water 3.0 ml Reaction mix A 500 µl Primer mix 250 µl Multi Taq2 DNA Polymerase 40 µl Control cDNA KASUMI-1 (500 ng/µl) 10 µl DNA Size Standard 550 (BTO) 50 µl Allelic ladder 25 µl

Ordering information Mentype® AMLplexQS 10 reactions Cat.No. 45-31220-0010 Mentype® AMLplexQS 25 reactions Cat.No. 45-31220-0025 Mentype® AMLplexQS 100 reactions Cat.No. 45-31220-0100

Storage

Store all components at -20 °C and avoid repeated thawing and freezing. Primer mix and allelic ladder must be stored protected from light. The DNA samples and post-PCR reagents (allelic ladder and DNA size standard) should be stored separately from PCR reagents. The expiry date is indicated on the kit cover.

Additionally required reagents Additional reagents are needed in order to use the Biotype® PCR Amplification Kit:

Reagent Supplier Order number

Hi-Di™ Formamide, 25 ml Life Technologies Corporation

4311320

Matrix Standards BT5 single-capillary instruments (5x25 µl)

Biotype Diagnostic GmbH 00-10411-0025

Matrix Standards BT5 multi-capillary instruments (25 µl)


Matrix Standards BT5 multi-capillary instruments (50 µl)


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Warnings and safety instructions

The PCR Amplification Kit contains the following potentially hazardous chemicals: Kit component Chemical Hazards Reaction mix Sodium azide NaN3 toxic if swallowed, develops toxic gases

when it gets in contact with acids

Observe the Material Safety Data Sheets (MSDS) for all Biotype® products, which are available on request. Please contact the respective manufacturers for copies of the MSDS for any additionally needed reagents.

Quality assurance

All kit components undergo an intensive quality assurance process at Biotype Diagnostic GmbH. The quality of the test kits is permanently monitored in order to ensure unrestricted usability. Please contact us if you have any questions regarding quality assurance. Trademarks and Patents

Mentype® is a registered trademark of Biotype Diagnostic GmbH. ABI PRISM®, GeneMapper®, GeneAmp® and Applied Biosystems® are registered trademarks of Applied Biosystems LLC. Under the law of Europe POP-4® is a registered trademark of Applied Biosystems LLC. POP-4™, POP-7™are registered as trademark of Life Technologies Corporation in the US. The PCR is covered by patents. Patentees are Hoffmann-La Roche Inc. and F. Hoffmann-La Roche (Roche).

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Outline of required working stages

Fig. 1 From sample to analysis – detection of fusion gene transcripts performed with the Mentype® AMLplexQS PCR Amplification Kit

sampling

cDNA synthesis

fragment length analysis

analysis of results

RNA isolation

multiplex PCR amplification

Mentype® AMLplexQS

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2. PCR amplification

2.1 Master mix preparation

The table below shows volumes of applied reagents per 1.0 µl sample volume (template-cDNA) in a total reaction volume of 25 µl. The number of reactions to be set up shall be determined taking into account positive and negative control reactions. Add one or two reactions to this number to compensate pipetting errors.

Component Volume Nuclease-free water 16.1 µl Reaction mix A* 5.0 µl Primer mix 2.5 µl Multi Taq2 DNA Polymerase (hot start, 2.5 U/µl) 0.4 µl Volume of master mix 24.0 µl

* contains Mg2+, dNTPs, BSA

All components should be mixed (vortex) and centrifuged for about 10 s before preparing the master mix.

Since performance of the Mentype® AMLplexQS analysis is mostly depending on quality and quantity of applied cDNA, we recommend standardised and already validated methods for sampling, RNA isolation and RNA to cDNA transcription e.g. of the Europe Against Cancer Program (EAC, see references p.33). The amount of cDNA used for the assay depends on the concentration and quality of prior isolated and applied RNA. For reference samples generated from cell culture the use of 1 µl cDNA will be sufficient if 1 µg of respective RNA was initially transcribed in a RT-PCR reaction volume of 20 µl. The amount of applied template can be extended in case of critical clinical samples. The maximum template amount should not exceed 1/10 of the RT-reaction volume. Adjust the final reaction volume to 25 µl with nuclease-free water. The primer mix is optimised to result in sufficient peak-heights if 25 PCR cycles in 25µl reaction volume are performed. The ABL-Control should not exceed the specified measuring range of the used instrument herein. Positive control

Dilute Control cDNA KASUMI-1 to 250 ng/µl in appropriate volume. Instead of template cDNA pipette diluted Control cDNA into reaction-tubes containing the PCR master mix. Negative control

Nuclease-free water serves as negative control. Pipette respective volume instead of the cDNA template into reaction tubes containing the PCR master mix. Template cDNA

Sometimes, measured value of the cDNA concentration varies depending on the quantification method used. In this instant it may be necessary to adjust the optimal cDNA amount.

Protocols for amplification, electrophoresis and analysis


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2.2 PCR amplification parameter

Perform a “hot start” PCR in order to activate the Multi Taq2 DNA Polymerase and to prevent the formation of non-specific amplification products. The number of PCR cycles depends on the amount of applied cDNA. 25 PCR cycles are recommended for all samples. For highly concentrated reference samples from cell cultures a reduction to 22 PCR cycles is recommended. In case of critical samples, we suggest to increase the number of PCR cycles to a maximum of 28 cycles. The internal ABL-Control may serve as point of reference to evaluate the optimal number of required PCR cycles. The optimal range of the internal ABL-Control should not exceed the specified measuring range of the used instrument herein (e.g. 500 to 5000 RFU on ABI3130) Very small amounts of cDNA may result in statistical dropouts and imbalances of the peaks. Increasing numbers of PCR cycles raise the risk of cross contamination caused by minimal amounts of impurities. Furthermore, unspecific amplification products could appear. Note: To provide an optimal kit balance the ramping rate of the thermal cycler should be adjusted to 4 °C/s.

Standard method - Recommended for all cDNA samples: Temperature Time 96 °C 4 min (hot start to activate Multi Taq2 DNA Polymerase) 96 °C 30 s

25 cycles 61 °C 120 s 72 °C 75 s 68 °C 10 min* 10 °C ∞ hold

Optional

Recommended for cDNA positive controls from cell culture Temperature Time 96 °C 4 min (hot start to activate Multi Taq2 DNA Polymerase) 96 °C 30 s

22 cycles 61 °C 120 s 72 °C 75 s 68 °C 10 min* 10 °C ∞ hold

Optional

Recommended for critical cDNA samples Temperature Time 96 °C 4 min (hot start to activate Multi Taq2 DNA Polymerase) 96 °C 30 s

max. 28 cycles 61 °C 120 s 72 °C 75 s 68 °C 10 min* 10 °C ∞ hold

* If a higher amount of minus-Adenine peaks is observed, extension up to 60 min is possible.


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3. Electrophoresis using the ABI PRISM® 310 Genetic Analyzer

For general instructions on instrument setup, matrix generation and application of the GeneMapper®software, please refer to the ABI PRISM® 310 Genetic Analyzer User’s Manual. Electrophoresis using the GeneMapper ID-X software is described below. The virtual filter set G5 shall be used for combined application of the five fluorescent labels 6-FAM, BTG, BTY, BTR, and BT0 (the matrix standard will be called BT5 hereinafter). Material Capillary 47 cm / 50 µm (green) Polymer POP-4™ for 310 Genetic Analyzer Buffer 10x Genetic Analyzer Buffer with EDTA

3.1 Matrix generation Prior to conducting DNA fragment size analysis with the filter set G5, a matrix with the five fluorescent labels 6-FAM, BTG, BTY, BTR, and BTO must be generated.

Color Matrix standard Blue (B) 6-FAM Green (G) BTG Yellow (Y) BTY Red (R) BTR Orange (O) BTO

Five electrophoresis runs shall be conducted, one for each fluorescent label, 6-FAM, BTG, BTY, BTR, and BTO; under same conditions as for samples and allelic ladders of the Biotype® test kit to generate suitable matrix files.

Matrix sample Component Volume

Matrix sample 1 Hi-Di™ Formamide 12.0 µl Matrix standard 6-FAM 1.0 µl

Matrix sample 2 Hi-Di™ Formamide 12.0 µl Matrix standard BTG 1.0 µl

Matrix sample 3 Hi-Di™ Formamide 12.0 µl Matrix standard BTY 1.0 µl

Matrix sample 4 Hi-Di™ Formamide 12.0 µl Matrix standard BTR 1.0 µl

Matrix sample 5 Hi-Di™ Formamide 12.0 µl Matrix standard BTO 1.0 µl

- Denaturation for 3 min at 95 °C - Cool down to 4 °C and place samples on the autosampler tray

- Create a Sample Sheet, choose 5 Dyes and enter a sample designation


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Injection list for matrix generation Parameter Set up Module File GS STR POP-4 (1 ml) G5 Matrix File NONE Size Standard* NONE Injection [s] 5 Injection [kV] 15.0 Run [kV] 15.0 Run [°C] 60 Run Time [min] 24

* Prepare matrix standards always without DNA Size Standard (BTO) Analysis of the matrix samples

- Run the GeneMapper® software - File Add Sample to Project (open folder of current run) - Select a matrix sample in the Sample File column - Sample Raw Data - Check the matrix samples for a flat baseline. As shown in the figure below there

should be at least five peaks with peak heights about 1000-4000 RFU (Y-axis) for each matrix sample (optimal range: 2000-4000 RFU)

Fig. 1 Electropherogram with raw data of the matrix standard 6-FAM - Select an analysis range with flat baseline and re-inject the matrix sample if

necessary - Note down start and end value (data points) of the analysis range, e.g. start value

2900, end value 5400 - Calculate the difference, e.g. 5400-2900 = 2500 data points

▼ 2900 Data Points (X) 5400▼


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Generation of a new matrix

- Tools GeneMapper Manager Matrices New - Create the matrix name, e.g. Matrix BT5 - Import matrix samples for all dyes (B, G, Y, R, O) (Click on the symbol)

Fig. 2 Matrix sample selection - Enter a Start At value, e.g. 2900 - Enter the calculated difference under Points, e.g. 2500


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Fig. 3 New matrix BT5 - Calculate the matrix with Create - Click on OK to save the new matrix Matrix check

Check the new matrix with current samples. - File Add Samples to Project (open folder of the respective run) - Select sample(s) in the Sample File column - Select the new matrix in the Sample Table - Re-analyse your samples There should be no pull-up peaks between the dye panels (B, G, Y, R, O) with the new matrix.


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3.2 Sample preparation Component Volume Hi-Di™ Formamide 12.0 µl DNA Size Standard 550 (BTO) 0.5 µl prepare 12 µl of the mix (formamide + DNA size standard) for all samples add 1 µl PCR product (dilute if necessary) or allelic ladder - Denaturation for 3 min at 95 °C - Cool down to 4 °C and place samples on the autosampler tray

Room temperature may influence the performance of PCR products on instruments, so that shoulder peaks or split peaks occur especially at low temperatures. Pay attention to keep ambient conditions as recommended by the instrument manufacturer. Optimal settings were reported >22 °C room temperature. Signal intensities

Options to increase the signal intensity: - Reduce the volume of the DNA Size Standard 550 (BTO) to peak heights of

about 500 relative fluorescent units (RFU) - Purify the PCR products before starting the analysis

3.3 Setting up the Data Collection Software

- Create a Sample Sheet and enter sample designation Injection list

Parameter Set up Module File GS STR POP-4 (1 ml) G5 Matrix File e.g. Matrix BT5 Size Standard e.g. SST-BTO_60-550bp Injection [s]* 5 Injection [kV] 15.0 Run [kV] 15.0 Run [°C] 60 Run Time [min]** 28

* Deviating from the standard settings, the injection time may range between 1 and 20 s depending on the type of sample. If reference samples with very high signal intensities are recorded, a shorter injection time may be selected in order to avoid pull-up peaks. For samples with low cDNA content or critical patient samples an injection time of up to 20 s may be necessary. ** Depending on the analysis conditions, the run time for Mentype® AMLplexQS should be modified in order to analyse fragments with lengths of up to 550 bp.


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4. Electrophoresis using the ABI PRISM® 3100-Avant/3100 Genetic Analyzer

For detailed instructions on instrument setup, spectral calibration, application of the Data Collection software and the GeneScan software, please refer to the ABI PRISM ® 3100-Avant/3100 Genetic Analyzer User’s Manual. This chapter describes the use of ABI PRISM ® 3100-Avant/3100 Genetic Analyzer in combination with Data Collection software version 1.0.1 and 1.1. For systems with Data Collection software 2.0 or 3.0 refer to chapter 6. The system with 4 capillaries is named ABI 3100-Avant, and the system with 16 capillaries is named ABI 3100. The virtual filter set G5 shall be used for combined application of the five fluorescent labels 6-FAM, BTG, BTY, BTR and BT0 (the matrix standard will be called BT5 hereinafter). Material Capillary* 36 cm Capillary Array for 3100-Avant/3100 Polymer* POP-4™ Polymer for 3100 Buffer 10x Genetic Analyzer Buffer with EDTA

*other instrument settings possible 4.1 Spectral calibration / matrix generation

Proper spectral calibration is critical to evaluate multicolor systems with the ABI PRISM® 3100-Avant/3100 Genetic Analyzer and shall be done prior to conducting fragment length analysis. The calibration procedure creates a matrix that is used to correct the overlap of fluorescence emission spectra of the dyes. Spectral calibration comprises the following steps: - Preparation of spectral calibration standards - Loading standards to the 96-well reaction plate (one sample per capillary) - Entering the plate composition - Performing a spectral calibration run and checking the matrix Setting up the spectral calibration standard

Example for 4 capillaries / ABI 3100-Avant Component Volume Hi-Di™ Formamide 60.0 µl Matrix standard BT5 5.0 µl - Load 12 μl of the mix to a 96-well reaction plate, e.g. position A1-D1 - Denaturation for 3 min at 95 °C - Cool down to 4 °C and place samples on the autosampler tray

Example for 16 capillaries / ABI 3100

Component Volume Hi-Di™ Formamide 204.0 µl Matrix standard BT5 17.0 µl - Load 12 μl of the mix to a 96-well reaction plate, e.g. position A1-H1 and A2-H2 - Denaturation for 3 min at 95 °C - Cool down to 4 °C and place samples on the autosampler tray


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Performing a spectral calibration run

First of all, the parameter file for DyeSetG5 must be modified once to achieve successful calibration with the Data Collection software version 1.0.1 or 1.1.

Spectral parameter

To change settings in the parameter file go to the following path: D:\AppliedBio\Support Files\Data Collection Support Files\CalibrationData\Spectral Calibration\ParamFiles - Select MtxStd{Genescan_SetG5} to open the PAR-file - Change Condition Bounds Range to [1.0; 20.0] - Select File Save As to save the parameter file under a new name, e.g.

MtxStd{Genescan_SetG5_BT5}.par Always use this parameter file for spectral calibration runs using Biotype® matrix standard BT5. Plate Editor for spectral calibration (I)

- Place the 96-well plate on the autosampler tray - Run the ABI PRISM® 3100 Data Collection software - In Plate View click New to open the Plate Editor dialog box - Enter a name of the plate - Select Spectral Calibration - Select 96-Well as plate type and click on Finish Plate editor for spectral calibration (II)

Parameter Set up Sample Name Enter name for the matrix samples Dye Set G5 Spectral Run Module Default (e.g. Spect36_POP4) Spectral Parameters MtxStd{GeneScan_SetG5_BT5}.par (parameters created before)

- Click into the column header to select the entire column, select Edit → Fill Down to

apply the information of the selected samples and confirm with OK - Link your reaction plate on the autosampler tray with the created plate ID and start

the run - On completion of the run check in the Spectral Calibration Result dialog box if all

capillaries have successfully passed calibration (label A). If individual capillaries are labelled X, refer to ABI PRISM ®Genetic Analyzer User’s Manual

- Click on OK to confirm completion of the run


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Matrix check

- Select Tools → Display Spectral Calibration → Dye Set → G5 to review the spectral calibration profile for each capillary

- The quality value (Q value) must be greater than 0.95 and the condition number (C value) must be between 1 and 20. Both values must be within the previously determined range

- Check the matrix samples for a flat baseline. There should be five peaks with peak heights of about 1000-5000 RFU (Y-axis) in each matrix sample (optimal range: 2000-4000 RFU)

- Check the new matrix with your current samples. There should be no pull-up peaks between the dye panels (B, G, Y, R, O) with the new matrix

- If all capillaries have passed the calibration, the last calibration file for Dye Set G5 must be activated manually under Tools → Set Active Spectral Calibration. Rename the calibration file under Set Matrix Name (e.g. BT5_Date of calibration)

- If calibration was not successful, try to re-inject the samples with higher injection voltage or injection time. The editing of the Spectral Run Module will be necessary. You can re-inject the same samples up to three times. Otherwise use more matrix standard for spectral calibration

4.2 Sample preparation Component Volume Hi-Di™ Formamide 12.0 µl DNA Size Standard 550 (BTO) 0.5 µl Prepare 12 µl of the mix (formamide + DNA size standard) for all samples Add 1 µl PCR product (dilute if necessary) or allelic ladder - Denaturation for 3 min at 95 °C - Cool down to 4 °C and place samples on the autosampler tray

Since injections take place simultaneously on all capillaries, 4 or 16 samples must be pipetted on the plate of multi-capillary analyzers. If fewer samples are analysed, the empty positions must be filled with 12 µl Hi-Di™ Formamide. Run several ladders to ensure a reliable allelic assignment on multi-capillary analyzers. Room temperature may influence the performance of PCR products on multi-capillary instruments, so that shoulder peaks or split peaks occur especially at low temperatures. Pay attention to keep ambient conditions as recommended by the instrument manufacturer. Optimal settings were reported >22 °C room temperature. Signal intensities

Options to increase the signal intensity: - Reduce the volume of the DNA Size Standard 550 (BTO) to peak heights of about 500

relative fluorescent units (RFU) - Purify the PCR products before starting the analysis


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Edit the default run module in Dye Set G5 once for the first run. - Select Module Editor to open the dialog box - Select the appropriate Run Module as template from the GeneScan table - Modify the Injection Voltage to 3 kV and the Injection Time to 10 s

Run Module 3kV_10s_550bp Parameter Set up Run Temperature [°C] Default Cap Fill Volume Default Maximum Current [A] Default Current Tolerance [A] Default Run Current [A] Default Voltage Tolerance [kV] Default Pre Run Voltage [kV] Default Pre Run Time [s] Default Injection Voltage [kV] 3.0 Injection Time [s]* 10 Run Voltage [kV] Default Number of Steps Default Voltage Step Interval Default Data Delay Time [s] Default Run Time [min]** 26

* Deviating from the standard settings, the injection time may range between 1 and 20 s depending on the type of sample. If reference samples with very high signal intensities are recorded, a shorter injection time may be selected in order to avoid pull-up peaks. For samples with low DNA content or critical patient samples an injection time of up to 20 s may be necessary. ** Depending on the analysis conditions, the run time for Mentype® AMLplexQS should be modified in order to analyse fragments with lengths of up to 550 bp.

- Click on Save As, enter the name of the new module (e.g. 3kV_10s_550bp) and confirm with OK

- Click on Close to exit the Run Module Editor Starting the run

- Place the prepared 96-well plate on the autosampler tray - Run the ABI PRISM® 3100 Data Collection software - In Plate View click on New to open the Plate Editor dialog box - Enter a name of the plate - Select GeneScan - Select 96-Well as plate type and click on Finish


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Plate Editor Parameter Set up Sample Name Enter name for the samples Dyes O Color Info Ladder or sample Project Name e.g. 3100_Project1 Dye Set G5 Run Module* 3kV_10s_550bp Analysis Module 1 DefaultAnalysis.gsp

* parameter see above

- Complete the table in the Plate Editor and click on OK - Click into the column header to select the entire column and select Edit → Fill

Down to apply the information of the selected samples - Link your reaction plate on the autosampler tray with the created plate ID and start

the run - On completion of the run, view data as Color Data in Array View of the 3100 Data

Collection software or as Analyzed Sample Files under D:/AppliedBio/3100/DataExtractor/ExtractRuns


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5. Electrophoresis using the ABI PRISM® 3130/3130xl Genetic Analyzer

For detailed instructions on instrument setup, spectral calibration, or application of the ABI PRISM® Data Collection software version 3.0 and the GeneMapper® ID/ID-X software, refer to the ABI PRISM ® 3130/3130xl Genetic Analyzers Getting Started Guide. The system with 4 capillaries is named ABI 3130 and the system with 16 capillaries is named ABI 3130xl. The virtual filter set Any5Dye shall be used for the combined application of the five fluorescent labels 6-FAM, BTG, BTY, BTR, and BT0 (the matrix standard will be called BT5 hereinafter). Material Capillary* 36 cm Capillary Array for 3130/3130xl Polymer* POP-4™ Polymer for 3130 Buffer 10x Genetic Analyzer Buffer with EDTA

* other instrument settings possible

5.1 Spectral calibration / matrix generation

Prior to conducting DNA fragment size analysis, it is necessary to perform a spectral calibration with the four fluorescent labels 6-FAM, BTG, BTY, BTR, and BTO for each analyzer. The calibration procedure creates a matrix which is used to correct the overlap of fluorescence emission spectra of the dyes. Spectral calibration comprises the following steps: - Preparation of spectral calibration standards - Loading the standards to the 96-well reaction plate (one sample per capillary) - Creating the instrument protocol for spectral calibration (Protocol Manager) - Defining the plate composition in the plate editor (Plate Manager) - Performing a spectral calibration run and checking the matrix


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Setting up the spectral calibration standards

Example for 4 capillaries / ABI 3130 Component Volume Hi-Di™ Formamide 60.0 µl Matrix standard BT5 5.0 µl - Load 12 μl of the mix to a 96-well reaction plate, e.g. position A1-D1 - Denaturation for 3 min at 95 °C - Cool down to 4 °C and place samples on the autosampler tray

Example for16 capillaries / ABI 3130xl

Component Volume Hi-Di™ Formamide 204.0 µl Matrix standard BT5 17.0 µl - Load 12 μl of the mix to a 96-well reaction plate, e.g. position A1-H1 and A2-H2 - Denaturation for 3 min at 95 °C - Cool down to 4 °C and place samples on the autosampler tray

Performing a spectral calibration run

- Place the 96-well plate on the autosampler tray - In the Protocol Manager of the Data Collection software click on New in

Instrument Protocol to open the Protocol Editor dialog box Instrument Protocol for spectral calibration

Protocol Editor Set up Name User (e.g. Spectral36_POP4_BT5) Type SPECTRAL Dye Set Any5Dye Polymer* User (e.g. POP4) Array Length* User (e.g. 36cm) Chemistry Matrix Standard Run Module* Default (e.g. Spect36_POP4_1)

* Depends on the type of polymer and length of capillary used

- Click on OK to leave the Protocol Editor dialog box - In the Plate Manager of the Data Collection software, click on New to open the

New Plate Dialog box Plate Editor for spectral calibration (I)

New Plate Dialog Set up Name e.g. Spectral_BT5_date Application Spectral Calibration Plate Type 96-Well Owner Name / Operator Name …

- Click on OK. A new table in the Plate Editor will open automatically


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Plate Editor for spectral calibration (II) Parameter Set up Sample Name Enter name for the matrix samples Priority e.g. 100 Instrument Protocol 1 Spectral36_POP4_BT5 (setting described before)

- Click into the column header to select the entire column, select Edit → Fill Down to apply the information to all selected samples, and click on OK

- In the Run Scheduler click on Find All, select Link to link the reaction plate on the autosampler to the newly created plate record (position A or B), and, start the run.

Fig. 5 Electropherogram of spectral calibration with matrix standard BT5 on an ABI 3130

Matrix check

- The quality value (Q value) of each capillary must be greater than 0.95 and the condition number range (C value) must be between 1 and 20 - Check the matrix samples for a flat baseline. As shown in the figure above, there

should be five peaks with peak heights of about 1000-5000 RFU (Y-axis) in each matrix sample (optimal range: 2000-4000 RFU)

- Check the new matrix with your current samples. There should be no pull-up peaks between the dye panels (B, G, Y, R, O) with the new matrix

- If all capillaries have passed the test, the last calibration file for the Dye Set Any5Dye is activated automatically in the Spectral Viewer. Rename the calibration file (e.g. BT5_Date of calibration) using the respective button

- If calibration was not successful, try to re-inject the samples with higher injection voltage or injection time. Editing of the Spectral Run Module will be necessary. You can re-inject the same samples up to three times. Otherwise use more matrix standard for spectral calibration


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5.2 Sample preparation

Components Volume Hi-Di™ Formamide 12.0 µl DNA Size Standard 550 (BTO) 0.5 µl prepare 12 µl of the mix (formamide + DNA size standard) for all samples add 1 µl PCR product (diluted if necessary) or allelic ladder - Denaturation for 3 min at 95 °C - Cool down to 4 °C and place samples on the autosampler tray

Since injections take place simultaneously on all capillaries, 4 or 16 samples must be pipetted on the plate of multi-capillary analyzers. If fewer samples are analysed, the empty positions must be filled with 12 µl Hi-Di™ Formamide. Run several ladders to ensure a reliable allelic assignment on multi-capillary analyzers. Room temperature may influence the performance of PCR products on multi-capillary instruments. Shoulder peaks or split peaks could occur especially at low temperatures. Pay attention to keep ambient conditions as recommended by the instrument manufacturer. Optimal settings were reported >22 °C room temperature. Signal intensities




26


Edit the Run Module as follows for the first run: - In the Module Manager of the Data Collection software click on New to open the

Run Module Editor dialog box Run Module 3kV_10s_550bp

Parameter Set up Oven Temperature [°C] Default Poly Fill Volume Default Current Stability [µA] Default PreRun Voltage [kV] Default PreRun Time [s] Default Injection Voltage [kV] 3.0 Injection Time [s]* 10 Voltage Number of Steps Default Voltage Step Interval Default Data Delay Time [s] Default Run Voltage [kV] Default Run Time [s]** 1560


- Click on Save As, enter the name of the new module (e.g. 3kV_10s_550bp) and confirm with OK

- Click on Close to exit the Run Module Editor Starting the run

- Place the prepared 96-well plate on the autosampler tray - In the Protocol Manager of the Data Collection software, click on New in the

Instrument Protocol window to open the Protocol Editor dialog box Instrument Protocol

Protocol Editor Set up Name e.g. Run36_POP4_BT5_26min Type REGULAR Run Module* 3kV_10s_550bp Dye Set Any5Dye

* parameter see above - Click on OK to exit the Protocol Editor


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Prior to each run, it is necessary to create a plate definition as follows: - In the Plate Manager of the Data Collection software click on New to open the New

Plate Dialog box Plate Editor (I)

New Plate Dialog Set up Name e.g. Plate_BT5_Date Application Select GeneMapper Application Plate Type 96-Well Owner Name / Operator Name …

- Click on OK. A new table in the Plate Editor will open automatically Plate Editor (II)

Parameter Set up Sample Name Enter name for the samples Priority e.g. 100 (Default) Sample Type Sample or allelic ladder Size Standard e.g. SST-BTO_60-550bp Panel e.g. AMLplex_Panels_v2 Analysis Method e.g. AMLplex_HID_3130_200rfu Snp Set - User-defined 1-3 - Results Group 1 (select results group) Instrument Protocol 1 Run36_POP4_BT5_26min (setting described before)

- Click into the column header to select the entire column, select Edit → Fill Down to

apply the information to all selected samples and click on OK - In the Run Scheduler, click on Find All, select Link to link the reaction plate on the

autosampler to the newly created plate record (position A or B) and start the run - During the run, view Error Status in the Event Log or examine the quality of the raw

data for each capillary in the Capillaries Viewer or the Cap/Array Viewer - View data as overview in Run History or Cap/Array Viewer of the Data Collection

software. Run data are saved in the Run Folder of the previously chosen Result Group


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6. Electrophoresis using the ABI PRISM® 3500/3500xL Genetic Analyzer

For detailed instructions on instrument setup, spectral calibration, or application of the Applied Biosystems 3500 Series Data Collection Software version 3.0 and the GeneMapper® ID-X software version 1.4, refer to the Applied Biosystems 3500/3500xL Genetic Analyzers User Guide. The system with 8 capillaries is named AB 3500 and the system with 24 capillaries is named AB 3500xL. The virtual filter set Any5Dye shall be used for the combined application of five fluorescent labels 6-FAM, BTG, BTY, BTR, and BT0 (the matrix standard will be called BT5 hereinafter). Material Capillary* 36 cm Capillary Array for 3500/3500xL Polymer POP-4™ Polymer for 3500/3500xL Buffer 10x Genetic Analyzer Buffer with EDTA for 3500/3500xL

* other instrument settings possible

6.1 Spectral calibration / matrix generation

Prior to conducting DNA fragment size analysis, it is necessary to perform a spectral calibration with the fluorescent labels 6-FAM, BTG, BTY, BTR, and BTO for each analyzer. The calibration procedure creates a matrix that is used to correct the overlap of fluorescence emission spectra of the dyes. Spectral calibration comprises the following steps: - Preparation of spectral calibration standards - Loading the standards to the multi-well reaction plate (one sample per capillary) - Preparation of instrument and creating a Dye Set BT5 - Performing a spectral calibration run and checking the matrix


29

Setting up the spectral calibration standards

Example for 8 capillaries / ABI 3500 Component Volume Hi-Di™ Formamide 108.0 µl Matrix standard BT5 9.0 µl - Load 12 μl of the mix to a 96-well reaction plate, e.g. position A1-H1 - Denaturation for 3 min at 95°C - Cool down to 4°C and place samples on the autosampler tray

Example for 24 capillaries / ABI 3500xL

Component Volume Hi-Di™ Formamide 300.0 µl Matrix standard BT5 25.0 µl - Load 12 μl of the mix to a 96-well reaction plate, e.g. position A1-H1, A2-H2 and A3-H3* - Denaturation for 3 min at 95°C - Cool down to 4°C and place samples on the autosampler tray

* When using a 384-well plate, load 10 μl of the mixtures to columns 1, 3, and 5 in rows A, C, E, G, I, K, M, and O. Performing a spectral calibration run

- Place the multi-well plate on the autosampler tray - Now prepare the instrument and specific spectral calibration run settings Preparation of the instrument Before starting the spectral calibration process ensure that the spatial calibration has been performed. This process is necessary if a new capillary array was installed before and is described in detail in the Applied Biosystems 3500/3500xL Genetic Analyzers User Guide. Preparation of dye set BT5 Prior to the spectral calibration, a dye set for the matrix standard BT5 needs to be setup. 1. To create a new dye set, go to Library and select Analyze, followed by Dye Sets and click Create. 2. Enter a Dye Set Name, e.g. BT5. 3. Select Matrix Standard as a chemistry and AnyDye Template as a dye set template. 4. Disable Purple in the field Arrange Dyes. Ensure that all other colors are enabled. 5. Under Calibration Peak Order the colors need to be arranged as follows: 5 – blue, 4 – green, 3 – yellow, 2 – red, and 1 – orange. 6. Do not alter the Parameter settings. 7. Click Save to confirm the changes.


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Fig. 6 Setup for dye set BT5

Performing a spectral calibration run Once the multi-well plate containing the spectral calibration mixture is placed in the autosampler tray the spectral calibration process can be started. 1. To access the Spectral Calibration screen, select Maintenance on the Dashboard of the 3500 Series Data Collection software. 2. The number of wells in the spectral calibration plate and their location in the instrument must be specified. 3. Select Matrix Standard as a chemistry standard and BT5 for dye set (defined before). 4. Enable Allow Borrowing (Optional). 5. Click Start Run.


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Fig. 7 Electropherogram of spectral calibration with matrix standard BT5 on an ABI 3500

Matrix check

- The quality value (Q value) of each capillary must be greater than 0.8 and the condition number range (C value) must be between 1 and 20 - Check the matrix samples for a flat baseline. As shown in the figure above, there

should be five peaks with peak heights of about 1000-5000 RFU (Y-axis) in each matrix sample (optimal range: 2000-4000 RFU)

- A successful calibration will be displayed in green in Overall and for each capillary - If all capillaries have passed the test, Accept Results - If calibration failed, Reject Results and refer to the “spectral calibration

troubleshooting” section in the Applied Biosystems 3500/3500xL Genetic Analyzer User Guide.

6.2 Sample preparation Component Volume Hi-Di™ Formamide 12.0 µl DNA Size Standard 550 (BTO) 0.5 µl prepare 12 µl of the mix (formamide + DNA size standard) for all samples add 1 µl PCR product (dilute if necessary) or allelic ladder - Denaturation for 3 min at 95 °C - Cool down to 4 °C and place samples on the autosampler tray

Since injections take place simultaneously on all capillaries, 8 or 24 samples must be pipetted on the plate of multi-capillary analyzers. If fewer samples are analysed empty positions need to be filled with 12 µl Hi-Di™ Formamide. To ensure a reliable allelic assignment on multi-capillary analyzers, several ladders should be run. Room temperature may influence the performance of PCR products on multi-capillary instruments, so that shoulder peaks or split peaks occur especially at low temperatures. Pay attention to keep ambient conditions as recommended by the instrument manufacturer. Optimal settings were reported >22 °C room temperature.


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Signal intensities



6.3 Setting up a run

For the first run using the Mentype® AMLplexQS you will need to setup a number of protocols within the 3500 Series Data Collection Software. Create Instrument protocol - Go to Library and select Analyze / Instrument protocol and click Create - Change the parameters according the table below Instrument protocol for Mentype® AMLplexQS

Parameter Set up Application Type HID or Fragment Capillary Length Default Polymer Default Dye Set BT5 Run Module Default Protocol Name e.g. Mentype AMLplexQS Oven Temperature [°C] Default Run Voltage [kV] Default Injection Voltage [kV] 3.0 Run Time [s]** 1560** PreRun Time [s] Default Injection Time [s]* 8* Data Delay Time [s] Default Advanced Options Default


- Click on Save to confirm the settings


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Create Size Standard - Go to Library and select Analyze / Size Standards and click Create - Change the parameters according the table below

Parameter Set up Size Standard BTO_550 Dye Color Orange

The DNA Size Standard 550 (BTO) should be used with the following lengths of fragments: 60, 80, 90, 100, 120, 140, 160, 180, 200, 220, 240, 250, 260, 280, 300, 320, 340, 360, 380, 400, 425, 450, 475, 500, 525, and 550 bp.


Create QC or Size Calling Protocol - Go to Library and select Analyze / QC or Size Calling Protocol and click Create - Change the parameters according the table below

Parameter Set up Protocol Name enter a name Size Standard BTO_550 (from above) Sizecaller Size Caller v.1.1.0

- Go to Analysis Settings / Peak Amplitude Threshold and disable purple. All

other colors should be enabled - Keep all other settings as Default - Click on Save to confirm the settings Create an Assay - Go to Library and select Manage / Assays and click Create - Change the parameters according the table below

Parameter Set up Assay Name e.g. Mentype AMLplexQS Color Default Application Type HID or Fragment Instrument Protocol e.g. Mentype AMLplexQS QC (Size Calling) Protocol e.g. BTO_550



34

Starting the run

- Place the prepared multi-well plate on the autosampler tray - In the Dashboard of the Data Collection software, click Create New Plate - Go to Define Plate Properties and select Plate Details - Change the parameters according the table below Plate Details

Property Set up Name e.g. Mentype AMLplexQS Number of Wells 96 or 384 Plate Type* HID or Fragment Capillary Length 36cm Polymer POP4

- Click Assign Plate Contents to confirm the settings - Define well position of each sample or ladder for data collection and processing by

entering sample names - Assign an Assay (required), a file name conventions, and a result group to all named

wells in the plate - Click Link the plate for Run and enter Run Name - Click Start Run


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7. Analysis

For general instructions on automatic sample analysis, please refer to the GeneScan or GeneMapper® ID/ID-X Software User’s Manual.

7.1 Analysis parameters / analysis method

The recommended analysis parameters are:

Peak Detection Algorithm Advanced

Allele No specific stutter ratio, set all to 0.0 Amelogenin cut off: 0.0

Ranges Analysis: Full Range Sizing: All Sizes

Smoothing and Baselining Smoothing: Light Baseline Window: 51 pts

Size Calling Method Local Southern Method

Peak Detection

Peak Amplitude Thresholds B:200 Y:200 G:200 R:200 O:50 Min. Peak Half Width: 2 pts Polynominal Degree: 3 Peak Window Size: 15 pts** Slope Thresholds: 0.0

Peak Quality Heterozygote Balance: 0.0 Max expected alleles: 22

* The peak amplitude threshold (cut-off value) corresponds to the minimum peak height that will be detected by the GeneMapper® ID software. For the Mentype® AMLplexQS 200 RFU is recommended and should be determined individually by the laboratory. Recommendation: The minimal peak height should be three times as high as the background noise of the baseline. ** If necessary, Peak Window Size can be minimised to 11 pts to improve peak detection. Note: Within the Mentype® AMLplexQS the red panel should be faded out. Finding the exact lengths of the amplified products depends on the device type, the conditions of electrophoresis, as well as the DNA size standard used. Therefore, determining the size should be based on evenly distributed references. The DNA Size Standard 550 (BTO) shall thus be used with the following lengths of fragments: 60, 80, 90, 100, 120, 140, 160, 180, 200, 220, 240, 250, 260, 280, 300, 320, 340, 360, 380, 400, 425, 450, 475, 500, 525, and 550 bp.

Fig. 8 Electropherogram of the DNA Size Standard 550 (BTO), fragments with lengths in bp.

Note: The provided template file for the DNA size standard SST-BTO_60-550bp can be applied for the evaluation and analysis of the Mentype® AMLplexQS using the GeneMapper® ID/ID-X Software.


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7.2 Biotype® template files

Allocation of fusion gene transcripts and variants should be carried out with suitable analysis software, e.g. GeneMapper® ID/ID-X software in combination with the Mentype® AMLplexQS template files from Biotype. The Biotype® template files with the respective manual are available on our homepage (www.biotype.de) for download or as CD-ROM on request. Recommended Biotype® templates for GeneMapper® ID/ID-X Software are:

Panels AMLplex_Panels_v2/v2X or higher version BinSets AMLplex_Bins_v2/v2X or higher version Size Standard SST-BTO_60-550bp Analysis Method

AMLplex_HID_310_200rfu recommended

AMLplex_HID_3130_200rfu recommended Plot Settings PlotsBT5_4dyes Table Settings Table for 10 Alleles Table für 22 Alleles

Panels and BinSets have to be used at any time, whereas other template files are optional.

Important Note: Import and allele calling with provided template files is only guarantied using GeneMapper® ID/ID-X software. If GeneMapper® software is applied you may experience import problems using some template files. You may have to adjust Panels and Bins with one ore more runs of the allelic ladder on your specific instrument setup. Contact us for support (support@biotype,de).

General procedure for the analysis 1. Check the DNA size standard 2. Check the allelic ladder 3. Check the positive control 4. Check the negative control 5. Analyse and interpret the sample data


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7.3 Controls

The Mentype® AMLplexQS PCR Amplification Kit includes a cDNA Control that represents the following aberrations: Table 3. Allocation with the Mentype® AMLplexQS

cDNA from cell culture* Aberration

KASUMI-1 (Asou et al. 1991) AML1-ETO

*Cell culture for preparation of cDNA was purchased from DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany. Use of provided cDNA is restricted to Mentype® AMLplexQS only.

7.4 Fragment lengths and aberration variants

Table 4 shows fragment lengths of the individual variants that refer to the DNA Size Standard 550 (BTO). All analyses have been performed on an ABI PRISM® 3130 Genetic Analyzer with POP-4® polymer. Different analysis instruments, DNA size standards or polymers may result in different fragment lengths. Due to instrument specific differences individual fine tuning of actually measured fragment sizes (home-based apparatus) is recommended. In addition, a visual alignment with the allelic ladder is also recommended. Scaling

Horizontal: 55-550 bp Vertical: Depending on signal intensity

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Figure 9

Fig. 9 Electropherogram of the Mentype® AMLplexQS using 250 ng cDNA Control KASUMI-1. Analysis was performed using the ABI PRISM® 3130 Genetic Analyzer and the DNA Size Standard 550 (BTO). Assignment was done with GeneMapper® ID Software and the Mentype® AMLplexQS template file.

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Figure 10

Fig. 10 Electropherogram of the Mentype® AMLplexQS allelic ladder. Analysis was performed using the ABI PRISM® 3130 Genetic Analyzer and the DNA Size Standard 550 (BTO). Assignment was done with GeneMapper® ID Software and the Mentype® AMLplexQS template file.


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Table 4. Fragment lengths of the Mentype® AMLplexQS allelic ladder measured using the ABI PRISM® 3130 Genetic Analyzer with POP-4® polymer. Please consider note under chapter 8.3.

Panel/Variants Size [bp]* Others Panel/Variants Size [bp]* Others

AMLplex Blue AMLplex Green

CBFB-MYH11_TypeG 63 DEK-CAN 78

CBFB-MYH11_TypeI 66 MLL-PTD_e9e3 87

QS-Control 72 MLL-AF9_6A_S‡ 113

BCR-ABL_b2a3 107 MLL-AF9_6B 191

CBFB-MYH11_TypeJ 141 MLL-PTD_e10e3 218

CBFB-MYH11_TypeC 146 MLL-ELL_e10e3 242

CBFB-MYH11_TypeD 160 MLL-AF9_7A 245

CBFB_MYH11_TypeH 165 MLL-ELL_e10e2 289

CBFB_MYH11_TypeF 175 MLL-AF6 303

BCR-ABL_b3a3 183 MLL-PTD_e11e3 333

BCR-ABL_e1a3 206 MLL-AF9_8A 360

AF10_240-CALM_2092

265 MLL-AF9_6A_L‡ 498

CBFB-MYH11_TypeA 271

BCR-ABL_b2a2 282 AMLplex Yellow

AML1-ETO 301 PML-RARA-bcr1 220

BCR-ABL_b3a2 358 PML-RARA_bcr3 288

CBFB-MYH11_TypeE 365 PML-

RARA_bcr2**

AF10_240-CALM_1987

371

BCR-ABL_e1a2 380

NPM1-MLF1 389

CBFB-MYH11_TypeB 486

ABL-Control 518

* rounded to integer

** Although this variant is detectable with Mentype® AMLplexQS primers, the varying length of the amplicon (apprx. 173 bp) prevents automated allocation. ‡ Two amplicons for variant MLL-AF9_6A

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8. Interpretation of results

As mentioned above, post PCR analysis and automatic allele assignment with suitable analysis software ensure a precise and reliable discrimination of fusion gene transcripts and variants. Please check for correct allelic ladder assignment within each run. Detection limit Applying plasmids, experimental data showed that 1000 copies resulted in peaks-heights > 200 RFU. Please note that Mentype® AMLplexQS was designed, validated and certified as a screening tool for subtype classification of AML. This application is not suited to quantify copy numbers or monitor Minimal Residual Disease (MRD). Pull-up peaks

Pull-up peaks may occur if peak heights of the PCR product are outside the linear detection range of the instrument, or if an incorrect matrix was applied. They appear at positions of specific peaks in other color channels, typically with lower signal intensities. If necessary please dilute the PCR product to confirm results. In case pull-up effects persist despite optimal peak heights, a new matrix run should be performed. Template-independent addition of nucleotides Because of its terminal transferase activity, the Multi Taq DNA Polymerase tends to add an adenosine radical at the 3’-end of the amplified DNA fragments. The artefact peak is one base shorter than expected (-1 bp peaks). All Biotype® primers are designed to minimise these artefacts. Artefact formation is further reduced by the final extension step of the PCR protocol at 68°C for 10 minutes. Peak height of the artefact correlates with the amount of cDNA. Laboratories should define their individual limits for analysis of the peaks. Artefacts

Room temperature may influence the performance of PCR products on multi-capillary instruments, shoulder peaks or split peaks occur. Furthermore, automated assignment could be influenced in some cases. If these effects occur we recommend injecting the sample again at higher room temperature and maybe using more than one allelic ladder sample per run. Pay attention to keep ambient conditions as recommended by the instrument manufacturer. Optimal settings were reported >22 °C room temperature. Influence of polymer types

The Mentype® AMLplexQS kit was validated and certified for the analysis on POP-4™ polymer. The use of other polymers (e.g. POP-7™ or POP-6™) might influence the run behaviour of specific PCR products. In case Biotype® Templates (Panels and BinSet) may have to be adjusted. Please contact our technical support ([email protected]). Furthermore background noise might increase through different behaviour of free fluorescent dyes.


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9. References

Asou H, Tashiro S, Hamamoto K, Otsuji A, Kita K, Kamada N (1991) Establishment of a human acute myeloid leukemia cell line (Kasumi-1) with 8;21 chromosome translocation. Blood 77(9): 2031-2036. Beillard E, Pallisgaard N, van der Velden VHJ, Bi W, Dee R, van der Schoot E, Delabesse E, Macintyre E, Gottardi E, Saglio G, Watzinger F, Lion T, van Dongen JJM, Hokland P, Gabert J (2003) Evaluation of candidate control genes for diagnosis and residual disease detection in leukemic patients using ‚real-time’ quantitative reverse-transcriptase polymerase chain reaction (RQ-PCR)- a Europe against cancer program. Leukemia 17:2474-2486. Van Dongen JJM, Macintyre EA, Gabert JA, Delabesse E, Rossi V, Saglio G, Gottardi E, Rambaldi A, DOtti G, Griesinger F, Parreira A, Gameiro P, Gonzalez Diaz M, Malec M, Langerak AW, San Miguel JF, Biondi A (1999) Standardized RT-PCR analysis of fusion gene transcripts from chromosome aberrations in acute leukemia for detection of minimal residual disease - Report of the BIOMED-1 Concerted Action: Investigation of minimal residual disease in acute leukemia. Leukemia 13:1901-1928.

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10. Explanation of Symbols

Manufacturer

Date of manufacture

Batch code

<N>

Contains sufficient reagents for <N> tests

Consult instructions (handbook) for use

Use by

Temperature limitations

Catalogue number

In-Vitro-Diagnostics


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A Analytical Validation

A a) Determination of the Standard Reaction and Batch specific Tolerance

Objective: Determination of the standard reaction and batch-specific tolerances of the multiplex PCR with respect to the absolute signal heights (RFU), the balance of the signal heights and the base line. In addition, the test-specific device settings for genotyping using capillary electrophoresis (bins and panels) are determined by the evaluation templates of the DNA sequencing machines.

Methods: A control cDNA of the cell line KASUMI-1 (ACC220, Leibniz Institute DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig) is included in the test kit and contains the gene fusion AML1-ETO with the chromosomal aberration t (8; 21) (q22 , Q22) [7]. Additionally, an artificial equimolar template mixture of plasmids containing 33 of the 34 detectable variants was applied. The standard reaction was performed with the control cDNA at the nominal concentration of 250 ng per PCR amplification with 25 PCR cycles. The template mixture was adjusted so that signal heights fall into the linear measuring range of the analyzers (5000 RFU max.) when using 25 PCR cycles. A four-fold determination with additionally four blank values (no template control, NTC) without DNA was carried out.

Results: The following specifications were determined for the batch-specific mixing of the PCR primers when template-mixes are applied: Using an ABI PRISM® 310 Genetic Analyzer, signal heights of 1000-4000 RFU and using an ABI PRISM® 3130 Genetic Analyzer were signal levels of 1000-5000 RFU. Specific signals are detected from a signal amplitude of 200 RFU. In the scaling range, no unspecific signals (free dyes, artefacts) > 200 RFU were detected for the blank values (baseline).

A b) Accuracy of the Measurement

Objective: Information of the accuracy of the method of measurement, and a sufficiently detailed summary of the data that enables to assess whether the means of ascertaining the accuracy are appropriate. Accuracy measurements for quantitative and qualitative tests can only be issued if a reference standard or method is available.

Methods: The kit is validated by the regular participation in ring trails with regard to the correct qualitative statement (diagnostics). Biotype has been participating regularly since June 3, 2013 in the United Kindom National Quality Assessment Scheme (UKNEQAS, www.ukneqas.org.uk) for the detection of BCR-ABL and AML translocations. Trails are regularly (2x) per year and are evaluated by the authority. The results (performance status) also in comparison with other participants are published.

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Results: Biotypes performance status is "Green". The product is demonstrably suitable for the detection of BCR-ABL variants and AML translocations and achieves the correct results (qualitative) in comparison with other molecular genetic methods.

A c) Analytical Specificity

A c) a) Analytical Specificity of negatively pre-typed cDNA Objective: The purpose of this study is to exclude false-positive results due to interference and cross-reactivity with selected cDNAs from negatively pre-typed samples (patients and healthy donors). Methods: 22 cDNAs negatively pre-typed for the translocation variants detectable with the test kit were tested. The amounts of cDNA used should cover the range of concentrations expected in clinical practice and ranged from 145 ng to max. 934 ng per PCR batch run with 25 cycles. Results: No cross-reactivity (> 200 RFU) was found in the allele range determined by the bins and panels. The measurement signal for the internal cDNA control (ABL gene) was > 200 RFU for 21 cDNAs, in one case approximately 50 RFU. The automatic allele allocation limit was set to 200 RFUs.

A c) b) Analytical Specificity of positively pre-typed cDNA Objective: The investigations served to exclude false-negative results as a result of interference and cross-reactivity of the primers with selected cDNAs from positively pre-typed patients. Methods: 20 cDNAs positively pre-typed for the translocation variants detectable with the test kit were tested. The amount of cDNA was adjusted to 250 ng per PCR amplification. The PCR program was performed with 25 cycles. Results: All somatic mutations were clearly identified. No cross-reactivity (> 50 RFU) was observed in the allele area. The measurement signals for the somatic mutations and the internal cDNA control (ABL gene) were> 200 RFU in 16/20 samples and> 50 RFU for 3/20 samples. One sample reached values below 50 RFU, but the fusion gene variant was still detectable. The automatic allele allocation limit was set to 200 RFUs.


46

A d) Analytical Sensitivity

Objective: The analytical detection limit of the test should be determined (sensitivity). Methods: A dilution series with 1 μg to 31.25 ng of reference cDNA (Kasumi-1) was tested in quadruplicates. The PCR program was performed with 25 cycles. In addition, for each transcription variant to be detected, the dilution series of an artificially prepared reference template (plasmide encoded gene fusion inserts, GeneArt/Life Technologies, Regensburg, DE)) with a fixed number of copies were tested in duplicates. Results: Up to a cDNA concentration of 62.5 ng, signal intensities > 200 RFU could be achieved for the specific translocations and for the ABL control. At 31.25 ng, the observed signal intensity of the specific variant were > 200 RFU, the ABL control reached > 50 RFU. Optimal values with respect to the measuring range of the capillary sequencer were achieved in the range of 150 ng-250 ng. The measurements of the plasmid dilutions showed a detection limit > 200 RFU and 100 copies that can be achieved for all translocation variants.

A e) Assay Performance with Different PCR-Thermocyclers

Objective: PCR thermocycler from different manufacturers differ in their specifications. In particular, different heating and cooling rates as well as different temperature control techniques can be present.

Methods: The standard reactions with control cDNA in the nominal concentration of 250 ng were carried out with the following thermocyclers in 4-fold determination with the same mastermix and 2 blank samples (without DNA): Thermocycler Eppendorf Mastercycler ep-S (Eppendorf AG, Hamburg), Applied Biosystems® GeneAmp 9700 with silver block (Life Technology GmbH, Darmstadt), Applied Biosystems® GeneAmp 9700 with aluminum block (Life Technology GmbH, Darmstadt).

Results: Correct assignments of all amplificates was observed on all types of thermocycler. All fragments of the template mixture were successfully amplified.

A f) PCR Annealing Temperatures

Objective: To determine the robustness of the PCRs, temperature fluctuations are simulated for the primer annealing step in the multiplex PCR. This temperature step is critical for the sensitivity and specificity of the PCRs.

47


Methods: The kite-specific annealing temperature of 60°C for the standard reaction with control cDNA in the nominal concentration of 250 ng was varied by ± 1°C and ± 2°C. A 3-fold determination with the same master mix was applied.

Results: The kit proved to be stable at ± 1°C by the specified annealing temperature. Optimum signal heights of all systems are reached with the annealing temperature of 61°C.

A g) Fluctuations of PCR buffer Batches

Objective: The concentration ratios of the ingredients of the PCR buffer REM A (dNTPs, ion concentrations, in particular Mg2+) are critical for the sensitivity, specificity and balance of the signals in the multiplex PCR. Therefore the robustness of the test is analysed towards batch fluctuations of the supplied PCR buffer.

Methods: 3 independent REM-A batches were tested in the standard reaction with control DNA of the nominal concentration of 250 ng, as well as the allelic-ladder and a cDNA line with weak expression (MLL-AF6).

Results: Each newly produced batch REM A will be tested with the Mentype® AMLplexQS amplification kit. Approval of respective REM A batch will only be provided, if the results obtained with the Mentype® AMLplexQS are within the specification.

A h) In-use stability

Objective: The stability of the reagents of the PCR kit was tested after repeated freezing and thawing.

Methods: The kit reagents were subjected to a 20-fold freezing and thawing cycle. The freezing was carried out for at least 1 h at -20°C. The mixture was thawed at room temperature and the reagents were homogenized by shaking before use. Subsequently, a standard reaction with control DNA of the nominal concentration of 250 ng and additional blank values without DNA was performed in triplicate determinations. The evaluation was carried out in comparison to a standard reaction without freezing and thawing cycle.

Results: The deviation of averaged peak heights compared to the standard reaction was a maximum of 20% (in particular signal loss). No additional peaks > 50 RFU were found within the scaling range for the blanc values.


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B Clinical Performance Data

B a) Study Design, ethics and regulatory aspects

A clinical performance study was conducted according to §§ 20 - 24 of German Medizinproduktegesetz. The protocol was approved by the National Competent Authory BfArM according to § 7 German Verordnung über klinische Prüfungen von Medizinprodukten and by the institutional ethics committee. All participants (10 volunteers, 297 patients) gave written informed consent.

B b) Reference Methods

The primary target is the determination of diagnostic sensitivities and specificities in comparison to the reference methods. Standardized cytogenetic methods (karyotyping, FISH analyzes) were available for a selection of the translocations [8]. Validated and established monoplex-nested-PCR assays were used for translocations that could not be addressed cytologically [9, 10].

B c) DNA-Extraction and Purification

Mononuclear cells (MNC) were collected from heparinised whole blood by density gradient centrifugation. Subsequently, total mRNA was isolated using commercially available mRNA extraction kits (RNeasy Mini Kit, Qiagen GmbH, Hilden, DE). Reverse transcription to cDNA was performed with commercially available kits. The quality of the cDNA was analyzed by real-time PCR (QuantiTect Reverse Transcription Kit, Qiagen GmbH, Hilden, DE). Validated in-house single PCR assays served to confirm the fusion genes and mutations.

B d) Results

The Mentype® AMLplexQS PCR amplification kit showed no false positive results by the analysis of the cDNA from 10 healthy volunteers. In total, 297 patient samples were examined. Out of these, 5 samples could not be evaluated (control signal for BCR-ABL below the recommended threshold). Of the remaining 292 samples, 199 were found to be correctly negative as compared to karyotyping, FISH and / or control PCR. Of the correctly negative samples, 56 in the karyogram showed genetic changes (chromosomal anomalies), which could not be recognized by the test kit. This can be explained by the fact that the Mentype® AMLplexQS PCR amplification kit, although containing the most frequent translocations, only covers approximately 37% of the genetic abnormalities frequently observed in AML [8]. The individual results of the comparison tests are summarized in Table 5.

49


Overall, a diagnostic sensitivity of 94% and a diagnostic specificity of 99.5% were achieved. All cytogenetic findings verified by control PCR [9, 10] were clearly confirmed.

Table 5: Conclusion of the clinical performance data.

Biomarker Bewertung der Leistungsbewertungsprüfung (n=292)

Genfusion Chromosomale

Aberration

Variante Prävalenz

bei AML [%]

(Grimwade

et al. 2010)

Richtig

positiv

Richtig

negativ

Falsch

postiv

Falsch

negativ

Diagnostische

Sensitivität [%]

Diagnostische

Spezifität [%]

AML1-ETO t(8;21) (q22;q22) n. b. 7 14 277 0 1 93.3 100.0

BCR-ABL t(9;22) (q34;q11) e1a3 1 1 291 0 0 100.0 100.0

e1a2

b3a2

b3a3

b2a2

b2a3

CALM-AF10 t(10;11) (p13;q14) AF10_240-CALM_1987 1 0 292 0 0 n.b. 100.0

AF10_240-CALM_2092

CBFB-MYH11 inv(16) (p13;q22) Type A 5 25 264 1 2 92.6 99.6

Type B

Type C

Type D

Type E

Type F

Type G

Type H

Type J

DEK-CAN t(6;9) (p23;q34) n. b. 1 3 289 0 0 100.0 100.0

MLL-AF6 t(6;11) (q27;q23) n. b. <0,5 0 292 0 0 n.b 100.0

MLL-AF9 t(9;11) (p22;q23) 6A_(THP-1) 1 4 287 0 1 80.0 100.0

7A_(10A)

8A_(MM6)

6B_(9B)

MLL-ELL t(11;19) (q23;p13.1) e10e2 1 0 291 0 1 0.0 100.0

e10e3

MLL-PTD Partial Tandem

Duplication

e9e3 5 bis 7 23 269 0 0 100.0 100.0

e10e3

e11e3

NPM1-MLF1 t(3;5) (q25.1;q34) n. b. <0,5 1 291 0 0 100.0 100.0

PML-RARA t(15;17) (q22;q21) bcr1 (PR-L) 13 8 284 0 0 100.0 100.0

bcr2 (PR-V)

bcr3 (PR-S)

Gesamt ca. 37 79 207 1 5 94.0 99.5


50

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Soekarman D, von Lindern M, Daenen S, de Jong B, Fonatsch C, Heinze B, Bartram C, Hagemeijer A, Grosveld G. The translocation (6;9) (p23;q34) shows consistent rearrangement of two genes and defines a myeloproliferative disorder with specific clinical features. Blood. 1992 Jun 1;79(11):2990-7. PubMed PMID: 1586743.

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Corbacioglu A, Scholl C, Schlenk RF, Eiwen K, Du J, Bullinger L, Fröhling S, Reimer P, Rummel M, Derigs HG, Nachbaur D, Krauter J, Ganser A, Döhner H, Döhner K. Prognostic impact of minimal residual disease in CBFB-MYH11-positive acute myeloid leukemia. J Clin Oncol. 2010 Aug 10;28(23):3724-9. Epub 2010 Jul 12. PubMed PMID: 20625124.

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Prasad R, Gu Y, Alder H, Nakamura T, Canaani O, Saito H, Huebner K, Gale RP, Nowell PC, Kuriyama K, et al. Cloning of the ALL-1 fusion partner, the AF-6 gene, involved in acute myeloid leukemias with the t(6;11) chromosome translocation. Cancer Res. 1993 Dec 1;53(23):5624-8. PubMed PMID: 8242616.

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53


References: MLL-AF9, t(9;11)(q22;q23):

Giugliano E, Rege-Cambrin G, Scaravaglio P, Serra A, Wlodarska I, Emanuel B, Saglio G, Hagemeijer A. MLL-AF6 fusion resulting from a new three-way translocation t(6;11;7) in a patient with acute myeloid leukemia. Leukemia. 2001 Oct;15(10):1674-6. PubMed PMID: 11587234.

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References: MLL-ELL, t(11;19)(q23;p13.1):

Huret JL, Brizard A, Slater R, Charrin C, Bertheas MF, Guilhot F, Hählen K, Kroes W, van Leeuwen E, Schoot EV, et al. Cytogenetic heterogeneity in t(11;19) acute leukemia: clinical, hematological and cytogenetic analyses of 48 patients--updated published cases and 16 new observations. Leukemia. 1993 Feb;7(2):152-60. Review. PubMed PMID: 8426468.

Mitani K, Kanda Y, Ogawa S, Tanaka T, Inazawa J, Yazaki Y, Hirai H. Cloning of several species of MLL/MEN chimeric cDNAs in myeloid leukemia with t(11;19)(q23;p13.1) translocation. Blood. 1995 Apr 15;85(8):2017-24. PubMed PMID: 7718874.

References: MLL-PTD, Partial Tandem Duplication:

Basecke J, Whelan JT, Griesinger F, Bertrand FE. The MLL partial tandem duplication in acute myeloid leukaemia. Br J Haematol. 2006 Nov;135(4):438-49. Epub 2006 Sep 11. Review. PubMed PMID: 16965385.


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Pajuelo-Gámez JC, Cervera J, García-Casado Z, Mena-Durán AV, Valencia A, Barragán E, Such E, Bolufer P, Sanz MA. MLL amplification in acute myeloid leukemia. Cancer Genet Cytogenet. 2007 Apr 15;174(2):127-31. PubMed PMID: 17452254.

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References: PML-RARA, t(15;17)(q22;q21):

Alcalay M, Zangrilli D, Pandolfi PP, Longo L, Mencarelli A, Giacomucci A, Rocchi M, Biondi A, Rambaldi A, Lo Coco F, et al. Translocation breakpoint of acute promyelocytic leukemia lies within the retinoic acid receptor alpha locus. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):1977-81. PubMed PMID: 1848017; PubMed Central PMCID: PMC51149.

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Notes


58

Notes

mentype amlplex qs...primer for each transcript is fluorescence-labelled with 6-fam, btg, bty. the...

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