PANA RealTyper HPV 32 Genotyping - 240625 - 105140
PANA RealTyper HPV 32 Genotyping - 240625 - 105140
Version 2.0
PNAM-1101
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PANA RealTyperTM HPV 32 Genotyping kit
Contents
IX. PROCEDURES......................................................................................... 9
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PANA RealTyperTM HPV 32 Genotyping kit
I. INTENDED USE
The PANA RealTyperTM HPV 32 Genotyping kit is an reagent for detecting human papilloma
virus (HPV) using peptide nucleic acid (PNA) probes. This kit is a DNA amplification test for the
qualitative detection of a total of 32 types of HPV by using a real-time PCR (polymerase chain
reaction) system. This kit enables target classification by type (20 high-risk and 12 low-risk types)
based on melting temperature (Tm) analysis.
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PANA RealTyperTM HPV 32 Genotyping kit
The PANA RealTyperTM HPV 32 Genotyping kit employs PNA-based fluorescence melting
curve analysis technology and a real-time PCR system. Each target-specific PNA probe, which is
conjugated with a fluorescent dye and a quencher, is used. The PNA probe is designed to hybridize
only to its specific target sequence and the specific binding is interfered by even a single base
mismatch. Therefore, the PNA probe shows highly specific target detection property and can be used
to detect multiple targets in single reaction tube.
The PANA RealTyperTM HPV 32 Genotyping kit determines whether the target HPV is detected
via melting curve analysis (measuring a melting temperature). Each specific PNA probe for detecting
a total of 32 types of HPV has unique Tm range and its own fluorescent dye, which enables improved
multi-detection. In detail, three tubes of reaction premix (HPV Mix #A, #B, and #O) contain
fluorescent dye (FAM, HEX, ROX, or Cy5) and quencher conjugated PNA probes designed for each
target. Clinical samples with multiple infections of different types of HPV could be assessed
accurately.
The PANA RealTyperTM HPV 32 Genotyping kit is designed to detect L1 gene fragment in HPV
genome. Viral and human DNA is extracted from clinical specimens simultaneously (Specimen
collection and DNA extraction kits are not part of the kit).
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PANA RealTyperTM HPV 32 Genotyping kit
For any questions including technical support, please contact the distributors or the manufacturer.
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PANA RealTyperTM HPV 32 Genotyping kit
◆ It is recommended to use PCR system and plastic consumables below for the best performance.
Company Model
Bio-Rad CFX96 real-time PCR detection system (CFX96)
ThermoFisher QuantStudio® 5 (QS5)
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PANA RealTyperTM HPV 32 Genotyping kit
✓ Please read instructions below carefully and become familiar with all components of the kit
prior to use.
✓ This kit (PANA RealTyperTM HPV 32 Genotyping kit) is for research use only.
✓ This kit should be used by trained laboratory professionals.
✓ All experiments should be performed under proper clean conditions in order to prevent
contamination. It is recommended that a user has separate, dedicated pipettes and pipette tips
with filter to add DNA template and prepare PCR reagents.
✓ Always wear powder-free gloves when you handle the kit.
✓ To avoid repeated freezing and thawing, aliquot all reagents into appropriate volumes and
store frozen until use. Thaw appropriate volumes of reagents before each experiment.
✓ All experimental procedures should be performed at room temperature. However, please
minimize the exposure time of Taq DNA polymerase to room temperature for the optimal
performance.
✓ Dissolve reagents completely and mix them thoroughly by vortex.
✓ Tubes should be briefly centrifuged before use.
✓ Tubes containing PNA probe should be protected from prolonged exposure to light.
✓ Use only recommended instrument and consumables only (page 6). If not, it may cause loss of
performance and increase the chance of false result.
✓ Additional validation test by a user may necessary when non-recommended instrument and
consumable is used.
✓ Do not use incorrect volume of reagent or target DNA; it may cause loss of performance and
increase the chance of false result.
✓ Do not interchange or mix reagents from different lots or other manufacture’s product.
✓ After the reaction is completed, do not reuse any of the reagents that you have prepared.
✓ Do not use the expired product.
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PANA RealTyperTM HPV 32 Genotyping kit
The PANA RealTyperTM HPV 32 Genotyping kit is shipped on ice packages and must still be
frozen on arrival. If the kit is not frozen on arrival please contacts HLB Panagene or the local
distributor. (see back cover)
The PANA RealTyperTM HPV 32 Genotyping kit should be stored immediately upon receipt at -
20℃ or below. When stored under the recommended storage conditions the kit is stable until the
labeled expiration date. After open the kit, reagents can be stored in their original packaging at -20℃
or below for 90 days or until the expiration date, whichever comes first.
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PANA RealTyperTM HPV 32 Genotyping kit
IX. PROCEDURES
Specimen collection, DNA extraction reagents and accessories for extracting DNA are not
included in the kit so they should be provided by the user.
2) Ideally, cervical specimens should be processed on the same day when they are collected.
Alternatively, they can be stored at 4°C for maximum seven days.
Maxwell® 16 Viral Total Nucleic Acid Purification Kit Promega (USA) AS1150
4) Extracted DNA can be stored at 4°C for up to seven days or at -20°C for long-term storage.
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PANA RealTyperTM HPV 32 Genotyping kit
* Prepare one extra volume for each component to compensate pipette error.
1) Prepare three reagent mixes (HPV Mix #A, #B, and #O) after thaw, vortex and spin down at
room temperature.
2) Prepare test sample (extracted DNA) and control samples (NC and PC).
3) Prepare 3 PCR tubes (or wells) for one DNA sample to be tested. Label them as A1, B1, and
O1, if it is necessary.
4) Load 19 µl of each reagent mix (HPV Mix #A, #B, or #O) into a strip tube or the PCR plate.
For example, A1 tube (or well) will contain HPV Mix #A, B1 tube (or well) will contain HPV
Mix #B, O1 tube (or well) will contain HPV Mix #O.
5) Add 1 µl of Taq DNA polymerase to the strip tubes or the PCR plate.
6) Add 5 µl of prepared test sample into each strip tubes or each well of the PCR plate to yield a
total 25 l of final volume.
7) One set of PC and NC for each HPV Mix should be included in each run. Add 5 µl of PC or
NC into strip tubes or wells of the PCR plate to yield a total 25 l of final volume.
8) Immediately seal the PCR plate tightly and spin down. Otherwise, the PCR mixture can be
evaporated and the result of the test may not accurate.
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PANA RealTyperTM HPV 32 Genotyping kit
3. Real-time PCR
1) Place the prepared strip tubes or the PCR plate on the block of a real-time PCR instrument.
2) Please set the PCR protocol according to following Table 5.
3) Select four fluorescent dyes (FAM, HEX(or VIC), ROX, and Cy5) for all reaction wells (*).
Table 5. Real-time PCR protocol for PANA RealTyperTM HPV 32 Genotyping kit.
ONE CYCLE
Pre-incubation 50°C 2 min
Initial denaturation 95°C 15 min
3-STEP CYCLING (45 CYCLES)
Denaturation 95°C 15 sec
Annealing and
55°C 45 sec
Detection*
Extension 72°C 15 sec
MELTING CURVE ANALYSIS
95°C 5 min
35°C 5 min
35°C to 80°C (0.5°C increment)* 5 sec / step
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PANA RealTyperTM HPV 32 Genotyping kit
4. Result analysis
1) Set the baseline cut-off (threshold) of melting peak analysis of each fluorescent dye in each
tube according to Table 6.
2) Determine whether each target HPV is detected according to the following criteria in Table 7.
Tm values are rounded to second decimal places and applied to the criterion.
Tm range “A – B” means “A ≤ Tm ≤ B”.
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PANA RealTyperTM HPV 32 Genotyping kit
3) Interpretation of results
Target HPV negative: 32 types of HPV tested are not detected (†)
Positive result of internal control (HBB) and negative results in all of three HPV Mixes indicate no
detection of HPV DNA in the clinical sample. However, it cannot rule out the possibility that non-
targeted HPV genotypes can be presence in the tested clinical sample. “Target HPV negative” result
does not preclude the presence of HPV in the clinical sample because results depend on adequate
specimen integrity, absence of inhibitors, and sufficient DNA to be detected.
Invalid (#)
A clinical test is invalid when internal control (HBB) and all of three HPV Mixes show negative
results. It may denote that the amplification of HPV DNA sample is failed or the amount of isolated
DNA is not sufficient. Please repeat the entire test procedure for that clinical sample, starting with
DNA isolation.
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PANA RealTyperTM HPV 32 Genotyping kit
[Step 2] For some multiple detections, correct the results according to the table below.
Multiple detection of
Ignore the detection result of HPV 43
HPV 34 and HPV 43
Multiple detection of
Ignore the detection result of HPV 32
HPV 43 and HPV 32
Additional criteria is necessary to accurately determine the results by considering some cross-
amplification due to high similarities in target sequence of specific HPV types.
The assay must be repeated if the results of NC and PC do not match the following.
Positive Control
HPV Mix #A HPV Mix #B HPV Mix #O
Fluorescent Dye
(Tm range, ℃) (Tm range, ℃) (Tm range, ℃)
FAM 55.0 - 60.0 60.0 - 65.0 -
HEX (or VIC) 45.0 - 50.0 47.0 - 51.0 43.5 - 49.0
ROX 56.0 - 61.0 56.0 - 65.0 -
Cy5 50.0 - 55.0 50.0 - 55.0 65.0 - 73.0
Tm range “A – B” means “A ≤ Tm ≤ B”.
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PANA RealTyperTM HPV 32 Genotyping kit
X. EXAMPLES OF ANALYSIS
1. CFX96
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A All - Negative
HPV Mix #B All - Negative Acceptable
HPV Mix #O Cy5 72.5℃ Valid
Fluorescent
Reagent Melting temperature Assessment Result
Dye
FAM 59°C
HEX 48.5°C
HPV Mix #A Positive
ROX 59°C
Cy5 52.5°C
FAM 62.5°C
Acceptable
HEX, 49.5°C
HPV Mix #B Positive
ROX 62.5°C
Cy5 54.5°C
HEX 47.5℃ Positive
HPV Mix #O
Cy5 72.5℃ Valid
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PANA RealTyperTM HPV 32 Genotyping kit
3) Sample 1
HPV Mix # A HPV Mix # B HPV # Mix O
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A FAM 59°C Positive
4) Sample 2
HPV Mix # A HPV Mix # B HPV # Mix O
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A All - Negative
FAM 64°C Type
HPV Mix #B Positive
Cy5 45.5°C 51 & 35
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PANA RealTyperTM HPV 32 Genotyping kit
5) Sample 3
HPV Mix # A HPV Mix # B HPV # Mix O
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A ROX 59.5°C Positive
Type
HPV Mix #B FAM 63.5°C Positive
18 & 35
HPV Mix #O Cy5 72.5℃ Valid
6) Sample 4
HPV Mix # A HPV Mix # B HPV # Mix O
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A All - Negative
HPV Mix #B All - Negative
Type
FAM 65.0℃ Positive
34 & 43
HPV Mix #O ROX 64.5℃ Positive
Cy5 70.5℃ Valid
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PANA RealTyperTM HPV 32 Genotyping kit
7) Sample 5
HPV Mix # A HPV Mix # B HPV # Mix O
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A All - Negative
HPV Mix #B HEX 53.5°C Positive Type 59
HEX 46.0°C Positive & 61
HPV Mix #O
Cy5 - Invalid
8) Sample 6
HPV Mix # A HPV Mix # B HPV # Mix O
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A All - Negative
HPV Not
HPV Mix #B All - Negative
detected
HPV Mix #O Cy5 70.5°C Valid
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PANA RealTyperTM HPV 32 Genotyping kit
2. QuantStudio® 5
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A All - Negative
HPV Mix #B All - Negative Acceptable
HPV Mix #O Cy5 72.7°C Valid
Fluorescent
Reagent Melting temperature Assessment Result
Dye
FAM 59.6°C
HEX 49.1°C
HPV Mix #A Positive
ROX 60.3°C
Cy5 52.1°C
FAM 64.8°C
Acceptable
HEX, 50.1°C
HPV Mix #B Positive
ROX 64.0°C
Cy5 54.1°C
HEX 47.2°C Positive
HPV Mix #O
Cy5 73.0°C Valid
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PANA RealTyperTM HPV 32 Genotyping kit
3) Sample 1
HPV Mix # A HPV Mix # B HPV # Mix O
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A HEX 49.1°C Positive
Type
HPV Mix #B All - Negative
16
HPV Mix #O Cy5 - Invalid
4) Sample 2
HPV Mix # A HPV Mix # B HPV # Mix O
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A All - Negative
Type
HPV Mix #B FAM 63.3°C Positive
35
HPV Mix #O Cy5 - Invalid
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PANA RealTyperTM HPV 32 Genotyping kit
5) Sample 3
HPV Mix # A HPV Mix # B HPV # Mix O
Fluorescent
Reagent Melting temperature Assessment Result
Dye
HPV Mix #A All - Negative
HPV Mix #B All - Negative Type
ROX 50.9°C Positibve 40
HPV Mix #O
Cy5 - Invalid
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PANA RealTyperTM HPV 32 Genotyping kit
Ⅺ. REFERENCES
1. Choi, J. J. et al. Peptide nucleic acid-based array for detecting and genotyping human
papillomaviruses. J. Clin. Microbiol. 2009; 1785-1790.
2. Gerard, J. et al. Correlation of Pap smear, cervical biopsy, and clinical follow-up with an HPV
typing microarray system. Diagn. Mol. Pathol. 2008; 17:107-111.
3. Debbie Saslow et al. American Cancer Society, American Society for Colposcopy and
Cervical Pathology, and American Society for Clinical Pathology Screening Guidelines for the
Prevention Early Detection of cancer. Am. J. Olin. Pathol/ 2012; 137 : 516-542.
4. Abreu, et al. A review of methods for detect human Papillomavirus infection. Virol. J. 2012,
9:262.
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PANA RealTyperTM HPV 32 Genotyping kit
XIII. ENDNOTE
The kit itself or any of the components in the kit cannot be modified, re-sold or transferred without
the approval of manufacturer. Information in this document is subject to change.
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