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PANA RealTyper HPV 32 Genotyping - 240625 - 105140

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0% found this document useful (0 votes)
452 views23 pages

PANA RealTyper HPV 32 Genotyping - 240625 - 105140

Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 23

PANA RealTyperTM HPV 32 Genotyping kit

PANA RealTyper™ HPV 32 Genotyping kit

For research use only

Instruction manual for product # PNAM-1101

Version 2.0

PNAM-1101

Store at -20°C or below

Instruction Version: 2.0


Date of Revision: Aug, 2023

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PANA RealTyperTM HPV 32 Genotyping kit

Contents

I. INTENDED USE ........................................................................................ 3

II. PRINCIPLE AND OVERVIEW .............................................................. 4

III. CONTACT INFORMATION ................................................................. 5

IV. SAFETY INFORMATION ...................................................................... 5

V. EQUIPMENT AND MATERIALS SUPPLIED BY THE USER ......... 6

VI. WARNINGS AND PRECAUTIONS ....................................................... 7

VII. STORAGE CONDITION AND STABILITY ........................................ 8

VIII. KIT CONTENTS ...................................................................................... 8

IX. PROCEDURES......................................................................................... 9

1. SAMPLE PREPARATION AND STORAGE ................................................. 9

2. PREPARATION OF THE REAL-TIME PCR MIXTURE ............................ 10

3. REAL-TIME PCR ......................................................................................... 11

4. RESULT ANALYSIS ..................................................................................... 12

X. EXAMPLES OF ANALYSIS .................................................................. 15

XI. REFERENCES ........................................................................................ 22

XII. EXPLANATION OF SYMBOLS ON THE LABEL ........................... 22

XIII. ENDNOTE .............................................................................................. 23

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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.

Detectable genotypes by PANA RealTyperTM HPV 32 Genotyping kit

[ High-risk genotypes (20 genotypes) ]


- 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 69, 70, 73, and 82

[ Low-risk genotypes (12 genotypes) ]


- 6, 11, 32, 34, 40, 42, 43, 44, 54, 61, 72 and 81

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PANA RealTyperTM HPV 32 Genotyping kit

II. PRINCIPLE AND OVERVIEW

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).

Figure 1. Principle of the PANA RealTyper™ HPV 32 Genotyping kit

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PANA RealTyperTM HPV 32 Genotyping kit

III. CONTACT INFORMATION

For any questions including technical support, please contact the distributors or the manufacturer.

Manufacturer: HLB Panagene Co., Ltd


54, Techno 10-ro, Yuseong-gu, Daejeon, 34027, Korea
Email: [email protected]
Tel: +82 42 861 9296

IV. SAFETY INFORMATION

Material Safety Data Sheets (MSDS) are available upon request.

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PANA RealTyperTM HPV 32 Genotyping kit

V. EQUIPMENT AND MATERIALS SUPPLIED BY THE USER

✓ Reagents and equipment for DNA extraction


✓ Pipettes (capacity 10 µl, 20 µl, and 200 µl)
✓ Pipette tips with filter
✓ Bench top micro-centrifuge
✓ Vortex mixer
✓ Disposable gloves (powder free)
✓ PCR tubes (DNase-free)

◆ It is recommended to use PCR system and plastic consumables below for the best performance.

➢ PCR plate, 96-well, recommended by each instrument


In case of CFX-96, Catalog No. MLL-9651, white, Bio-Rad
In case of QuantStudio® 5, Catalog No. N8010560, ThermoFisher
➢ Adhesive seals, recommended by each instrument
In case of CFX-96, Catalog No. MSB-1001, Bio-Rad
In case of QuantStudio® 5, Catalog No. 4311971, ThermoFisher
➢ Real-time PCR system (Table 2)

Table 1. Compatible real-time PCR instruments

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

VI. WARNINGS AND PRECAUTIONS

✓ 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

VII. STORAGE CONDITION AND STABILITY

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.

VIII. KIT CONTENTS

◆ A total of 48 samples can be tested using a kit.

Table 2. Reagents provided in the PANA RealTyperTM HPV 32 Genotyping kit.

No. Name of content Description Volume Label & color of cap

1 HPV Mix #A HPV PNA probes and primers 1000 l HPV #A

2 HPV Mix #B HPV PNA probes and primers 1000 l HPV #B

HPV PNA probes, HBB PNA


3 HPV Mix #O 1000 l HPV #O
probe, and primers
4 Taq DNA polymerase Taq DNA polymerase 170 l Taq

5 Positive Control (PC) Positive Control 100 l P.C

6 Negative Control (NC) Negative Control 100 l N.C

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PANA RealTyperTM HPV 32 Genotyping kit

IX. PROCEDURES

Figure 2. Workflow of the PANA RealTyperTM HPV 32 Genotyping kit.

1. Sample preparation and storage

Specimen collection, DNA extraction reagents and accessories for extracting DNA are not
included in the kit so they should be provided by the user.

1) A Swab Sampler should be used for the collection of cervical specimen.

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.

3) DNA can be isolated using one of recommended kits in Table 3.

Table 3. The list of recommended DNA isolation kit.

Model Company Catalog number


GeneAll
Exgene Tissue SV 104-152
(Republic of Korea)
QIAamp DNA Blood Mini Kit Qiagen (USA) 51104

Insta Gene Matrix Bio-Rad (USA) 732-6030

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

2. Preparation of the real-time PCR reaction mixture

Table 4. Set up reaction mixture per one reaction.


Reagent Volume*
HPV mix (HPV Mix #A, #B, or #O, respectively) 19 l
Taq DNA polymerase 1 l
Extracted DNA, PC, or NC 5 l
Total volume 25 l

* 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.

Table 6. Baseline cut-off values for Tm determination


HPV Mix Fluorescent Dye Baseline cut-off criteria
CFX96 QS5
FAM ≥ 100 ≥ 10,000
HEX (or VIC) ≥ 50 ≥ 5,000
HPV Mix #A
ROX ≥ 50 ≥ 5,000
Cy5 ≥ 150 ≥ 15,000
FAM ≥ 100 ≥ 10,000
HEX (or VIC) ≥ 50 ≥ 5,000
HPV Mix #B
ROX ≥ 50 ≥ 5,000
Cy5 ≥ 80 ≥ 8,000
FAM ≥ 100 ≥ 10,000
HEX (or VIC) ≥ 50 ≥ 5,000
HPV Mix #O
ROX ≥ 70 ≥ 7,000
Cy5 ≥ 100 ≥ 10,000

2) Determine whether each target HPV is detected according to the following criteria in Table 7.

Table 7. Criteria for target HPV detection.

HPV Mix #A HPV Mix #B HPV Mix #O


Fluorescent Tm range Fluorescent Tm range Fluorescent Tm range
Type Type Type
Dye (℃) Dye (℃) Dye (℃)
HPV 33 45.0 - 49.5 HPV 53 48.0 - 56.0 HPV 32 43.0 - 50.0
FAM
HPV 11 FAM 55.0 - 60.0 HPV 35 60.0 - 65.0 HPV 42 FAM 54.0 - 60.0
HPV 58 60.5 - 67.0 HPV 39 47.0 - 51.0 HPV 34 62.0 - 68.0
HPV 16 45.0 - 50.0 HPV 59 HEX 52.0 - 55.0 HPV 61 43.5 - 49.0
HEX
HPV 73 61.0 - 65.0 HPV 31 58.0 - 64.0 HPV 81 HEX 53.0 - 58.5
HPV 45 43.0 - 49.0 HPV 68 39.0 - 49.5 HPV 72 59.0 - 71.0
HPV 18 ROX 56.0 - 61.0 HPV 70 ROX 50.0 - 55.0 HPV 40 42.0 - 52.0
HPV 69 66.0 - 70.0 HPV 56 56.0 – 65.0 HPV 44 ROX 55.0 - 60.5
HPV 26 42.0 - 46.0 HPV 51 43.0 - 47.0 HPV 43 62.0 - 67.5
HPV 6 Cy5 50.0 - 55.0 HPV 66 Cy5 50.0 - 55.0 HPV 54 52.0 - 56.0
Cy5
HPV 52 59.5 - 64.0 HPV 82 58.0 – 62.0 HBB 65.0 - 73.0

 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

[Step 1] Test results are interpreted as shown in Table 8.

Table 8. Results interpretation of PANA RealTyperTM HPV 32 Genotyping kit


Target HPV
Internal control (HBB) Interpretation
(in Mix #A, #B, or #O)
Detected Detected Target HPV positive (Valid)*
Detected Not detected Target HPV negative (Valid)†
Not detected Detected Target HPV positive (Valid)*
Not detected Not detected Invalid#

Target HPV positive (*)


Positive results in HPV Mixes indicate presence of HPV DNA in the clinical sample even internal
control shows negative result. Type of target HPV should be identified from criteria in Table 7.

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.

Table 9. Additional criteria for correcting multiple detection results

Case Additional criteria

If the detection signal (melting peak height) of HPV 32


Multiple detection of
does not exceed 200 (CFX96) / 20,000 (QS5),
HPV 34 and HPV 32
ignore the detection result of HPV 32

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.

4) Assessment of results by negative control (NC) and positive control (PC)

The assay must be repeated if the results of NC and PC do not match the following.

Table 10. Acceptable results for NC and PC


Negative Control
HPV Mix #A HPV Mix #B HPV Mix #O
Fluorescent Dye
(Tm range, ℃) (Tm range, ℃) (Tm range, ℃)
FAM - - -
HEX (or VIC) - - -
ROX - - -
Cy5 - - 65.0 - 73.0

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

1) Negative Control (NC)


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 Acceptable
HPV Mix #O Cy5 72.5℃ Valid

2) Positive Control (PC)


HPV Mix # A HPV Mix # B HPV # Mix O

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

HPV Mix #B All - Negative Type 11

HPV Mix #O Cy5 71℃ Valid

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

HPV Mix #O Cy5 70.5℃ Valid

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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

1) Negative Control (NC)


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 Acceptable
HPV Mix #O Cy5 72.7°C Valid

2) Positive Control (PC)


HPV Mix # A HPV Mix # B HPV # Mix O

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.

Ⅻ. EXPLANATION OF SYMBOLS ON THE LABEL

Batch Code Use by (YYYY.MM.DD)

Manufacturer Research Use Only product

Temperature Limitation Catalogue number

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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.

HLB Panagene Co., Ltd

54, Techno 10-ro, Yuseong-gu, Daejeon, 34027, Korea


Tel: +82-42-861-9296
Fax: +82-42-861-9297
E-mail: [email protected] (for general inquiry)
[email protected] (for order and quotation inquiry)
[email protected] (for technical inquiry)
Website: www.hlbpanagene.com

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