WO2010058357A1 - Séquences nucléotidiques, procédés et kits pour détecter le vph - Google Patents

Séquences nucléotidiques, procédés et kits pour détecter le vph Download PDF

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Publication number
WO2010058357A1
WO2010058357A1 PCT/IB2009/055158 IB2009055158W WO2010058357A1 WO 2010058357 A1 WO2010058357 A1 WO 2010058357A1 IB 2009055158 W IB2009055158 W IB 2009055158W WO 2010058357 A1 WO2010058357 A1 WO 2010058357A1
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WO
WIPO (PCT)
Prior art keywords
hpv
nucleic acid
acid molecule
probes
subtypes
Prior art date
Application number
PCT/IB2009/055158
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English (en)
Inventor
Joseph Tam
Kwok Fai Joseph Chow
Rhys Cheuk Yu Chan
Original Assignee
Diagcor Bioscience Incorporation Ltd.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Diagcor Bioscience Incorporation Ltd. filed Critical Diagcor Bioscience Incorporation Ltd.
Priority to EP09827253.7A priority Critical patent/EP2358910B1/fr
Priority to CN200980144854.4A priority patent/CN102209793B/zh
Priority to PL09827253T priority patent/PL2358910T3/pl
Publication of WO2010058357A1 publication Critical patent/WO2010058357A1/fr

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • C12Q1/708—Specific hybridization probes for papilloma
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • This invention relates to nucleotide sequences, methods and kits for detecting human papillomavirus (HPV), particularly those for detecting multiple subtypes of HPV with a relatively small number of nucleotide sequences as probes.
  • HPV human papillomavirus
  • Cervical cancer is one of the most common cancers in woman. The worldwide death rate was estimated to be 273,500 in 2002, and increased to 320,000 in 2004. It was estimated that
  • Cervical cancer was found to be closely related to human papillomavirus (HPV) infection, which causes a precancerous stage, cervical intraepithelial neoplasia (CIN), during the cancer development. Therefore, HPV detection plays an important role in preventing and treating cervical cancer.
  • HPV human papillomavirus
  • the methods for detection of HPV in human using nucleotide sequences can be classified into two groups. Those of the first group differentiate the subtypes of HPV while detecting the presence of HPV in human samples, and examples includes Roche® AMPLICORTM HPV Test and LINEAR ARRAYTM HPV Genotyping Test; Innogentics® INNO-LiP ATM HPV Genotyping Extra; CN200410037617.7 of Decipher Bioscience (Shenzhen) LTD; and CN200610061044.0 of Longyang Bioscience (Shenzhen) LTD. This group of methods generally require the presence of one nucleotide probe specific for each of the subtypes of HPV to be detected and these probes must be in separate locations (i.e.
  • HCII Digene Hybrid Capture® II
  • the HCII is further subdivided into high risk and low risk types, which detect HPV DNA directly using liquid hybridization in clinical samples without amplification of the target viral DNA and instead it uses the chemiluminescence signal amplification technology.
  • the signal to noise ratio is low at relatively low target concentration and therefore the detection sensitivity is much lower that that of the PCR based test.
  • RNA probe may pose low stability of the kit and the possibility of contamination (the HCII is dependent on the cellular content of samples, rendering occasionally false positive and false negative results, i.e. nearby its detection cut off concentration the false positive/negative rates are reportedly higher), the HCII is also expensive.
  • specific RNA probes are used to capture the target subtype DNA to be tested, and therefore HCII also faces development limitations similar to those of the first group above (the genotyping assay), except that it is done in the liquid mixture without genotyping.
  • the HCII is able to detect only 18 subtypes of HPV (13 in HCII high risk type, and 5 in HCII low risk type), which are far less than the most commonly seen 38 subtypes of HPV in human. Some of the 150 plus rare subtypes of HPV are already confirmed high risk for cancer induction, and hence the ability of detecting these subtypes is also important to the diagnosis and prevention of cervical cancer.
  • HPV HPV in a sample at reduced costs.
  • this invention provides an isolated nucleic acid molecule selected from the group consisting of: (a) a sequence selected from the group consisting of SEQ ID NOS: 1-24 and 32; and (b) a sequence fully complementary to any of said nucleic acid molecule of (a).
  • an HPV detection kit which includes: a) at least one HPV probe for detecting HPV, each HPV probe being an isolated nucleic acid molecule selected from the group consisting of: (a) a sequence selected from the group consisting of SEQ ID NOS: 1-24; and (b) a sequence fully complementary to any of said nucleic acid molecule of (a); b) primers for amplifying HPV in sample DNA by polymerase chain reaction; and c) labels for labeling DNA that is amplified and hybridized to said DNA chip.
  • each HPV probe being an isolated nucleic acid molecule selected from the group consisting of: (a) a sequence selected from the group consisting of SEQ ID NOS: 1-24; and (b) a sequence fully complementary to any of said nucleic acid molecule of (a).
  • the current invention also provides an HPV detection kit including: a) at least two HPV probes for detecting at least thirty-six subtypes of HPV, each of said at least two HPV probes being an isolated nucleic acid molecule; b) primers for amplifying HPV in sample DNA by polymerase chain reaction; and c) labels for labeling DNA that is amplified and hybridized to said DNA chip.
  • the HPV detection kit and/or DNA chip consist of four HPV probes for detecting thirty-eight subtypes of HPV. More preferably, these four HPV probes respectively have sequences of SEQ ID NOS: 1-4 or SEQ ID NOS: 21-24.
  • the isolated nucleic acid molecule is DNA.
  • Figure 1 shows the images of the detection of various subtypes of HPV by exemplary nucleotide sequences of the current invention.
  • the present inventors have prepared detection probes for various subtypes of HPV having nucleotide sequences complementary to the DNA of HPV such that relatively few probes can detect most of the commonly seen subtypes of HPV. In a particular embodiment, at least 36 most commonly seen subtypes of HPV can be detected by various combinations of 2 to 4 HPV probes of the current invention.
  • the probes of the present invention comprise nucleotide sequences set forth in SEQ ID NOS: 1 - 24 (Table 1).
  • LNA modified base is marked by (+) in front of the base)
  • Probe 1 Type Probe 1 Probe 2 Probe 1 Probe 3 Probe 1 Probe 4 Probe 1 16 Probe 1 24 (HPV (HPV (HPV (HPV (HPV (HPV)
  • Tables 2 and 3 The results of the detection of multiple subtypes of HPV by each of the SEQ ID NOS: 1-24 are shown in Tables 2 and 3, in which Table 2 shows the results for the detection of common 38 subtypes of HPV, while Table 3 shows the results for rare subtypes of HPV.
  • Table 2 shows the results for the detection of common 38 subtypes of HPV
  • Table 3 shows the results for rare subtypes of HPV.
  • the results show that each of the sequences set forth in SEQ ID NOS: 1 - 24 is able to detect multiple subtypes of HPV.
  • various combinations of at least 2 to 4 of the sequences set forth in SEQ ID NOS: 1 - 24 is able to detect at least 36 common subtypes of HPV, which can be noted from the results of Tables 2 and 3.
  • a combination of HPV probes 1 and 2 can detect at least 36 subtypes of HPV, while other combinations of 2 HPV probes of the current invention can detect at least 37 or 38 subtypes of HPV.
  • Table 5 shows similar results for various combinations of 3 HPV probes of the current invention, that is, a combination of at least 3 HPV probes to detect at least 36, more specifically 37 or 38, subtypes of HPV.
  • the use of a combination of 4 HPV probes having respective sequences set forth in SEQ ID NOS: 1 - 4, that is, one probe has a sequence sets forth in SEQ ID NO 1, one probe has a sequence sets forth in SEQ ID NO 2, one probe has a sequence sets forth in SEQ ID NO 3, and one probe has a sequence sets forth in SEQ ID NO 4, is able to detect 38 common subtypes of HPV, including the high risk types 16, 18, 31, 33, 35, 45, 51, 52, 58, and 59.
  • sequences complementary to any of the sequences set forth in SEQ ID NOS: 1 - 24 are also useful for either detecting HPV, or for making nucleic acid molecules having the sequences set forth in SEQ ID NOS: 1 - 24. If desired, RNA of having the sequences set forth in SEQ ID NOS: 1 - 24 may be used, although DNA is generally preferred due to higher stability in the resulting detection kit and chip.
  • DNA wherein the nucleotide base includes those modified by various groups used for labeling signal generating; those used for modulating the Tm value of the annealing temperature and/or increase the stability of the molecules such as Locked Nucleic Acid (LNA) and Peptide Nucleic Acid (PNA) and RNA molecule.
  • LNA Locked Nucleic Acid
  • PNA Peptide Nucleic Acid
  • the detection kit of the current invention includes: a DNA chip with at least one probe that have nucleotide sequences complementary to DNA of HPV, more specifically the at least one HPV probe being an isolated nucleic acid molecule selected from the group consisting of: (a) a sequence selected from the group consisting of SEQ ID NOS: 1-24; and (b) a sequence fully complementary to any of said nucleic acid molecule of (a).
  • Primers for amplifying DNA obtained from clinical samples by PCR are also included.
  • known primers for amplifying DNA from the samples for detecting HPV shown in Table 7 below are used:
  • the detection kit also includes labeling agents for labeling amplified DNA hybridized with the probes of the DNA chip.
  • the DNA chip may further include position markers to locate probes, and staining or labeling is performed by using labeling agents such as biotin-binding material, for example a conjugate of a fluorophore and a protein with biotin-binding sites such as streptavidin-R-phycoerythrin, horseradish peroxidase, digoxigenin, chemiluminescence or fluorescent (FAM, HEX, Cys3, Cys5) and detected with a scanner.
  • labeling agents such as biotin-binding material, for example a conjugate of a fluorophore and a protein with biotin-binding sites such as streptavidin-R-phycoerythrin, horseradish peroxidase, digoxigenin, chemiluminescence or fluorescent (FAM, HEX, Cys3, Cys5) and detected with a scanner.
  • globin primers and probe may be included for monitoring the quality of the PCR process. These globin primers and probe are used to check whether the sample has DNA, and whether the DNA in the sample can be satisfactorily amplified. Examples of globin primers and probe are listed in Table 8 below, which can be used in the current invention:
  • the forward primer IC-F (New) is designed in the current invention that can replace the existing forward primer IC-F. With the use of this new primer IC-F (New), a larger PCR amplification is resulted, and is more compatible to the HPV detection kit of the current invention and hence to improve the kit detection efficiency.
  • the DNA chip used in the detection kit of the current invention may be prepared with the following known processes: 1. 5' terminal amine-linked DNA probes which have an isolated nucleic acid molecule selected from the group consisting of: (a) a sequence selected from the group consisting of SEQ ID NOS: 1-24; and (b) a sequence fully complementary to any of said nucleic acid molecule of (a) are prepared. 2. The prepared DNA probes are then affixed to an aldehyde-derivatized solid surface, for example glass.
  • the probes can be affixed to the surface of the solid support via Schiff s base reaction between an aldehyde group on the surface of solid support and an amine group at 5' terminal of the probes under 20 to 35 C and 50 to 70% humidity, while controlling the concentration of probes, for example in a range of preferably 100 to 300 ⁇ mol/ ⁇ L, more preferably 200 ⁇ mol/ ⁇ L.
  • HPV infection can be detected by the HPV detection kit of the current invention.
  • DNA in a sample for example a clinical sample
  • a sample for example a clinical sample
  • suitable primers for example those in Table 2.
  • the amplified DNA are then applied to the DNA chip for hybridization.
  • the amplified DNA are bound on the surface of the DNA chip after labeling.
  • the amplified sample DNA hybridized with the probes can be labeled with, for example, Streptavidin-R-phycoerythrin and detected with a laser scanner.
  • sequences of the HPV probes can be used in the reversed flow-through detection methods developed by the inventors and described in WO 2007/115491A and WO 2009/044370A, which allow 64 samples to be detected simultaneously, and results of the detection can be available within 5 to 15 minutes.
  • the current invention provides various sequences capable of detecting
  • HPV in which each of the sequences is able to detect multiple subtypes of HPV.
  • sequences of the current invention it is possible to detect commonly seen 38 subtypes of HPV, including those of high risk, with various combinations of four sequences of the current invention. This allows reduction of the costs of the resulting detection kits and DNA chips.
  • HPV detection As relatively few sequences are used as detection probe, complexity of the detection process can be reduced, and more accurate results can be obtained. These can reduce the overall costs of HPV detection, which is important for developing countries. After HPV infection is detected in a patient, the specific subtype of the HPV infection in the patient can then be detected by genotyping if necessary.

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Virology (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
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  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La présente invention concerne différentes séquences en tant que sonde de détection pour le VPH, où chacune de ces séquences est capable de détecter plusieurs sous-types de VPH. L'invention concerne aussi des puces de détection du VPH, des kits de détection comprenant ces sondes. Avec les séquences de la présente invention, il est possible de détecter 38 sous-types couramment observés de VPH, comprenant ceux à risque élevé, avec différentes combinaisons des séquences de la présente invention.
PCT/IB2009/055158 2008-11-19 2009-11-19 Séquences nucléotidiques, procédés et kits pour détecter le vph WO2010058357A1 (fr)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP09827253.7A EP2358910B1 (fr) 2008-11-19 2009-11-19 Séquences nucléotidiques, procédés et kits pour détecter le vph
CN200980144854.4A CN102209793B (zh) 2008-11-19 2009-11-19 用于检测hpv的核苷酸序列、方法和试剂盒
PL09827253T PL2358910T3 (pl) 2008-11-19 2009-11-19 Sekwencje nukleotydów, sposoby i zestawy do wykrywania HPV

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
HK08112649.2 2008-11-19
HK08112649 2008-11-19

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WO2010058357A1 true WO2010058357A1 (fr) 2010-05-27

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EP (1) EP2358910B1 (fr)
CN (1) CN102209793B (fr)
PL (1) PL2358910T3 (fr)
WO (1) WO2010058357A1 (fr)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110592279A (zh) * 2019-09-11 2019-12-20 圣湘生物科技股份有限公司 检测hpv的组合物、试剂盒及方法

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014139330A1 (fr) * 2013-03-15 2014-09-18 Diagcor Bioscience Incorporation Limited Analyse rapide de typage génétique et ses trousses
CN108929869B (zh) * 2018-08-09 2022-03-08 亚能生物技术（深圳）有限公司 Hpv全长基因组质控品的制备方法、扩增引物及检测试剂

Citations (6)

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WO1999014377A2 (fr) 1997-09-16 1999-03-25 Innogenetics N.V. Detection et identification du virus du papillome humain au moyen d'une pcr et d'une hybridation inverse specifique de type
US20050175989A1 (en) * 2001-06-20 2005-08-11 Ching-Yu Lin Method and detector for identifying subtypes of human papilloma viruses
US20060121516A1 (en) 2004-12-08 2006-06-08 Gen-Probe Incorporated Detection of nucleic acids from multiple types of human papillomaviruses
CN1814796A (zh) * 2005-12-02 2006-08-09 浙江大学 一种用于26种人乳头瘤病毒的检测与分型的方法
WO2007100198A1 (fr) 2006-03-03 2007-09-07 Gyngen Bio Co., Ltd. Trousses et procédé de détection du papilloma virus humain avec analyse de cordon de nucléotides
CN101177701A (zh) * 2007-09-29 2008-05-14 潮州凯普生物化学有限公司 人乳头状瘤病毒基因分型检测试剂盒及其基因芯片制备方法

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DK0746627T3 (da) * 1994-02-21 2002-12-16 Stichting Res Fonds Pathologie Påvisning af human papillomavirus ved hjælp af en nukleinsyreamplifikationsproces, som anvender generelle primere

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999014377A2 (fr) 1997-09-16 1999-03-25 Innogenetics N.V. Detection et identification du virus du papillome humain au moyen d'une pcr et d'une hybridation inverse specifique de type
US20050175989A1 (en) * 2001-06-20 2005-08-11 Ching-Yu Lin Method and detector for identifying subtypes of human papilloma viruses
US20060121516A1 (en) 2004-12-08 2006-06-08 Gen-Probe Incorporated Detection of nucleic acids from multiple types of human papillomaviruses
CN1814796A (zh) * 2005-12-02 2006-08-09 浙江大学 一种用于26种人乳头瘤病毒的检测与分型的方法
WO2007100198A1 (fr) 2006-03-03 2007-09-07 Gyngen Bio Co., Ltd. Trousses et procédé de détection du papilloma virus humain avec analyse de cordon de nucléotides
CN101177701A (zh) * 2007-09-29 2008-05-14 潮州凯普生物化学有限公司 人乳头状瘤病毒基因分型检测试剂盒及其基因芯片制备方法

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* Cited by examiner, † Cited by third party
Title
FRANC,OIS COUTLE'E ET AL.: "Enhanced Detection and Typing of Human Papillomavirus (HPV) DNA in Anogenital Samples with PGMY Primers and the Linear Array HPV Genotyping Test", JOURNAL OF CLINICAL MICROBIOLOGY, 30 June 2006 (2006-06-30), pages 1998 - 2006, XP008148664 *
KORNEGAY ET AL., J. CLIN. MICROBIOL., vol. 39, no. 10, 2001, pages 3530
See also references of EP2358910A4 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110592279A (zh) * 2019-09-11 2019-12-20 圣湘生物科技股份有限公司 检测hpv的组合物、试剂盒及方法

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Publication number Publication date
EP2358910A1 (fr) 2011-08-24
PL2358910T3 (pl) 2018-05-30
CN102209793B (zh) 2014-09-03
EP2358910A4 (fr) 2012-10-03
CN102209793A (zh) 2011-10-05
EP2358910B1 (fr) 2017-11-22

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