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WO1997039010A1 - Sondes pour la detection des papillomavirus humains - Google Patents

Sondes pour la detection des papillomavirus humains Download PDF

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Publication number
WO1997039010A1
WO1997039010A1 PCT/US1997/006354 US9706354W WO9739010A1 WO 1997039010 A1 WO1997039010 A1 WO 1997039010A1 US 9706354 W US9706354 W US 9706354W WO 9739010 A1 WO9739010 A1 WO 9739010A1
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Prior art keywords
variant nucleotide
hpv
nucleic acid
nucleotide
variant
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PCT/US1997/006354
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English (en)
Inventor
Cosette M. Wheeler
M. Michele Manos
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The University Of New Mexico
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Application filed by The University Of New Mexico filed Critical The University Of New Mexico
Priority to AU26725/97A priority Critical patent/AU2672597A/en
Priority to EP97918677A priority patent/EP1007538A4/fr
Publication of WO1997039010A1 publication Critical patent/WO1997039010A1/fr

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    • 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

Definitions

  • the present invention relates probes constituted by labelled, mono-stranded DNA or RNA nucleic acid sequences.
  • HPVs Human papillomaviruses
  • HPV- 16 Human papillomaviruses
  • HPVs are characterized by a circular double strand DNA genome, about 8000 bases long, wrapped in a protein capsid 55-60 nm in diameter.
  • the virus can be found in non-malignant lesions in the unintegrated episomal state. In these cases disturbance of the cellular differentiation is observed and production of viral particles at late stages of the differentiation is observed.
  • Papillomaviruses are defined by genomic sequence similarities rather than by classical serology.
  • HPV genome is defined as a new type if it is separated by a Hamming distance or dissimilarity of more than 10% in its nucleotide sequence compared with other known HPV types in the E6, E7, and Ll open reading frames (ORFs) combined. Isolates within the same type differing by 0 to 2% in their nucleotide sequences compared with the reference sequence are referred to as variants, and those differing by 2 to 10% are referred to as subtypes.
  • Probes for HPVs made from DNA sequences may be obtained by various routes, particularly by genetic engineering or by manual or automatic direct synthesis. These nucleic acid sequences have the property of being matched and of forming hybrids with complementary DNA or RNA sequences, as the case may be denatured previously, if the latter were initially double stranded or mRNA. This denaturation can be done after incubation in a medium of high ionic strength and at high temperature or in a basic medium. These hybrids are then detectable.
  • the detection of hybrids can be done by different methods.
  • the probe may be labelled by one of the known methods for the labelling of nucleic acid probes. It may be radioactive labelling, for example, with phosphorus 32, or in the case of a cold probe, no radioactive labelling, for example enzymatic, as is also known. In certain cases, the probe is not labelled during its use proper, but modified chemically to be detectable after hybridization, for example with biotin.
  • HPV in the cervix is carried out by the use of molecular probes constituted by synthetic HPV-specific oligonucleotides or cloned viral DNA fragments that are labelled.
  • molecular probes constituted by synthetic HPV-specific oligonucleotides or cloned viral DNA fragments that are labelled.
  • synthetic DNA probes labelled non-isotopically or isotopically and usable in situ or in liquid or solid-phase assays.
  • there are identified at the level of the DNA specific regions of different types of HPV virus to deduce therefrom complementary homologous synthetic probes.
  • Figure 1 shows the genetic variation within HPV-18 in tabular form
  • Figure 2 shows the genetic variation within HPV-33 in tabular form
  • Figure 3 shows the genetic variation within HPV-35 in tabular form
  • Figure 4 shows the genetic variation within HPV-39 in tabular form
  • Figure 5 shows the genetic variation within HPV-45 in tabular form
  • Figure 6 shows the genetic variation within HPV-51 in tabular form
  • Figure 7 shows the genetic variation within HPV-52 in tabular form
  • Figure 8 shows the genetic variation within HPV-58 in tabular form
  • Figure 9 shows the genetic variation within HPV-59 in tabular form
  • Figure 10 shows the genetic variation within HPV-68 in tabular form
  • Figure 1 1 shows the genetic variation within MM4 in tabular form
  • Figure 12 shows the genetic variation within MM9/W13B in tabular form
  • Figure 13 is a table comparing intratypic nucleotide and amino acid sequence variation in the MY09/11 Ll region for 13 HPV types and novel sequences, including a reference type, HPV- 16.
  • RNA equivalent refers to a nucleic acid sequence substituting "U” (Uracil) for "T” in a corresponding DNA sequence.
  • Figures 1 to 12 present a nucleotide comparison with the corresponding reference HPV sequences for the 12 HPVs for which the present invention provides probes.
  • the first nucleotide of the specific HPV sequence has been used as nt 1 for each individual HPV type.
  • variations within a single HPV type or novel sequence range from no changes (HPV-33, HPV-35, HPV-45, HPV-51 HPV-52, HPV-58, HPV-59, HPV-68, and MM4) to a maximum of 19 changes (HPV-52).
  • Nucleotide changes between two individual specimens range from no changes (HPV-18, HPV-33, HPV-35, HPV-45, HPV-51, hPV- 52, HPV-58, HPV-59, HPV-68 and MM4) to a maximum of 9 changes in IS464 (an HPV-52 variant).
  • isolates can be classified into variant clusters.
  • Figure 13 is a table comparing intratypic nucleotide and amino acid sequence variation in the MY09/11 Ll region for the 12 HPV types of Figs. 1 to 12 and a reference type, HPV- 16
  • ORF Ll nucleotide positions at which variations have been observed are given across the top of each figure.
  • the numbering refers to the first nucleotide of each specific HPV genome for all HPV types except HPV-68, MM4, and MM9 for which the numbering refers to the first nucleotide of the sequence for each type as presented in the MY09/11 Ll fragment deposited in GenBank and as reported in a human papillomaviruses 1994 compendium, (Myers, G. et al.
  • HPV-73 The following HPVs were analyzed: HPV-18, HPV-33, HPV-35, HPV-39, HPV-45, HPV-51 , HPV-52, HPV- 58, HPV-59, HPV-68 (ME180), MM4/W13B (novel partial genomic sequence) and MM9/PAP238A (recently designated HPV-73).
  • PCR products were subjected to electrophoresis in 1 % Nusieve agarose 1 X TAE buffer and visualized under UV light Amplimers of the expected 450-bp size were excised from the gels and extracted with Gelase (Epicentre Technologies, Madison, WI) as described by the manufacturer. Gel- purified amplimers were ligated to a pGEM-T vector (Promega, Madison, WI). Individual transformants were subjected to colony direct PCR with Ml 3 forward and reverse p ⁇ mers.
  • Plasmid min ⁇ reps of cloned HPVs with correct insert size and positive by hyb ⁇ dization assays were prepared as desc ⁇ bed in Stewart, A., et al , 1995, Generation of Entire Human Papillomavirus Genomes by Long PCR and Frequency of Errors Produced in Amplification, Genome Research, 5:79-88.
  • Phylogenetic analyses were performed over the MY09/1 1 Ll region with 53 distinct HPV sequences.
  • the 53 HPV sequences were obtained from 53 separate clinical specimens. Twelve different HPV types and novel sequences and the co ⁇ esponding reference sequences were represented in the analyses For each type an alignment of the distinct MY09/11 sequences (Including the sequence of the reference clone from GenBank) was constructed by using the complete MY09/1 1 region except for the primer binding sites.
  • the most parsimonious phylogenetic trees were determined with PAUP 3.1.1 software on a Power Macintosh 7100 using the branch- and-bound search strategy, which is guaranteed to find the most parsimonious tree(s). In some cases, several equally parsimonious trees were obtained.
  • HPV-18 variants do not seem to form intermediate classes between the two major HPV-18 groups but may be representative of unique groups of HPV-18 variants.
  • HPV-18 reference does not account for variations at nt 6579, 6581, 6625, 6626, 6677, 6697, 6719, 6749, 6842, 6877, 6917, 6943, 6986 (nt 22, 24, 68, 69, 120, 140, 162, 192, 285, 320, 360, 386, 429 of SEQ ID NO: l below).
  • the present invention provides nucleic acid probes for HPV-18 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 21, 25 to 67, 70 to 1 19, 121 to 139, 163 to 191, 193 to 284, 286 to 319, 321 to 359, 361 to 385, 387 to 428 and 430 to 455 of SEQ ID NO: l and their RNA equivalents.
  • These probes avoid the region of variation in HPV-18 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for HPV-18 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting ofthe nucleic acid sequences contained within SEQ ID NO:l which include a variant nucleotide located at at least one of numbered positions 22, 24, 68, 69, 120, 340, 162, 192, 285, 320, 360, 386, and 429 wherein: when the variant nucleotide is at nt 22, the variant nucleotide is A; when the variant nucleotide is at nt 24, the variant nucleotide is C; when the variant nucleotide is at nt 68, the variant nucleotide is G; when the variant nucleotide is at nt 69, the variant nucleotide is T or U; when the variant nucleotide is at nt 120, the variant nucleotide is G; when the variant nucleotide is at ntide is at
  • the present invention provides nucleic acid probes for HPV- 33 comprising an oligonucleotide of 18 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 98, 100 to 125, 127 to 165, 167 to 399 and 401 to 449 of SEQ ID NO:2 and their RNA equivalents.
  • These probes avoid the region of variation in HPV-33 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for HPV-33 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO:2 which include a variant nucleotide located at at least one of numbered positions 99, 126, 166, and 400 wherein: when the variant nucleotide is at nt 99, the variant nucleotide is C; when the variant nucleotide is at nt 126, the variant nucleotide is G; when the variant nucleotide is at nt 166, the variant nucleotide is T; and when the variant nucleotide is at nt 400, the variant nucleotide is A; and RNA equivalents ofthe nucleic acid sequences.
  • These probes are capable of hybridizing with the HPV-33 variants shown in Figure 2.
  • the present invention provides nucleic acid probes for HPV-35 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 102 and 104 to 452 of SEQ ID NO:3 and their RNA equivalents. These probes avoid the region of variation in HPV-35 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for HPV-35 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO:3 which include nt 103. These probes are capable of hybridizing with the HPV-35 variants shown in Figure 3.
  • Four of the specimens were prototype-like and had either one change each at nt 6638 (T to A) and 6903 (C to T) (ISO73 and IS270, respectively) or both of these changes (ISI 14 and IS281) (Fig. 4)
  • the remaining six specimens had three to six changes each .all but one (IS270) HPV-39 specimens had the C-to-T substitution at nt 6903, and none of the specimens were identical to the HPV-39 reference sequence.
  • HPV-39 reference does not account for variations at nt 6638, 6733, 6785, 6853, 6854, 6903, 6996 (54, 149, 201 , 269, 270, 319, and 412 of SEQ ID NO:4 below).
  • the present invention provides nucleic acid probes for HPV-35 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 53, 55 to 148, 150 to 200, 202 to 268, 271 to 318, 320 to 41 1 and 413 to 455 of SEQ ID NO:4 and their RNA equivalents.
  • These probes avoid the region of variation in HPV-33 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for HPV-39 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting ofthe nucleic acid sequences contained within SEQ ID NO:4 which include a variant nucleotide located at at least one of numbered positions 54, 149, 201, 269, 270, 319 and 412 wherein: when the variant nucleotide is at nt 54, the variant nucleotide is A; when the variant nucleotide is at nt 149, the variant nucleotide is T; when the variant nucleotide is at nt 201 , the variant nucleotide is A; when the variant nucleotide is at nt 269, the variant nucleotide is C; when the variant nucleotide is at nt 270, the variant nucleotide is C; when the variant nucleotide is at nt 319, the variant
  • the remaining five specimens appear as an intermediate groups between the prototype/prototype-like group and the group containing African specimens sharing some of the maker substitutions from both groups. It was not possible to make any geographical assignments to any of the variants except for those of African origin, since the two other groups included specimens from various continents.
  • HPV-45 reference does not account for variations at nt 6621, 6661, 6665, 6676, 6677, 6687, 6705, 6816, 6837, 6852, 6861, 6862, 6910, 6914, 6951, 6996 (60, 100, 104, 1 15, 116, 126, 144, 255, 276, 291, 300, 301, 349, 353, 390, and 435 of SEQ ID NO:5 below).
  • the present invention provides nucleic acid probes for HPV-45 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 59, 61 to 99, 145 to 254, 256 to 275, 302 to 348, 354 to 389, 391 to 434 and 436 to 455 of SEQ ID NO:5 and their RNA equivalents.
  • These probes avoid the region of variation in HPV-45 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for HPV-45 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO:5 which include a variant nucleotide located at at least one of numbered positions 60, 100, 104, 1 15, 116, 126, 144, 255, 276, 291, 300, 301, 349, 353, 390, and 435 wherein: when the variant nucleotide is at nt 60, the variant nucleotide is T; when the variant nucleotide is at nt 100, the variant nucleotide is G; when the variant nucleotide is at nt 104, the variant nucleotide is C; when the variant nucleotide is at nt 1 15, the variant nucleotide is G; when the variant nucleotide is at nt 116, the variant nucleotide is A
  • the present invention provides nucleic acid probes for HPV-51 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO:6 which include nt 348. These probes are capable of hybridizing with the HPV-51 variants shown in Figure 6.
  • HPV-52 reference does not account for the variations at nt 6698, 6701, 6703, 6711, 6712, 6764, 6794, 6824, 6833, 6848, 6917, 6920, 6935, 6941, 6944, 6959, 6980, 6983, 6992 (96, 99, 101, 109, 110, 162, 192, 222, 231, 246, 315, 318, 333, 339, 342, 357, 378, 381, 390 of SEQ ID NO:7 below).
  • the present invention provides nucleic acid probes for HPV-52 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 95, 1 1 1 to 161 , 163 to 191 , 193 to 221, 247 to 314, 358 to 377 and 391 to 449 of SEQ ID NO:7 and their RNA equivalents.
  • These probes avoid the region of variation in HPV-52 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for HPV-52 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO:7 which include a variant nucleotide located at at least one of numbered positions 96, 99, 101, 109; 1 10, 162, 192, 222, 231 , 246, 315, 318, 333, 339, 342, 357, 378, 381 , and 390 wherein: when the variant nucleotide is at nt 96, the variant nucleotide is A; when the variant nucleotide is at nt 99, the variant nucleotide is G; when the variant nucleotide is at nt 101, the variant nucleotide is C; when the variant nucleotide is at nt 109, the variant nucleotide is G; when the variant nucleotide is at n
  • Specimens within the HPV-58 group did not form any natural groups, with the exception of prototype or prototype-like (Fig.8). The majority of the samples (56%)) could be considered prototype or prototype-like, whereas the remaining sequences (44%) had three to eight nucleotide changes and share only one nucleotide substitution at position 240 (C to A). Overall, it has been found that the HPV-58 reference does not account for the variations at nt 6641, 6692, 6697, 671 1, 6798, 6822, 6827, 6828, 6881 , 7016 (54, 105, 110, 124, 211, 235, 240, 241 , 294, 429 of SEQ ID NO.8 below).
  • the present invention provides nucleic acid probes for HPV-58 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 53, 55 to 104, 125 to 210, 212 to 234, 242 to 293, 295 to 428 and 430 to 449 of SEQ ID NO:8 and their RNA equivalents.
  • These probes avoid the region of variation in HPV-58 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for HPV-58 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO:8 which include a variant nucleotide located at at least one of numbered positions 54, 105, 110, 124, 21 1, 235, 240, 241, 294, and 429 wherein: when the variant nucleotide is at nt 54, the variant nucleotide is A; when the variant nucleotide is at nt 105, the variant nucleotide is A; when the variant nucleotide is at nt 110, the variant nucleotide is A; when the variant nucleotide is at nt 124, the variant nucleotide is A; when the variant nucleotide is at nt 21 1, the variant nucleotide is G; when the variant nucleotide is at nt 235
  • the present invention provides nucleic acid probes for HPV-59 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 65, 67 to 101, 104 to 399 and 401 to 455 of SEQ ID NO:9 and their RNA equivalents. These probes avoid the region of variation in HPV-59 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for HPV-59 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO:9 which include a variant nucleotide located at at least one of numbered positions 66, 102, 103, and 400 wherein: when the variant nucleotide is at nt 66, the variant nucleotide is C; when the variant nucleotide is at nt 102, the variant nucleotide is G; when the variant nucleotide is at nt 103, the variant nucleotide is C or G; and when the variant nucleotide is at nt 400, the variant nucleotide is A; and RNA equivalents of the nucleic acid sequences.
  • These probes are capable of hybridizing with the HPV-59 variants shown in Figure 9.
  • the present invention provides nucleic acid probes for HPV-68 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 209, 1 1 1 to 344, 346 to 377 and 379 to 455 of SEQ ID NO: 10 and their RNA equivalents.
  • These probes avoid the region of variation in HPV-68 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for HPV-68 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO: 10 which include a variant nucleotide located at at least one of numbered positions 210, 345 and 378 wherein: when the variant nucleotide is at nt 210, the variant nucleotide is A; when the variant nucleotide is at nt 345, the variant nucleotide is G; and when the variant nucleotide is at nt 378, the variant nucleotide is C; and RNA equivalents of the nucleic acid sequences.
  • These probes are capable of hybridizing with the HPV-68 variants shown in Figure 10.
  • the present invention provides nucleic acid probes for MM4 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences from numbered positions 1 to 11 1 , 1 13 to 139, 145 to 248, 250 to 267, 269 to 290, 292 to 369 and 317 to 455 of SEQ ID NO:l 1 and their RNA equivalents.
  • These probes avoid the region of variation in MM4 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for MM4 comprising oligonucleotides of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO:l l which include a variant nucleotide located at at least one of numbered positions 1 12, 140, 144, 249, 268, 291 , and 370 wherein: when the variant nucleotide is at nt 1 12, the variant nucleotide is A; when the variant nucleotide is at nt 140, the variant nucleotide is G; when the variant nucleotide is at nt 144, the variant nucleotide is G or T; when the variant nucleotide is at nt 249, the variant nucleotide is C; when the variant nucleotide is at nt 268, the variant nucleotide is C; when the variant nucleotide is at nt 291, the variant nucleotide
  • the present invention provides nucleic acid probes for MM9 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting ofthe nucleic acid sequences from numbered positions 1 to 101, 102 to 143, 145 to 169, 188 to 302, 304 to 334, 336 to 374, 376 to 416 and 418 to 458 of SEQ ID NO: 12 and their RNA equivalents.
  • These probes avoid the region of variation in MM9 while providing a probe of a convenient size for conventional hybridization techniques.
  • the present invention provides nucleic acid probes for MM9 comprising an oligonucleotide of 15 to 30 nucleotides selected from the group consisting of the nucleic acid sequences contained within SEQ ID NO: 12 which include a variant nucleotide located at at least one of numbered positions 102, 144, 170, 187, 303, 333, 375, and 417 wherein: when the variant nucleotide is at nt 102, the variant nucleotide is A; when the variant nucleotide is at nt 144, the variant nucleotide is A; when the variant nucleotide is at nt 170, the variant nucleotide is A; when the variant nucleotide is at nt 187, the variant nucleotide is T; when the variant nucleotide is at nt 303, the variant nucleotide is G; when the variant nucleotide is at ntide
  • a desired sequence region of all known HPV types is aligned using a conventional nucleic acid alignment program, such as the PileUp program produced by the Wisconsin Genetics Computer Group (GCG).
  • GCG Wisconsin Genetics Computer Group
  • Potential type-specific oligonucleotide probes are marked using the following criteria: length of 15 to 30 bp, preferably 18 to 22 bp; preferably a G/C to A/T ratio of 50:50, if possible; preferably no strings of consecutive A, T or A and T longer than 4, if possible;
  • One G or C is weighted as 4°C
  • One A or T is weighted as 2°C
  • probes are compared against all known HPV sequences in the selected regions.
  • a suitable program is the FASTA program of GCG.
  • probes having at least four nucleotide mismatches when compared with all known HPV types are chosen, with a preference for probes with greater than four mismatches.
  • probes produced by this process are designed for a predicted hybridization temperature (50 to 55°C), this procedure can be changed slightly for other hybridization parameters. For example, a lower hybridization temperature will require the oligonucleotide type- or allele-specific probe to have a greater number of mismatches and different length.
  • A represents adenine
  • C represents cytosine
  • G represents guanine
  • T represents thymine
  • U represents uracil
  • M represents A or C
  • R represents A or G
  • W represents A or T/U
  • S represents C or G
  • Y represents C or T/U
  • K represents G or T/U
  • V represents A or C or G, not T/U
  • H represents A or C or T/U, not G
  • D represents A or G or T/U, not C
  • B represents C or G or T/U, not A
  • N represents (A or C or G or T/U) or (unknown or other).
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • CAACTATGCA AAGTTACCTT AACTGCAGAA GTTATGACAT ATATTCATGC TATGAATCCA 240
  • MOLECULE TYPE DNA (genomic)
  • GCACAAGGCC ATAATAATGG TATTTGTTGG AGTAACCAAT TGTTTGTTAC TGTAGTTGAT 60
  • MOLECULE TYPE DNA (genomic)
  • AATTCCTCTA TATTGGACAA TTGGAATTYY GCTGTAGCTC CTCCACCATC TGCCAGTTTG 300
  • MOLECULE TYPE DNA (genomic)
  • GATTCTACMA TTTTAGAACA GTGGAATYTT GGATTAACCT TGCCCCCCTC MGCTAGTTTG 300
  • CAGGCTAAAS AAGACCCTTT GGCAAAATAT AAATTTTGGA ATGTAGACCT TAAGGAACGC 420
  • MOLECULE TYPE DNA (genomic)

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Abstract

L'invention concerne des sondes destinées aux papillomavirus humains HPV-18, HPV-33, HPV-35, HPV-39, HPV-45, HPV-51, HPV-52, HPV-58, HPV-59, HPV-68 (ME180), MM4/W13B et MM9/PAP238A, qui s'hybrident avec les régions homologues de l'ADN de ces HPV. Elle concerne également des sondes destinées aux papillomavirus humains, qui peuvent s'hybrider avec des régions variantes récemment découvertes de l'ADN de ces HPV.
PCT/US1997/006354 1996-04-15 1997-04-14 Sondes pour la detection des papillomavirus humains WO1997039010A1 (fr)

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AU26725/97A AU2672597A (en) 1996-04-15 1997-04-14 Probes for the detection of human papillomavirus
EP97918677A EP1007538A4 (fr) 1996-04-15 1997-04-14 Sondes pour la detection des papillomavirus humains

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Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1082466A1 (fr) * 1998-05-30 2001-03-14 Visible Genetics Inc. Procede, reactif et kit servant a determiner le genotype de papillomavirus humains
WO2006077102A3 (fr) * 2005-01-18 2007-07-19 Delft Diagnostic Lab Bv Methode de detection et matieres associees
US20120009562A1 (en) * 2004-05-07 2012-01-12 Roche Molecular Systems, Inc. High-Risk Human Papillomavirus Detection
US20130078618A1 (en) * 2004-12-08 2013-03-28 Gen-Probe Incorporated Compositions, reaction mixtures and methods for detecting nucleic acids from type a1 and/or type c1 human papillomavirus

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5182377A (en) * 1988-09-09 1993-01-26 Hoffmann-La Roche Inc. Probes for detection of human papillomavirus
US5447839A (en) * 1988-09-09 1995-09-05 Hoffmann-La Roche Inc. Detection of human papillomavirus by the polymerase chain reaction
US5527898A (en) * 1988-09-09 1996-06-18 Hoffmann-La Roche Inc. Detection of human papillomavirus by the polymerase chain reaction
US5643715A (en) * 1988-10-26 1997-07-01 Lancaster; Wayne D. Human papillomavirus type 52 DNA sequences and methods for employing the same

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ES2181765T3 (es) * 1994-02-21 2003-03-01 Stichting Res Fonds Pathologie Deteccion de papiloma virus humano en un proceso de amplificacion de acido nucleico utilizando cebadores generales.

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5182377A (en) * 1988-09-09 1993-01-26 Hoffmann-La Roche Inc. Probes for detection of human papillomavirus
US5447839A (en) * 1988-09-09 1995-09-05 Hoffmann-La Roche Inc. Detection of human papillomavirus by the polymerase chain reaction
US5527898A (en) * 1988-09-09 1996-06-18 Hoffmann-La Roche Inc. Detection of human papillomavirus by the polymerase chain reaction
US5643715A (en) * 1988-10-26 1997-07-01 Lancaster; Wayne D. Human papillomavirus type 52 DNA sequences and methods for employing the same

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See also references of EP1007538A4 *

Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1082466A1 (fr) * 1998-05-30 2001-03-14 Visible Genetics Inc. Procede, reactif et kit servant a determiner le genotype de papillomavirus humains
EP1082466A4 (fr) * 1998-05-30 2004-10-06 Bayer Healthcare Llc Procede, reactif et kit servant a determiner le genotype de papillomavirus humains
US20120009562A1 (en) * 2004-05-07 2012-01-12 Roche Molecular Systems, Inc. High-Risk Human Papillomavirus Detection
US8202975B2 (en) * 2004-05-07 2012-06-19 Roche Molecular Systems, Inc. High-risk human papillomavirus detection
US20130078618A1 (en) * 2004-12-08 2013-03-28 Gen-Probe Incorporated Compositions, reaction mixtures and methods for detecting nucleic acids from type a1 and/or type c1 human papillomavirus
US8574841B2 (en) * 2004-12-08 2013-11-05 Gen-Probe Incorporated Compositions, reaction mixtures and methods for detecting nucleic acids from type A1 and/or type C1 human papillomavirus
WO2006077102A3 (fr) * 2005-01-18 2007-07-19 Delft Diagnostic Lab Bv Methode de detection et matieres associees

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