RAPID GENOTYPING ANALYSIS FOR HUMAN PAPILLOMAVIRUS AND THE DEVICE THEREOF

• US 20110111389A1
• Filed: 04/29/2010
• Published: 05/12/2011
• Est. Priority Date: 11/07/2001
• Status: Abandoned Application

• Current Assignee: DiagCor Bioscience Incorporation Limited
• Original Assignee: DiagCor Bioscience Incorporation Limited
• Inventors: CHOW, Joseph Kwok Fai, CHAN, Rhys Cheuk Yu, TAM, Joseph Wing On
• Application Number:
  US12/770,034
• Publication Number:
  US 20110111389A1
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6888 for detection or identification of organisms
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 1/705 for herpetoviridae, e.g. herpes simplex, varicella zoster
• CPC Class Codes: C12Q 1/706 for hepatitis
• CPC Class Codes: C12Q 1/708 for papilloma
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation

Abstract

The present invention discloses methods and devices for rapid genotyping. In one embodiment, the present invention is applied to human papillomavirus (HPV) genotyping, comprising the use of viral genotype-specific-oligonucleotide probes, reversed-dot-blotting genotype array format and flow through hybridization process, thereby providing a more efficient, faster and less expensive method for HPV genotyping. The genotyping method further comprises the use of generic probes to expand the detection of HPV genotypes.

Claims

1. A method for rapid detection of human papillomavirus (HPV), comprising the steps of:

(a) obtaining a sample comprising a template nucleic acid;

(b) amplifying the template nucleic acid with primers having the sequences of SEQ ID NOs;

116-118, thereby generating HPV L1 amplicons; and

(c) hybridizing the HPV L1 amplicons with immobilized oligonucleotide probes selected from the group consisting of SEQ ID NOs;

121-173, wherein the resulting hybridization profile would indicate the presence of HPV.

2. The method of claim 1, wherein the primers further comprise primers complimentary to an internal control.

3. The method of claim 2, wherein the primers complimentary to the internal control have the sequences of SEQ ID NOs:

119-120.

4. The method of claim 1, wherein the primers comprise a signal generating label.

5. The method of claim 1, wherein the oligonucleotide probes further comprise probes capable of capturing generic HPV viral DNA.

6. The method of claim 5, wherein the probes capable of capturing generic HPV viral DNA are selected from the group consisting of SEQ ID NOs:

170-173.

7. The method of claim 1, wherein hybridization of the HPV L1 amplicons with the plurality of immobilized oligonucleotide probes is carried out in a flow-through process or a lateral flow-through process.

8. The method of claim 1, wherein hybridization of the HPV L1 amplicons with the plurality of immobilized oligonucleotide probes is carried out in a flow-through process with recirculation of target analyte solution, thereby resulting in increased sensitivity.

9. The method of claim 1, wherein the method can detect the presence of HPV with a HPV genotype selected from the group consisting of HPV6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 66, 68, 70, 71, 72, 73, 81, 82, and 84.

10. The method of claim 9, wherein the HPV genotypes are separately detected, or the genotypes are detected collectively in one or more groups.

11. The method of claim 9, wherein HPV genotypes 16 and 18 are separately detected, and HPV genotypes 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 73 and 82 are detected collectively in one or more groups.

12. The method of claim 11, wherein the method further detects HPV genotypes 6, 11, 26, 40, 42, 43, 44, 53, 54, 55, 57, 61, 66, 70, 71, 72, 73, 81 and 84 collectively in one or more groups.

13. A kit for human papillomavirus (HPV) genotyping, comprising primers having the sequences of SEQ ID NOs:

116-118 and oligonucleotide probes selected from the group consisting of SEQ ID NOs;

121-173.

14. The kit of claim 13, wherein the primers further comprise primers complimentary to an internal control.

15. The kit of claim 14, wherein the primers complimentary to the internal control have the sequences of SEQ ID NOs:

119-120.

16. The kit of claim 13, wherein the primers comprise a signal generating label.

17. The kit of claim 13, wherein the oligonucleotide probes further comprise probes capable of capturing generic HPV viral DNA.

18. The kit of claim 17, wherein the probes capable of capturing generic HPV viral DNA are selected from the group consisting of SEQ ID NOs:

170-173.

19. The kit of claim 13, wherein the kit can detect a HPV genotype selected from the group consisting of HPV6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 66, 68, 70, 71, 72, 73, 81, 82, and 84.

20. The kit of claim 19, wherein the HPV genotypes are separately detected, or the genotypes are detected collectively in one or more groups.