A polymer-based DNA biochip platform for human papilloma virus genotyping

Journal of Virological Methods

Volumn 163, Issue 1, 2010, Pages 40-48

  Brandstetter, Thomas ^a   Böhmer, Sebastian ^a   Prucker, Oswald ^a   Bissé, Emmanuel ^b   zur Hausen, Axel ^b   Alt Mörbe, Juliane ^c   Rühe, Jürgen ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b UNIVERSITY OF FREIBURG   (Germany)

^c Laboratory for DNA Analytics   (Germany)

Author keywords

3D plastic DNA biochip; HPV chip genotyping; Human papilloma virus (HPV); Polymer network

Indexed keywords

POLYMER; SINGLE STRANDED DNA;

AMPLICON; ARTICLE; BIOCHIP; CALIBRATION; CONTROLLED STUDY; DNA ISOLATION; DNA MICROARRAY; DNA PROBE; EQUIPMENT DESIGN; GENOTYPE; IMMOBILIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RELIABILITY; SENSITIVITY AND SPECIFICITY; ULTRAVIOLET RADIATION; VALIDATION PROCESS; VIRUS DETECTION; VIRUS STRAIN; WART VIRUS;

DNA, VIRAL; FEMALE; GENOTYPE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PAPILLOMAVIRIDAE; PAPILLOMAVIRUS INFECTIONS; REAGENT KITS, DIAGNOSTIC; SENSITIVITY AND SPECIFICITY; UTERINE CERVICAL NEOPLASMS;

HUMAN PAPILLOMAVIRUS;

EID: 70749083518     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2009.07.027     Document Type: Article

References (37)

1. An H.J., Kim K.R., Kim I.S., Kim D.W., Park M.H., Park I.A., Suh K.S., Seo E.J., Sung S.H., Sohn J.H., Yoon H.K., Chang E.D., Cho H.I., Han J.Y., Hong S.R., and Ahn G.H. Prevalence of human papillomavirus DNA in various histological subtypes of cervical adenocarcinoma: a population-based study. Mod. Pathol. 18 (2005) 528-534
2. An H.J., Cho N.H., Lee S.Y., Kim I.H., Lee C., Kim S.J., Mun M.S., Kim S.H., and Jeong J.K. Correlation of cervical carcinoma and precancerous lesions with human papillomavirus (HPV) genotypes detected with the HPV DNA chip microarray method. Cancer 97 (2003) 1672-1680
3. Baek T.J., Park P.Y., Han K.N., Kwon H.T., and Seong G.H. Development of a photodiode array biochip using a bipolar semiconductor and its application to detection of human papilloma virus. Anal. Bioanal. Chem. 390 5 (2008) 1373-1378 (Epub 2008 January 13)
4. Brenton J.D., Aparicio S.A., and Caldas C. Molecular profiling of breast cancer: portraits but not physiognomy. Breast Cancer Res. 3 (2001) 77-80
5. Castellsagué X., Díaz M., de Sanjosé S., Muñoz N., Herrero R., Franceschi S., Peeling R.W., Ashley R., Smith J.S., Snijders P.J.F., Meijer C.J.L.M., and Bosch F.X. Worldwide human papillomavirus etiology of cervical adenocarcinoma and its cofactors: implications for screening and prevention. J. Natl. Cancer Inst. 98 5 (1, 2006) 303-315
6. Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N., Lane C.R., Lim E.P., Kalayanaraman N., Nemesh J., Ziaugra L., Friedland L., Rolfe A., Warrington J., Lipshutz R., Daley G.Q., and Lander E.S. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22 (1999) 231-238
7. Dalstein V., Merlin S., Bali C., Saunier M., Dachez R., and Ronsin C. Analytical evaluation of the PapilloCheck test, a new commercial DNA chip for detection and genotyping of human papillomavirus. J. Virol. Methods 156 1-2 (2009) 77-83
8. Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A., Bloomfield C.D., and Lander E.S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286 (1999) 531-537
9. Gwynne P., and Heebner G. Biochips-array of applications. Science 307 5714 (4, 2005) (special advertising section)
10. Hoheisel J.D. Microarray technology: beyond transcript profiling and genotype analysis. Nat. Rev. Genet. 7 3 (2006) 200-210 (Review)
11. Hwang T.S., Jeong J.K., Park M., Han H.S., Choi H.K., and Park T.S. Detection and typing of HPV genotypes in various cervical lesions by HPV oligonucleotide microarray. Gynecol. Oncol. 90 (2003) 51-56
12. Jeffreys A.J., Wilson V., and Thein S.L. Individual-specific 'fingerprints' of human DNA. Nature 316 6023 (1985) 76-79
13. Kleter B., van Doorn L.J., Schrauwen L., Molijn A., Sastrowijoto S., ter Schegget J., Lindeman J., ter Harmsel B., Burger M., and Quint W. Development and clinical evaluation of a highly sensitive PCR-reverse hybridisation line probe assay for detection and identification of anogenital human papillomavirus. J. Clin. Microbiol. 37 (1999) 2508-2517
14. Kuebler D.L., Illingworth A., Blenc A.M., and Wilbur D.C. A peer comparison program for the quality assurance of human papillomavirus DNA detection using the Digene Hybrid Capture II/SurePath method shows excellent analytic interlaboratory correlation. Cancer 111 October (5) (2007) 339-343
15. Lehr H.-P., Reimann M., Brandenburg A., Sulz G., and Klapproth H. Real-time detection of nucleic acid interactions by total internal reflection fluorescence. Anal. Chem. 75 (2003) 2414-2420
16. Matthews-Greer J., Rivette D., Reyes R., Vanderloos C.F., and Turbat-Herrera E.A. Human papillomavirus detection: verification with cervical cytology. Clin. Lab. Sci. Winter 17 1 (2004) 8-11
17. Menzo S., Marinelli K., Bagnarelli P., Rolla S., and Clementi M. Human papillomavirus infections: new perspectives for prevention and treatment. New Microbiol. 30 3 (2007) 189-212
18. Muñoz N., Bosch F.X., Castellsagué X., Díaz M., de Sanjose S., Hammouda D., Shah K.V., and Meijer C.J. Against which human papillomavirus types shall we vaccinate and screen? The international perspective. Int. J. Cancer 111 2 (2004) 278-285
19. Nuwaysir M.E., Bittner M., Trent J., Barrett J.C., and Afshari C.A. Microarrays and toxicology: the advent of toxicogenomics. Mol. Carcinog. 24 (1999) 153-159 (Review)
20. Pascual A., Pariente M., Godínez J.M., Sánchez-Prieto R., Atienzar M., Segura M., and Poblet E. High prevalence of human papillomavirus 16 in penile carcinoma. Histol. Histopathol. 22 2 (2007) 177-183
21. Qu W., Jiang G., Cruz Y., Chang C.J., Ho G.Y.F., Klein R.S., and Burk R.D. PCR detection of human papillomavirus: comparison between MY09/MY11 and GP5_/GP6_ primer systems. J. Clin. Microbiol. 35 (1997) 1304-1310
22. Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 October (5235) (1995) 467-470
23. Schenk T., Brandstetter T., Zur Hausen A., Alt-Mörbe J., Huzly D., and Rühe J. Performance of a polymer-based DNA chip platform in detection and genotyping of human papillomavirus in clinical samples. J. Clin. Microbiol. 47 5 (2009) 1428-1435
24. Scherf U., Ross D.T., Waltham M., Smith L.H., Lee J.K., Tanabe L., Kohn K.W., Reinhold W.C., Myers T.G., Andrews D.T., Scudiero D.A., Eisen M.B., Sausville E.A., Pommier Y., Botstein D., Brown P.O., and Weinstein J.N. A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 24 (2000) 236-244
25. Shoemaker D.D., Schadt E.E., Armour C.D., He Y.D., Garrett-Engele P., McDonagh P.D., Loerch P.M., Leonardson A., Lum P.Y., Cavet G., Wu L.F., Altschuler S.J., Edwards S., King J., Tsang J.S., Schimmack G., Schelter J.M., Koch J., Ziman M., Marton M.J., Li B., Cundiff P., Ward T., Castle J., Krolewski M., Meyer M.R., Mao M., Burchard J., Kidd M.J., Dai H., Phillips J.W., Linsley P.S., Stoughton R., Scherer S., and Boguski M.S. Experimental annotation of the human genome using microarray technology. Nature 409 (2001) 922-927
26. Tavazoie S., Hughes J.D., Campbell M.J., Cho R.J., and Church G.M. Systematic determination of genetic network architecture. Nat. Genet. 22 (1999) 281-285
27. The Chipping Forecast II. Nat. Genet. 32 4s (2002)
28. The Chipping Forecast. Nat. Genet. 21 1s (1999)
29. Toomey R., Freidank D., and Rühe J. Swelling behavior of thin, surface-attached polymer networks. Macromolecules 37 (2004) 882-887
30. Villa L.L. Overview of the clinical development and results of a quadrivalent HPV (types 6, 11, 16, 18) vaccine. Int. J. Infect. Dis. 11 Suppl. 2 (2007) 17-25 (Review)
31. Wang D., Coscoy L., Zylberberg M., Avila P.C., Boushey H.A., Ganem D., and DeRisi J.L. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. U.S.A. 26 (2002) 15687-15692
32. Wu T.C. Therapeutic human papillomavirus DNA vaccination strategies to control cervical cancer. Eur. J. Immunol. 37 2 (1, 2007) 310-314
33. Wulfkuhle J.D., Liotta L.A., and Petricoin E.F. Proteomic applications for the early detection of cancer. Nat. Rev. Cancer 3 4 (2003) 267-275 (Review)
34. Xu L., Yu H., Akhras M.S., Han S.J., Osterfeld S., White R.L., Pourmand N., and Wang S.X. Giant magnetoresistive biochip for DNA detection and HPV genotyping. Biosens. Bioelectron. 15/24 1 (2008) 99-103
35. Yang G., Liang C.H., Cui J.H., and Chen S. The development and clinical application of papillomavirus genotyping by DNA chip. Zhonghua Liu Xing Bing Xue Za Zhi 27 1 (2006) 47-49
36. zur Hausen H. Papillomaviruses and cancer: from basic studies to clinical application. Nat. Rev. Cancer 2 5 (2002) 342-350 (Review)
37. zur Hausen H. Papillomaviruses causing cancer: evasion from host-cell control in early events in carcinogenesis. J. Natl. Cancer Inst. 92 May (9) (2000) 690-698 (Review)