Generation of a DNA microarray for determination of E6 natural variants of human papillomavirus type 16.
Infection with high-risk types of human papillomavirus (HPV) is necessary for the development of cervical cancer. However, the majority of the HPV infections are efficiently cleared by the immune system and only a minority persist and induce the development of malignant lesions. Several studies provided evidence that intratype genetic variations are implicated in determining the clinical outcome of HPV infections. In this study, we describe a DNA chip based on arrayed primer extension (APEX) for the analysis of the natural variants of HPV16, the most frequently detected type in cervical cancer world-wide. We show that HPV16 E6 variants are detected efficiently by APEX. In addition, APEX is a valid assay for the simultaneous detection of different HPV16 variants. Thus, it could be used for clinical studies aiming to analyse multiple infections with different HPV16 subtypes. Finally, since APEX combines the advantages of dideoxy DNA sequencing with the high-throughput potential of the microarray, it is suitable for the simultaneous analysis of a number of variable regions of HPV16 genome in large-scale studies.
Gemignani
Federica
F
International Agency for Research on Cancer, World Health Organization, 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France.
Landi
Stefano
S
Chabrier
Amélie
A
Smet
Anouk
A
Zehbe
Ingeborg
I
Canzian
Federico
F
Tommasino
Massimo
M
D004279:DNA, Viral / Q000032:analysis; D005260:Female; D014644:Genetic Variation; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009856:Oncogene Proteins, Viral / Q000235:genetics*; D012097:Repressor Proteins
D004279:DNA, Viral; C068651:E6 protein, Human papillomavirus type 16; D009856:Oncogene Proteins, Viral; D012097:Repressor Proteins