BACKGROUND: Restriction fragment length polymorphism (RFLP) methods for genotyping genital human papillomavirus (HPV) are considered labor consuming and constrained by the reduced set of restriction enzymes capable of detecting specific mutations. However, we think that these methods have not taken full advantage of the high diversity of the known restriction enzymes. OBJECTIVE: We have set out to find the best restriction enzyme for HPV typing. STUDY DESIGN: An extensive search for enzymes was carried out by combining statistical methods and database information. The search maximized the discrimination between high- and low-risk types by examining the sequence of the L1 gene flanked by primers MY09/11. Different electrophoretic resolutions and two variations of the RFLP method were considered. RESULTS: HpyCH4V is the best enzyme for discriminating between risk types. Moreover, HpyCH4V generates different patterns for virtually all the HPV types. The typical pattern consists of two or three fragments, which facilitates typing in mixed infections. The typing of a set of clinical samples confirmed the expectations. CONCLUSIONS: This result illustrates the possibilities of statistical methods to exploit the high diversity of restriction enzymes in order to classify samples in a pre-established hierarchy of types for which DNA sequences are known.
BACKGROUND: Restriction fragment length polymorphism (RFLP) methods for genotyping genital human papillomavirus (HPV) are considered labor consuming and constrained by the reduced set of restriction enzymes capable of detecting specific mutations. However, we think that these methods have not taken full advantage of the high diversity of the known restriction enzymes. OBJECTIVE: We have set out to find the best restriction enzyme for HPV typing. STUDY DESIGN: An extensive search for enzymes was carried out by combining statistical methods and database information. The search maximized the discrimination between high- and low-risk types by examining the sequence of the L1 gene flanked by primers MY09/11. Different electrophoretic resolutions and two variations of the RFLP method were considered. RESULTS: HpyCH4V is the best enzyme for discriminating between risk types. Moreover, HpyCH4V generates different patterns for virtually all the HPV types. The typical pattern consists of two or three fragments, which facilitates typing in mixed infections. The typing of a set of clinical samples confirmed the expectations. CONCLUSIONS: This result illustrates the possibilities of statistical methods to exploit the high diversity of restriction enzymes in order to classify samples in a pre-established hierarchy of types for which DNA sequences are known.
Authors: André L P de Abreu; Paula R B Nogara; Raquel P Souza; Mariana C da Silva; Nelson S Uchimura; Rodrigo L Zanko; Erika C Ferreira; Maria C B Tognim; Jorge J V Teixeira; Fabrícia Gimenes; Marcia E L Consolaro Journal: Am J Trop Med Hyg Date: 2012-11-05 Impact factor: 2.345
Authors: André Lp de Abreu; Natália Malaguti; Raquel P Souza; Nelson S Uchimura; Érika C Ferreira; Monalisa W Pereira; Maria Db Carvalho; Sandra M Pelloso; Marcelo G Bonini; Fabrícia Gimenes; Marcia El Consolaro Journal: Am J Cancer Res Date: 2016-06-01 Impact factor: 6.166
Authors: Edilson Damke; Fábio A Kurscheidt; Valério A Balani; Karen I Takeda; Mary M T Irie; Fabrícia Gimenes; Marcia E L Consolaro Journal: Biomed Res Int Date: 2017-08-01 Impact factor: 3.411
Authors: Sheila C Rocha-Brischiliari; Fabrícia Gimenes; André L P de Abreu; Mary M T Irie; Raquel P Souza; Rosangela G Santana; Angela A F Gravena; Maria D de B Carvalho; Marcia E L Consolaro; Sandra M Pelloso Journal: Infect Agent Cancer Date: 2014-02-11 Impact factor: 2.965
Authors: Raquel P Souza; Fabrícia Gimenes; André Lp de Abreu; Sheila C Rocha-Brischiliari; Maria Db de Carvalho; Erika C Ferreira; Marcelo G Bonini; Sandra M Pelloso; Marcia El Consolaro Journal: Infect Agent Cancer Date: 2013-10-07 Impact factor: 2.965