title: Human papillomavirus genotyping by Linear Array and Next-Generation Sequencing in cervical samples from Western Mexico.
abstract: BACKGROUND
  The Linear Array® (LA) genotyping test is one of the most used methodologies for Human papillomavirus (HPV) genotyping, in that it is able to detect 37 HPV genotypes and co-infections in the same sample. However, the assay is limited to a restricted number of HPV, and sequence variations in the detection region of the HPV probes could give false negatives results. Recently, 454 Next-Generation sequencing (NGS) technology has been efficiently used also for HPV genotyping; this methodology is based on massive sequencing of HPV fragments and is expected to be highly specific and sensitive. In this work, we studied HPV prevalence in cervixes of women in Western Mexico by LA and confirmed the genotypes found by NGS.
  
  
  METHODS
  Two hundred thirty three cervical samples from women Without cervical lesions (WCL, n = 48), with Cervical intraepithelial neoplasia grade 1 (CIN I, n = 98), or with Cervical cancer (CC, n = 87) were recruited, DNA was extracted, and HPV positivity was determined by PCR amplification using PGMY09/11 primers. All HPV- positive samples were genotyped individually by LA. Additionally, pools of amplicons from the PGMY-PCR products were sequenced using 454 NGS technology. Results obtained by NGS were compared with those of LA for each group of samples.
  
  
  RESULTS
  We identified 35 HPV genotypes, among which 30 were identified by both technologies; in addition, the HPV genotypes 32, 44, 74, 102 and 114 were detected by NGS. These latter genotypes, to our knowledge, have not been previously reported in Mexican population. Furthermore, we found that LA did not detect, in some diagnosis groups, certain HPV genotypes included in the test, such as 6, 11, 16, 26, 35, 51, 58, 68, 73, and 89, which indicates possible variations at the species level.
  
  
  CONCLUSIONS
  There are HPV genotypes in Mexican population that cannot be detected by LA, which is, at present, the most complete commercial genotyping test. More studies are necessary to determine the impact of HPV-44, 74, 102 and 114 on the risk of developing CC. A greater number of samples must be analyzed by NGS for the most accurate determination of Mexican HPV variants.
authors.affiliation: División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico. nereyda_2404@hotmail.com.|Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco, Mexico. nereyda_2404@hotmail.com.
authors.forename: María Guadalupe
authors.initials: MG
authors.lastname: Flores-Miramontes
authors.affiliation: División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico. torres_reyes_88@hotmail.com.|Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco, Mexico. torres_reyes_88@hotmail.com.
authors.forename: Luis Alberto
authors.initials: LA
authors.lastname: Torres-Reyes
authors.affiliation: División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico. lilit1585@hotmail.com.|Programa de Doctorado en Ciencias Biomédica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Jalisco, Mexico. lilit1585@hotmail.com.
authors.forename: Liliana
authors.initials: L
authors.lastname: Alvarado-Ruíz
authors.affiliation: Diagnostics Division, Roche México, Mexico City, Mexico. salvador.angel.rm@gmail.com.
authors.forename: Salvador Angel
authors.initials: SA
authors.lastname: Romero-Martínez
authors.affiliation: Diagnostics Division, Roche México, Mexico City, Mexico. verenice.ramirez@roche.com.
authors.forename: Verenice
authors.initials: V
authors.lastname: Ramírez-Rodríguez
authors.affiliation: Unidad de Investigación Médica en Epidemiología Clínica, UMAE Hospital de Especialidades, Centro Médico Nacional de Occidente (CMNO)-IMSS, Guadalajara, Jalisco, Mexico. luz.ma.adriana@gmail.com.
authors.forename: Luz María Adriana
authors.initials: LM
authors.lastname: Balderas-Peña
authors.affiliation: Centro de Investigación Biomédica de Oriente (CIBIOR)-IMSS, Metepec, Puebla, Mexico. veronica_vallejo@yahoo.com.
authors.forename: Verónica
authors.initials: V
authors.lastname: Vallejo-Ruíz
authors.affiliation: Laboratorio de Oncología Molecular, Unidad de Investigación Médica en Enfermedades Oncológicas (UIMEO)-IMSS, Mexico City, Mexico. patricia_1307@yahoo.com.mx.
authors.forename: Patricia
authors.initials: P
authors.lastname: Piña-Sánchez
authors.affiliation: Centro de Investigación Biomédica del Noreste (CIBIN)-IMSS, Monterrey, Nuevo León, Mexico. elvacortes@cibinmty.net.
authors.forename: Elva Irene
authors.initials: EI
authors.lastname: Cortés-Gutiérrez
authors.affiliation: División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico. lfjave@yahoo.com.
authors.forename: Luis Felipe
authors.initials: LF
authors.lastname: Jave-Suárez
authors.affiliation: División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO)-Instituto Mexicano del Seguro Social (IMSS), Sierra Mojada No. 800, Col. Independencia, 44340, Guadalajara, Jalisco, Mexico. adry.aguilar.lemarroy@gmail.com.
authors.forename: Adriana
authors.initials: A
authors.lastname: Aguilar-Lemarroy
mesh_terms: D000328:Adult; D000368:Aged; D002584:Cervix Uteri / Q000821:virology*; D005260:Female; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008800:Mexico / Q000453:epidemiology; D008875:Middle Aged; D017720:Molecular Epidemiology / Q000379:methods; D027383:Papillomaviridae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D030361:Papillomavirus Infections / Q000453:epidemiology / Q000821:virology*; D015995:Prevalence