title: Assessment of Epstein-Barr virus nucleic acids in gastric but not in breast cancer by next-generation sequencing of pooled Mexican samples.
abstract: Gastric (GC) and breast (BrC) cancer are two of the most common and deadly tumours. Different lines of evidence suggest a possible causative role of viral infections for both GC and BrC. Wide genome sequencing (WGS) technologies allow searching for viral agents in tissues of patients with cancer. These technologies have already contributed to establish virus-cancer associations as well as to discovery new tumour viruses. The objective of this study was to document possible associations of viral infection with GC and BrC in Mexican patients. In order to gain idea about cost effective conditions of experimental sequencing, we first carried out an in silico simulation of WGS. The next-generation-platform IlluminaGallx was then used to sequence GC and BrC tumour samples. While we did not find viral sequences in tissues from BrC patients, multiple reads matching Epstein-Barr virus (EBV) sequences were found in GC tissues. An end-point polymerase chain reaction confirmed an enrichment of EBV sequences in one of the GC samples sequenced, validating the next-generation sequencing-bioinformatics pipeline.
authors.affiliation: Unidad de Investigación en Virología y Cáncer, Hospital Infantil de México Federico Gómez, México, DF, México.
authors.forename: Ezequiel M
authors.initials: EM
authors.lastname: Fuentes-Pananá
authors.affiliation: Laboratorio de Biotecnología y Bioinformática Genómica, Unidad Profesional Lázaro Cárdenas, Escuela Nacional de Ciencias Biológicas, México, DF, México.
authors.forename: Violeta
authors.initials: V
authors.lastname: Larios-Serrato
authors.affiliation: Laboratorio de Biotecnología y Bioinformática Genómica, Unidad Profesional Lázaro Cárdenas, Escuela Nacional de Ciencias Biológicas, México, DF, México.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Méndez-Tenorio
authors.affiliation: Unidad de Investigación en Virología y Cáncer, Hospital Infantil de México Federico Gómez, México, DF, México.
authors.forename: Abigail
authors.initials: A
authors.lastname: Morales-Sánchez
authors.affiliation: Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, México.
authors.forename: Carlos F
authors.initials: CF
authors.lastname: Arias
authors.affiliation: Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, México, DF, México.
authors.forename: Javier
authors.initials: J
authors.lastname: Torres
mesh_terms: D001943:Breast Neoplasms / Q000821:virology*; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation / Q000191:economics; D003201:Computers; D003362:Cost-Benefit Analysis / Q000379:methods; D004279:DNA, Viral / Q000302:isolation & purification*; D005260:Female; D004854:Herpesvirus 4, Human / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008800:Mexico; D009696:Nucleic Acids / Q000302:isolation & purification; D016133:Polymerase Chain Reaction / Q000379:methods; D012367:RNA, Viral / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods; D013274:Stomach Neoplasms / Q000821:virology*
chemical_list: D004279:DNA, Viral; D009696:Nucleic Acids; D012367:RNA, Viral