title: No significant viral transcription detected in whole breast cancer transcriptomes.
abstract: BACKGROUND
  Studies evaluating the presence of viral sequences in breast cancer (BC), including various strains of human papillomavirus and human herpes virus, have yielded conflicting results. Most were based on RT-PCR and in situ hybridization.
  
  
  METHODS
  In this report we searched for expressed viral sequences in 58 BC transcriptomes using five distinct in silico methods. In addition, we complemented our RNA sequencing results with exome sequencing, PCR and immunohistochemistry (IHC) analyses. A control sample was used to test our in silico methods.
  
  
  RESULTS
  All of the computational methods correctly detected viral sequences in the control sample. We identified a small number of viral sequences belonging to human herpesvirus 4 and 6 and Merkel cell polyomavirus. The extremely low expression levels-two orders of magnitude lower than in a typical hepatitis B virus infection in hepatocellular carcinoma-did not suggest active infections. The presence of viral elements was confirmed in sample-matched exome sequences, but could not be confirmed by PCR or IHC.
  
  
  CONCLUSIONS
  Our results show that no viral sequences are expressed in significant amounts in the BC investigated. The presence of non-transcribed viral DNA cannot be excluded.
authors.affiliation: IRIBHM - Université Libre de Bruxelles, ULB, Campus Erasme CP602, 808 route de Lennik, 1070, Brussels, Belgium. dfimerel@ulb.ac.be.
authors.forename: Danai
authors.initials: D
authors.lastname: Fimereli
authors.affiliation: IRIBHM - Université Libre de Bruxelles, ULB, Campus Erasme CP602, 808 route de Lennik, 1070, Brussels, Belgium. dgacquer@ulb.ac.be.
authors.forename: David
authors.initials: D
authors.lastname: Gacquer
authors.affiliation: Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium. fumagalli@bordet.be.
authors.forename: Debora
authors.initials: D
authors.lastname: Fumagalli
authors.affiliation: Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium. roberto.salgado@bordet.be.|Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium. roberto.salgado@bordet.be.
authors.forename: Roberto
authors.initials: R
authors.lastname: Salgado
authors.affiliation: Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium. francoise.rothe@bordet.be.
authors.forename: Françoise
authors.initials: F
authors.lastname: Rothé
authors.affiliation: Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium. denis.larsimont@bordet.be.
authors.forename: Denis
authors.initials: D
authors.lastname: Larsimont
authors.affiliation: Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium. christos.sotiriou@bordet.be.
authors.forename: Christos
authors.initials: C
authors.lastname: Sotiriou
authors.affiliation: IRIBHM - Université Libre de Bruxelles, ULB, Campus Erasme CP602, 808 route de Lennik, 1070, Brussels, Belgium. vdetours@ulb.ac.be.|WELBIO, 808 route de Lennik, 1070, Brussels, Belgium. vdetours@ulb.ac.be.
authors.forename: Vincent
authors.initials: V
authors.lastname: Detours
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D004263:DNA Tumor Viruses / Q000235:genetics*; D005260:Female; D004854:Herpesvirus 4, Human / Q000235:genetics; D006801:Humans; D008875:Middle Aged; D014158:Transcription, Genetic / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*