title: Reads from: GSM4284684: pat 46 non-tumor [HDV_46B_S23]; Homo sapiens; RNA-Seq
design: Background: Infection with adeno-associated virus (AAV) has been identified as a possible risk for hepatocellular carcinoma (Nault et al. 2015; Bayard et al. 2018; La Bella et al. 2020) if the AAV genome integrates into the host genome. However, evaluation of such AAV integrations is complex because they are of a type called hit and run, meaning that only a fragment of the AAV genome remains integrated for a long time in the host DNA (Starrett and Buck 2019; Cantalupo et al. 2018). It is likely, but not absolutely proven, that a necessary condition for AAV integration in DNA to pose a risk for oncogenesis, it must also affect one mRNA. One possible effect on mRNA that can be detected by sequence analysis is the inclusion of AAV fragments in transcribed mRNA.  Hypothesis: The laboratory of Dr. Xin Wei Wang originally submitted this bioproject  PRJNA603277 and GEO data set GSE144269 in conjunction with the paper (Candia et al. 2020). In a new study of several data sets, the laboratory of Dr. Wang collaborated with the laboratory of Dr. Eytan Ruppin (also in the National Cancer Institute) to assess whether the RNASeq reads in this dataset show any evidence of AAV integration.  Contact Information (copied from GSE144269):   Contact name: Xin W. Wang  Contact E-mail: xw3u@nih.gov  Organization name: National Institutes of Health  Department: Center for Cancer Research  Lab: Laboratory of Human Carcinogenesis  Address: 37 Convent Dr.; Bethesda, MD 20892 USA