title: Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells.
abstract: Forward genetic screens using retroviral (or transposon) gene-trap vectors in a haploid genome revolutionized the investigation of molecular networks in mammals. However, the sequencing data generated by Phenotypic interrogation followed by Tag sequencing (PhiT-seq) were not well characterized. The analysis of human and mouse haploid screens allowed us to describe PhiT-seq data and to define quality control steps. Moreover, we identified several blind spots in both haploid genomes where gene-trap vectors can hardly integrate. Integration of transcriptomic data improved the performance of candidate gene identification. Furthermore, we experimented with various statistical tests to account for biological replicates in PhiT-seq and investigated the effect of normalization methods and other parameters on the performance. Finally, we developed: VISITs, a dedicated pipeline for analyzing PhiT-seq data (https://sourceforge.net/projects/visits/).
authors.affiliation: Swiss Federal Institute of Technology Zurich, Department of Biology, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland.|Life Science Zurich Graduate School, Molecular and Translational Biomedicine program, University of Zurich, Zurich, Switzerland.
authors.forename: Jian
authors.initials: J
authors.lastname: Yu
authors.affiliation: Swiss Federal Institute of Technology Zurich, Department of Biology, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland.
authors.forename: Constance
authors.initials: C
authors.lastname: Ciaudo
mesh_terms: D000818:Animals; D019992:Databases as Topic; D053263:Gene Regulatory Networks; D005821:Genetic Techniques; D005822:Genetic Vectors / Q000378:metabolism*; D006238:Haploidy; D006801:Humans; D008322:Mammals / Q000378:metabolism*; D051379:Mice; D058977:Molecular Sequence Annotation; D010641:Phenotype; D011401:Promoter Regions, Genetic / Q000235:genetics; D012372:ROC Curve; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics