Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells

Sci Rep. 2017 Mar 17;7:44736. doi: 10.1038/srep44736.


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 (

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases as Topic
  • Gene Regulatory Networks
  • Genetic Techniques*
  • Genetic Vectors / metabolism*
  • Haploidy*
  • Humans
  • Mammals / metabolism*
  • Mice
  • Molecular Sequence Annotation
  • Phenotype
  • Promoter Regions, Genetic / genetics
  • ROC Curve
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Transcriptome / genetics