title: Sources of Error in Mammalian Genetic Screens.
abstract: Genetic screens are invaluable tools for dissection of biological phenomena. Optimization of such screens to enhance discovery of candidate genes and minimize false positives is thus a critical aim. Here, we report several sources of error common to pooled genetic screening techniques used in mammalian cell culture systems, and demonstrate methods to eliminate these errors. We find that reverse transcriptase-mediated recombination during retroviral replication can lead to uncoupling of molecular tags, such as DNA barcodes (BCs), from their associated library elements, leading to chimeric proviral genomes in which BCs are paired to incorrect ORFs, shRNAs, etc This effect depends on the length of homologous sequence between unique elements, and can be minimized with careful vector design. Furthermore, we report that residual plasmid DNA from viral packaging procedures can contaminate transduced cells. These plasmids serve as additional copies of the PCR template during library amplification, resulting in substantial inaccuracies in measurement of initial reference populations for screen normalization. The overabundance of template in some samples causes an imbalance between PCR cycles of contaminated and uncontaminated samples, which results in a systematic artifactual depletion of GC-rich library elements. Elimination of contaminating plasmid DNA using the bacterial endonuclease Benzonase can restore faithful measurements of template abundance and minimize GC bias.
authors.affiliation: Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115.
authors.forename: Laura Magill
authors.initials: LM
authors.lastname: Sack
authors.affiliation: Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115.
authors.forename: Teresa
authors.initials: T
authors.lastname: Davoli
authors.affiliation: Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115.
authors.forename: Qikai
authors.initials: Q
authors.lastname: Xu
authors.affiliation: Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115.
authors.forename: Mamie Z
authors.initials: MZ
authors.lastname: Li
authors.affiliation: Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115 selledge@genetics.med.harvard.edu.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Elledge
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques / Q000592:standards; D058893:DNA Barcoding, Taxonomic / Q000592:standards*; D005820:Genetic Testing / Q000592:standards*; D005822:Genetic Vectors; D016678:Genome; D008322:Mammals / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000592:standards; D034741:RNA, Small Interfering / Q000235:genetics
chemical_list: D034741:RNA, Small Interfering
keywords: GC bias; barcode screening; genetic libraries; lentivirus; pooled shRNA or CRISPR screens