title: Passenger Mutations Confound Interpretation of All Genetically Modified Congenic Mice.
abstract: Targeted mutagenesis in mice is a powerful tool for functional analysis of genes. However, genetic variation between embryonic stem cells (ESCs) used for targeting (previously almost exclusively 129-derived) and recipient strains (often C57BL/6J) typically results in congenic mice in which the targeted gene is flanked by ESC-derived passenger DNA potentially containing mutations. Comparative genomic analysis of 129 and C57BL/6J mouse strains revealed indels and single nucleotide polymorphisms resulting in alternative or aberrant amino acid sequences in 1,084 genes in the 129-strain genome. Annotating these passenger mutations to the reported genetically modified congenic mice that were generated using 129-strain ESCs revealed that nearly all these mice possess multiple passenger mutations potentially influencing the phenotypic outcome. We illustrated this phenotypic interference of 129-derived passenger mutations with several case studies and developed a Me-PaMuFind-It web tool to estimate the number and possible effect of passenger mutations in transgenic mice of interest.
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium. Electronic address: tom.vandenberghe@irc.vib-ugent.be.
authors.forename: Tom
authors.initials: T
authors.lastname: Vanden Berghe
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
authors.forename: Paco
authors.initials: P
authors.lastname: Hulpiau
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
authors.forename: Liesbet
authors.initials: L
authors.lastname: Martens
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
authors.forename: Roosmarijn E
authors.initials: RE
authors.lastname: Vandenbroucke
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
authors.forename: Elien
authors.initials: E
authors.lastname: Van Wonterghem
authors.affiliation: Department of Biomedical Engineering, University of Rochester, Rochester NY 14627, USA.
authors.forename: Seth W
authors.initials: SW
authors.lastname: Perry
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
authors.forename: Inge
authors.initials: I
authors.lastname: Bruggeman
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
authors.forename: Tatyana
authors.initials: T
authors.lastname: Divert
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
authors.forename: Sze Men
authors.initials: SM
authors.lastname: Choi
authors.affiliation: GNOMIXX bvba, Statistics for Genomics, 9000 Ghent, Belgium.
authors.forename: Marnik
authors.initials: M
authors.lastname: Vuylsteke
authors.affiliation: Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, University of Miami School of Medicine, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, Vavilov Institute for General Genetics, Moscow 119333, Russia.
authors.forename: Valery I
authors.initials: VI
authors.lastname: Shestopalov
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium.
authors.forename: Claude
authors.initials: C
authors.lastname: Libert
authors.affiliation: Inflammation Research Center, VIB, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium; Methusalem Program, Ghent University, 9000 Ghent. Electronic address: peter.vandenabeele@irc.vib-ugent.be.
authors.forename: Peter
authors.initials: P
authors.lastname: Vandenabeele
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D020169:Caspases / Q000235:genetics; D053471:Caspases, Initiator; D002874:Chromosome Mapping; D055028:Comparative Genomic Hybridization; D017630:Connexins / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D005838:Genotype; D053509:Matrix Metalloproteinase 13 / Q000235:genetics; D020784:Matrix Metalloproteinase 8 / Q000235:genetics; D051379:Mice; D020297:Mice, Congenic / Q000235:genetics; D008810:Mice, Inbred C57BL / Q000235:genetics*; D018345:Mice, Knockout; D009154:Mutation / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide
chemical_list: D017630:Connexins; D009419:Nerve Tissue Proteins; C503631:Panx1 protein, mouse; C101136:Casp4 protein, mouse; D020169:Caspases; D053471:Caspases, Initiator; D053509:Matrix Metalloproteinase 13; C507081:Mmp13 protein, mouse; C576328:MMP8 protein, mouse; D020784:Matrix Metalloproteinase 8