Author: "Seavitt, John" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Seavitt, John"' showing total 208 results

Start Over Author "Seavitt, John"

208 results on '"Seavitt, John"'

1. Impact of essential genes on the success of genome editing experiments generating 3313 new genetically engineered mouse lines

Author: Elrick, Hillary, Peterson, Kevin A., Willis, Brandon J., Lanza, Denise G., Acar, Elif F., Ryder, Edward J., Teboul, Lydia, Kasparek, Petr, Birling, Marie-Christine, Adams, David J., Bradley, Allan, Braun, Robert E., Brown, Steve D., Caulder, Adam, Codner, Gemma F., DeMayo, Francesco J., Dickinson, Mary E., Doe, Brendan, Duddy, Graham, Gertsenstein, Marina, Goodwin, Leslie O., Hérault, Yann, Lintott, Lauri G., Lloyd, K. C. Kent, Lorenzo, Isabel, Mackenzie, Matthew, Mallon, Ann-Marie, McKerlie, Colin, Parkinson, Helen, Ramirez-Solis, Ramiro, Seavitt, John R., Sedlacek, Radislav, Skarnes, William C., Smedley, Damien, Wells, Sara, White, Jacqueline K., Wood, Joshua A., Murray, Stephen A., Heaney, Jason D., and Nutter, Lauryl M. J.
Published: 2024
Full Text: View/download PDF

2. Whole genome analysis for 163 gRNAs in Cas9-edited mice reveals minimal off-target activity

Author: Peterson, Kevin A, Khalouei, Sam, Hanafi, Nour, Wood, Joshua A, Lanza, Denise G, Lintott, Lauri G, Willis, Brandon J, Seavitt, John R, Braun, Robert E, Dickinson, Mary E, White, Jacqueline K, Lloyd, KC Kent, Heaney, Jason D, Murray, Stephen A, Ramani, Arun, and Nutter, Lauryl MJ
Subjects: Biological Sciences, Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Generic health relevance, Mice, Animals, CRISPR-Cas Systems, Gene Editing, Genome, Mutation, Mutagenesis, Biological sciences, Biomedical and clinical sciences
Abstract: Genome editing with CRISPR-associated (Cas) proteins holds exceptional promise for "correcting" variants causing genetic disease. To realize this promise, off-target genomic changes cannot occur during the editing process. Here, we use whole genome sequencing to compare the genomes of 50 Cas9-edited founder mice to 28 untreated control mice to assess the occurrence of S. pyogenes Cas9-induced off-target mutagenesis. Computational analysis of whole-genome sequencing data detects 26 unique sequence variants at 23 predicted off-target sites for 18/163 guides used. While computationally detected variants are identified in 30% (15/50) of Cas9 gene-edited founder animals, only 38% (10/26) of the variants in 8/15 founders validate by Sanger sequencing. In vitro assays for Cas9 off-target activity identify only two unpredicted off-target sites present in genome sequencing data. In total, only 4.9% (8/163) of guides tested have detectable off-target activity, a rate of 0.2 Cas9 off-target mutations per founder analyzed. In comparison, we observe ~1,100 unique variants in each mouse regardless of genome exposure to Cas9 indicating off-target variants comprise a small fraction of genetic heterogeneity in Cas9-edited mice. These findings will inform future design and use of Cas9-edited animal models as well as provide context for evaluating off-target potential in genetically diverse patient populations.
Published: 2023

3. Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen

Author: Wotton, Janine M, Peterson, Emma, Flenniken, Ann M, Bains, Rasneer S, Veeraragavan, Surabi, Bower, Lynette R, Bubier, Jason A, Parisien, Marc, Bezginov, Alexandr, Haselimashhadi, Hamed, Mason, Jeremy, Moore, Michayla A, Stewart, Michelle E, Clary, Dave A, Delbarre, Daniel J, Anderson, Laura C, D'Souza, Abigail, Goodwin, Leslie O, Harrison, Mark E, Huang, Ziyue, Mckay, Matthew, Qu, Dawei, Santos, Luis, Srinivasan, Subhiksha, Urban, Rachel, Vukobradovic, Igor, Ward, Christopher S, Willett, Amelia M, Consortium, The International Mouse Phenotyping, Braun, Robert E, Brown, Steve DM, Dickinson, Mary E, Heaney, Jason D, Kumar, Vivek, Lloyd, KC Kent, Mallon, Ann-Marie, McKerlie, Colin, Murray, Stephen A, Nutter, Lauryl MJ, Parkinson, Helen, Seavitt, John R, Wells, Sara, Samaco, Rodney C, Chesler, Elissa J, Smedley, Damian, Diatchenko, Luda, Baumbauer, Kyle M, Young, Erin E, Bonin, Robert P, Mandillo, Silvia, and White, Jacqueline K
Subjects: Biomedical and Clinical Sciences, Neurosciences, Clinical Sciences, Human Genome, Pain Research, Genetics, Biotechnology, Chronic Pain, 2.1 Biological and endogenous factors, Generic health relevance, Animals, Freund's Adjuvant, Mice, Mice, Knockout, Nociception, Pain, Pain Measurement, Nocifensive behavior, Sensitization, Formalin, Hargreaves, von Frey, Complete Freund's adjuvant, Single-gene knockout mouse, Screen, IMPC, Comorbidity, Autism, International Mouse Phenotyping Consortium, Medical and Health Sciences, Psychology and Cognitive Sciences, Anesthesiology, Biomedical and clinical sciences, Health sciences, Psychology
Abstract: AbstractIdentifying the genetic determinants of pain is a scientific imperative given the magnitude of the global health burden that pain causes. Here, we report a genetic screen for nociception, performed under the auspices of the International Mouse Phenotyping Consortium. A biased set of 110 single-gene knockout mouse strains was screened for 1 or more nociception and hypersensitivity assays, including chemical nociception (formalin) and mechanical and thermal nociception (von Frey filaments and Hargreaves tests, respectively), with or without an inflammatory agent (complete Freund's adjuvant). We identified 13 single-gene knockout strains with altered nocifensive behavior in 1 or more assays. All these novel mouse models are openly available to the scientific community to study gene function. Two of the 13 genes (Gria1 and Htr3a) have been previously reported with nociception-related phenotypes in genetically engineered mouse strains and represent useful benchmarking standards. One of the 13 genes (Cnrip1) is known from human studies to play a role in pain modulation and the knockout mouse reported herein can be used to explore this function further. The remaining 10 genes (Abhd13, Alg6, BC048562, Cgnl1, Cp, Mmp16, Oxa1l, Tecpr2, Trim14, and Trim2) reveal novel pathways involved in nociception and may provide new knowledge to better understand genetic mechanisms of inflammatory pain and to serve as models for therapeutic target validation and drug development.
Published: 2022

4. Co-expression of prepulse inhibition and Schizophrenia genes in the mouse and human brain

Author: Aguilar-Pimental, Juan A., Amarie, Oana V., Becker, Lore, Calzada-Wack, Julia, Da Silva-Buttkus, Patricia, Dragano, Nathalia, Kraiger, Markus, Lengger, Christoph, Leuchtenberger, Stefanie, Marschall, Susan, Oestereicher, Manuela A., Rathkolb, Birgit, Sanz-Moreno, Adrián, Seisenberger, Claudia, Spielmann, Nadine, Stoeger, Claudia, Kumar, Vivek, Keskivali, Piia, King, Ruairidh, Haselimashhadi, Hamed, Bezginov, Alexandr, Norris, Clare, Taylor, Sarah, Pimm, Dale, Kelsey, Lois, Berberovic, Zorana, Qu, Dawei, D'Souza, Abigail, Bradaschia, Vivian, Eskandarian, Mohammed, Shang, Xueyuan, Duffin, Kyle, Roberton, Kyle, Xu, Catherine, Baguinat, Gloria, Laurin, Valerie, Lan, Qing, Sleep, Gillian, Lintott, Lauri, Gertsenstein, Marina, Tondat, Sandra, Cruz, Maribelle, Miller, David, Sorg, Tania, Riet, Fabrice, Tolentino, Heather, Tolentino, Todd, Schuchbauer, Mike, Hockenbury, Nichole, Beeman, Karrie, Pedroia, Sheryl, Salazar, Jason, Heffner, Mollie, Hsu, Joanne, Fletcher, Colin, Vanzanten, Maya, Golini, Elisabetta, Seavitt, John R., Lanza, Denise G., Lorenzo, Isabel, Gaspero, Angelina, Rios, Amanda, Garrett, Lillian, Trümbach, Dietrich, Lee, Donghyung, Mandillo, Silvia, Samaco, Rodney, Flenniken, Ann M., Stewart, Michelle, White, Jacqueline K., McKerlie, Colin, Nutter, Lauryl M.J., Vukobradovic, Igor, Veeraragavan, Surabi, Yuva, Lisa, Heaney, Jason D., Dickinson, Mary E., Meziane, Hamid, Hérault, Yann, Wells, Sara, Lloyd, K.C. Kent, Bower, Lynette, Lanoue, Louise, Clary, Dave, Zimprich, Annemarie, Gailus-Durner, Valerie, Fuchs, Helmut, Brown, Steve D.M., Chesler, Elissa J., Wurst, Wolfgang, Hrabě de Angelis, Martin, and Hölter, Sabine M.
Published: 2024
Full Text: View/download PDF

5. A resource of targeted mutant mouse lines for 5,061 genes

Author: Birling, Marie-Christine, Yoshiki, Atsushi, Adams, David J, Ayabe, Shinya, Beaudet, Arthur L, Bottomley, Joanna, Bradley, Allan, Brown, Steve DM, Bürger, Antje, Bushell, Wendy, Chiani, Francesco, Chin, Hsian-Jean Genie, Christou, Skevoulla, Codner, Gemma F, DeMayo, Francesco J, Dickinson, Mary E, Doe, Brendan, Donahue, Leah Rae, Fray, Martin D, Gambadoro, Alessia, Gao, Xiang, Gertsenstein, Marina, Gomez-Segura, Alba, Goodwin, Leslie O, Heaney, Jason D, Hérault, Yann, de Angelis, Martin Hrabe, Jiang, Si-Tse, Justice, Monica J, Kasparek, Petr, King, Ruairidh E, Kühn, Ralf, Lee, Ho, Lee, Young Jae, Liu, Zhiwei, Lloyd, KC Kent, Lorenzo, Isabel, Mallon, Ann-Marie, McKerlie, Colin, Meehan, Terrence F, Fuentes, Violeta Munoz, Newman, Stuart, Nutter, Lauryl MJ, Oh, Goo Taeg, Pavlovic, Guillaume, Ramirez-Solis, Ramiro, Rosen, Barry, Ryder, Edward J, Santos, Luis A, Schick, Joel, Seavitt, John R, Sedlacek, Radislav, Seisenberger, Claudia, Seong, Je Kyung, Skarnes, William C, Sorg, Tania, Steel, Karen P, Tamura, Masaru, Tocchini-Valentini, Glauco P, Wang, Chi-Kuang Leo, Wardle-Jones, Hannah, Wattenhofer-Donzé, Marie, Wells, Sara, Wiles, Michael V, Willis, Brandon J, Wood, Joshua A, Wurst, Wolfgang, Xu, Ying, Teboul, Lydia, and Murray, Stephen A
Subjects: Biological Sciences, Genetics, Infectious Diseases, Biotechnology, 2.1 Biological and endogenous factors, Animals, Gene Deletion, Genetic Association Studies, Genome, Genotype, Information Dissemination, International Cooperation, Internet, Mice, Mice, Knockout, Mouse Embryonic Stem Cells, Mutagenesis, Phenotype, International Mouse Phenotyping Consortium, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract: The International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for over 5,000 genes, including 2,850 novel null, 2,987 novel conditional- ready, and 4,433 novel reporter alleles.
Published: 2021

6. Soft windowing application to improve analysis of high-throughput phenotyping data

Author: Haselimashhadi, Hamed, Mason, Jeremy C, Munoz-Fuentes, Violeta, López-Gómez, Federico, Babalola, Kolawole, Acar, Elif F, Kumar, Vivek, White, Jacqui, Flenniken, Ann M, King, Ruairidh, Straiton, Ewan, Seavitt, John Richard, Gaspero, Angelina, Garza, Arturo, Christianson, Audrey E, Hsu, Chih-Wei, Reynolds, Corey L, Lanza, Denise G, Lorenzo, Isabel, Green, Jennie R, Gallegos, Juan J, Bohat, Ritu, Samaco, Rodney C, Veeraragavan, Surabi, Kim, Jong Kyoung, Miller, Gregor, Fuchs, Helmult, Garrett, Lillian, Becker, Lore, Kang, Yeon Kyung, Clary, David, Cho, Soo Young, Tamura, Masaru, Tanaka, Nobuhiko, Soo, Kyung Dong, Bezginov, Alexandr, About, Ghina Bou, Champy, Marie-France, Vasseur, Laurent, Leblanc, Sophie, Meziane, Hamid, Selloum, Mohammed, Reilly, Patrick T, Spielmann, Nadine, Maier, Holger, Gailus-Durner, Valerie, Sorg, Tania, Hiroshi, Masuya, Yuichi, Obata, Heaney, Jason D, Dickinson, Mary E, Wolfgang, Wurst, Tocchini-Valentini, Glauco P, Lloyd, Kevin C Kent, McKerlie, Colin, Seong, Je Kyung, Yann, Herault, de Angelis, Martin Hrabé, Brown, Steve DM, Smedley, Damian, Flicek, Paul, Mallon, Ann-Marie, Parkinson, Helen, and Meehan, Terrence F
Subjects: Biological Sciences, Genetics, Animals, Genetic Association Studies, Humans, Mice, Phenotype, Population Health, Software, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences
Abstract: MotivationHigh-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors.ResultsHere we introduce 'soft windowing', a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype-phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources.Availability and implementationThe method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin.Supplementary informationSupplementary data are available at Bioinformatics online.
Published: 2020

7. Human and mouse essentiality screens as a resource for disease gene discovery

Author: Cacheiro, Pilar, Muñoz-Fuentes, Violeta, Murray, Stephen A, Dickinson, Mary E, Bucan, Maja, Nutter, Lauryl MJ, Peterson, Kevin A, Haselimashhadi, Hamed, Flenniken, Ann M, Morgan, Hugh, Westerberg, Henrik, Konopka, Tomasz, Hsu, Chih-Wei, Christiansen, Audrey, Lanza, Denise G, Beaudet, Arthur L, Heaney, Jason D, Fuchs, Helmut, Gailus-Durner, Valerie, Sorg, Tania, Prochazka, Jan, Novosadova, Vendula, Lelliott, Christopher J, Wardle-Jones, Hannah, Wells, Sara, Teboul, Lydia, Cater, Heather, Stewart, Michelle, Hough, Tertius, Wurst, Wolfgang, Sedlacek, Radislav, Adams, David J, Seavitt, John R, Tocchini-Valentini, Glauco, Mammano, Fabio, Braun, Robert E, McKerlie, Colin, Herault, Yann, de Angelis, Martin Hrabě, Mallon, Ann-Marie, Lloyd, KC Kent, Brown, Steve DM, Parkinson, Helen, Meehan, Terrence F, and Smedley, Damian
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Pediatric, Biotechnology, Human Genome, 2.1 Biological and endogenous factors, Generic health relevance, Good Health and Well Being, Animals, Disease, Genes, Essential, Genetic Association Studies, Genomics, Humans, Mice, Mice, Knockout, Genomics England Research Consortium, International Mouse Phenotyping Consortium
Abstract: The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery.
Published: 2020

8. Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density

Author: Swan, Anna L, Schütt, Christine, Rozman, Jan, del Mar Muñiz Moreno, Maria, Brandmaier, Stefan, Simon, Michelle, Leuchtenberger, Stefanie, Griffiths, Mark, Brommage, Robert, Keskivali-Bond, Piia, Grallert, Harald, Werner, Thomas, Teperino, Raffaele, Becker, Lore, Miller, Gregor, Moshiri, Ala, Seavitt, John R, Cissell, Derek D, Meehan, Terrence F, Acar, Elif F, Lelliott, Christopher J, Flenniken, Ann M, Champy, Marie-France, Sorg, Tania, Ayadi, Abdel, Braun, Robert E, Cater, Heather, Dickinson, Mary E, Flicek, Paul, Gallegos, Juan, Ghirardello, Elena J, Heaney, Jason D, Jacquot, Sylvie, Lally, Connor, Logan, John G, Teboul, Lydia, Mason, Jeremy, Spielmann, Nadine, McKerlie, Colin, Murray, Stephen A, Nutter, Lauryl MJ, Odfalk, Kristian F, Parkinson, Helen, Prochazka, Jan, Reynolds, Corey L, Selloum, Mohammed, Spoutil, Frantisek, Svenson, Karen L, Vales, Taylor S, Wells, Sara E, White, Jacqueline K, Sedlacek, Radislav, Wurst, Wolfgang, Lloyd, KC Kent, Croucher, Peter I, Fuchs, Helmut, Williams, Graham R, Bassett, JH Duncan, Gailus-Durner, Valerie, Herault, Yann, Mallon, Ann-Marie, Brown, Steve DM, Mayer-Kuckuk, Philipp, and Hrabe de Angelis, Martin
Subjects: Biological Sciences, Genetics, Aging, Osteoporosis, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Musculoskeletal, Animals, Bone Density, Female, Gene Expression Regulation, Gene Ontology, Genetic Pleiotropy, Genome-Wide Association Study, Genotype, Male, Mice, Mice, Transgenic, Mutation, Osteoblasts, Osteoclasts, Phenotype, Promoter Regions, Genetic, Protein Interaction Maps, Sex Characteristics, Transcriptome, IMPC Consortium, Developmental Biology
Abstract: The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease.
Published: 2020

9. Bi-allelic Variants in TONSL Cause SPONASTRIME Dysplasia and a Spectrum of Skeletal Dysplasia Phenotypes

Author: Burrage, Lindsay C, Reynolds, John J, Baratang, Nissan Vida, Phillips, Jennifer B, Wegner, Jeremy, McFarquhar, Ashley, Higgs, Martin R, Christiansen, Audrey E, Lanza, Denise G, Seavitt, John R, Jain, Mahim, Li, Xiaohui, Parry, David A, Raman, Vandana, Chitayat, David, Chinn, Ivan K, Bertuch, Alison A, Karaviti, Lefkothea, Schlesinger, Alan E, Earl, Dawn, Bamshad, Michael, Savarirayan, Ravi, Doddapaneni, Harsha, Muzny, Donna, Jhangiani, Shalini N, Eng, Christine M, Gibbs, Richard A, Bi, Weimin, Emrick, Lisa, Rosenfeld, Jill A, Postlethwait, John, Westerfield, Monte, Dickinson, Mary E, Beaudet, Arthur L, Ranza, Emmanuelle, Huber, Celine, Cormier-Daire, Valérie, Shen, Wei, Mao, Rong, Heaney, Jason D, Orange, Jordan S, Genomics, University of Washington Center for Mendelian, Network, Undiagnosed Diseases, Adams, David R, Aday, Aaron, Alejandro, Mercedes E, Allard, Patrick, Ashley, Euan A, Azamian, Mahshid S, Bacino, Carlos A, Baker, Eva, Balasubramanyam, Ashok, Barseghyan, Hayk, Batzli, Gabriel F, Beggs, Alan H, Behnam, Babak, Bellen, Hugo J, Bernstein, Jonathan A, Berry, Gerard T, Bican, Anna, Bick, David P, Birch, Camille L, Bonner, Devon, Boone, Braden E, Bostwick, Bret L, Briere, Lauren C, Brokamp, Elly, Brown, Donna M, Brush, Matthew, Burke, Elizabeth A, Butte, Manish J, Chen, Shan, Clark, Gary D, Coakley, Terra R, Cogan, Joy D, Colley, Heather A, Cooper, Cynthia M, Cope, Heidi, Craigen, William J, D’Souza, Precilla, Davids, Mariska, Davidson, Jean M, Dayal, Jyoti G, Dell’Angelica, Esteban C, Dhar, Shweta U, Dipple, Katrina M, Donnell-Fink, Laurel A, Dorrani, Naghmeh, Dorset, Daniel C, Douine, Emilie D, Draper, David D, Dries, Annika M, Duncan, Laura, Eckstein, David J, Emrick, Lisa T, Enns, Gregory M, Eskin, Ascia, and Esteves, Cecilia
Subjects: Biological Sciences, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Clinical Research, Congenital Structural Anomalies, Pediatric, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Alleles, Animals, Cells, Cultured, Child, Child, Preschool, Chromosomal Instability, DNA Damage, Female, Fibroblasts, Genetic Association Studies, Genetic Variation, Humans, Mice, Mice, Knockout, Musculoskeletal Abnormalities, NF-kappa B, Osteochondrodysplasias, Exome Sequencing, Young Adult, Zebrafish, University of Washington Center for Mendelian Genomics, Undiagnosed Diseases Network, DNA repair, DNA replication, SPONASTRIME dysplasia, TONSL, exome sequencing, skeletal dysplasia, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract: SPONASTRIME dysplasia is an autosomal-recessive spondyloepimetaphyseal dysplasia characterized by spine (spondylar) abnormalities, midface hypoplasia with a depressed nasal bridge, metaphyseal striations, and disproportionate short stature. Scoliosis, coxa vara, childhood cataracts, short dental roots, and hypogammaglobulinemia have also been reported in this disorder. Although an autosomal-recessive inheritance pattern has been hypothesized, pathogenic variants in a specific gene have not been discovered in individuals with SPONASTRIME dysplasia. Here, we identified bi-allelic variants in TONSL, which encodes the Tonsoku-like DNA repair protein, in nine subjects (from eight families) with SPONASTRIME dysplasia, and four subjects (from three families) with short stature of varied severity and spondylometaphyseal dysplasia with or without immunologic and hematologic abnormalities, but no definitive metaphyseal striations at diagnosis. The finding of early embryonic lethality in a Tonsl-/- murine model and the discovery of reduced length, spinal abnormalities, reduced numbers of neutrophils, and early lethality in a tonsl-/- zebrafish model both support the hypomorphic nature of the identified TONSL variants. Moreover, functional studies revealed increased amounts of spontaneous replication fork stalling and chromosomal aberrations, as well as fewer camptothecin (CPT)-induced RAD51 foci in subject-derived cell lines. Importantly, these cellular defects were rescued upon re-expression of wild-type (WT) TONSL; this rescue is consistent with the hypothesis that hypomorphic TONSL variants are pathogenic. Overall, our studies in humans, mice, zebrafish, and subject-derived cell lines confirm that pathogenic variants in TONSL impair DNA replication and homologous recombination-dependent repair processes, and they lead to a spectrum of skeletal dysplasia phenotypes with numerous extra-skeletal manifestations.
Published: 2019

10. Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts

Author: Moore, Bret A, Leonard, Brian C, Sebbag, Lionel, Edwards, Sydney G, Cooper, Ann, Imai, Denise M, Straiton, Ewan, Santos, Luis, Reilly, Christopher, Griffey, Stephen M, Bower, Lynette, Clary, David, Mason, Jeremy, Roux, Michel J, Meziane, Hamid, Herault, Yann, McKerlie, Colin, Flenniken, Ann M, Nutter, Lauryl MJ, Berberovic, Zorana, Owen, Celeste, Newbigging, Susan, Adissu, Hibret, Eskandarian, Mohammed, Hsu, Chih-Wei, Kalaga, Sowmya, Udensi, Uchechukwu, Asomugha, Chinwe, Bohat, Ritu, Gallegos, Juan J, Seavitt, John R, Heaney, Jason D, Beaudet, Arthur L, Dickinson, Mary E, Justice, Monica J, Philip, Vivek, Kumar, Vivek, Svenson, Karen L, Braun, Robert E, Wells, Sara, Cater, Heather, Stewart, Michelle, Clementson-Mobbs, Sharon, Joynson, Russell, Gao, Xiang, Suzuki, Tomohiro, Wakana, Shigeharu, Smedley, Damian, Seong, JK, Tocchini-Valentini, Glauco, Moore, Mark, Fletcher, Colin, Karp, Natasha, Ramirez-Solis, Ramiro, White, Jacqueline K, de Angelis, Martin Hrabe, Wurst, Wolfgang, Thomasy, Sara M, Flicek, Paul, Parkinson, Helen, Brown, Steve DM, Meehan, Terrence F, Nishina, Patsy M, Murray, Stephen A, Krebs, Mark P, Mallon, Ann-Marie, Kent Lloyd, KC, Murphy, Christopher J, and Moshiri, Ala
Subjects: Biomedical and Clinical Sciences, Biotechnology, Genetics, International Mouse Phenotyping Consortium, Biological sciences, Biomedical and clinical sciences
Abstract: [This corrects the article DOI: 10.1038/s42003-018-0226-0.].
Published: 2019

11. Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts.

Author: Moore, Bret A, Leonard, Brian C, Sebbag, Lionel, Edwards, Sydney G, Cooper, Ann, Imai, Denise M, Straiton, Ewan, Santos, Luis, Reilly, Christopher, Griffey, Stephen M, Bower, Lynette, Clary, David, Mason, Jeremy, Roux, Michel J, Meziane, Hamid, Herault, Yann, International Mouse Phenotyping Consortium, McKerlie, Colin, Flenniken, Ann M, Nutter, Lauryl MJ, Berberovic, Zorana, Owen, Celeste, Newbigging, Susan, Adissu, Hibret, Eskandarian, Mohammed, Hsu, Chih-Wei, Kalaga, Sowmya, Udensi, Uchechukwu, Asomugha, Chinwe, Bohat, Ritu, Gallegos, Juan J, Seavitt, John R, Heaney, Jason D, Beaudet, Arthur L, Dickinson, Mary E, Justice, Monica J, Philip, Vivek, Kumar, Vivek, Svenson, Karen L, Braun, Robert E, Wells, Sara, Cater, Heather, Stewart, Michelle, Clementson-Mobbs, Sharon, Joynson, Russell, Gao, Xiang, Suzuki, Tomohiro, Wakana, Shigeharu, Smedley, Damian, Seong, JK, Tocchini-Valentini, Glauco, Moore, Mark, Fletcher, Colin, Karp, Natasha, Ramirez-Solis, Ramiro, White, Jacqueline K, de Angelis, Martin Hrabe, Wurst, Wolfgang, Thomasy, Sara M, Flicek, Paul, Parkinson, Helen, Brown, Steve DM, Meehan, Terrence F, Nishina, Patsy M, Murray, Stephen A, Krebs, Mark P, Mallon, Ann-Marie, Kent Lloyd, KC, Murphy, Christopher J, and Moshiri, Ala
Subjects: International Mouse Phenotyping Consortium, Genetics
Abstract: [This corrects the article DOI: 10.1038/s42003-018-0226-0.].
Published: 2019

12. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation

Author: Muñoz-Fuentes, Violeta, Cacheiro, Pilar, Meehan, Terrence F, Aguilar-Pimentel, Juan Antonio, Brown, Steve DM, Flenniken, Ann M, Flicek, Paul, Galli, Antonella, Mashhadi, Hamed Haseli, Hrabě de Angelis, Martin, Kim, Jong Kyoung, Lloyd, KC Kent, McKerlie, Colin, Morgan, Hugh, Murray, Stephen A, Nutter, Lauryl MJ, Reilly, Patrick T, Seavitt, John R, Seong, Je Kyung, Simon, Michelle, Wardle-Jones, Hannah, Mallon, Ann-Marie, Smedley, Damian, Parkinson, Helen E, and the IMPC consortium
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Generic health relevance, Life on Land, Cheetah, Endangered species, Loss-of-function, Non-model species, Panda, Polar bear, Phenotype, Wolf, Essential genes, IMPC, Knockout, Mouse, IMPC consortium, Environmental Sciences, Evolutionary Biology, Biological sciences, Environmental sciences
Abstract: The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.
Published: 2018

13. Co-expression of prepulse inhibition and schizophrenia genes in the mouse and human brain

Author: Garrett, Lillian, primary, Trümbach, Dietrich, additional, Lee, Dongyhung, additional, Mandillo, Silvia, additional, Samaco, Rodney, additional, Flenniken, Ann M., additional, Stewart, Michelle, additional, Aguilar-Pimental, Juan A., additional, Amarie, Oana V., additional, Becker, Lore, additional, Calzada-Wack, Julia, additional, Da Silva-Buttkus, Patricia, additional, Dragano, Nathalia, additional, Kraiger, Markus, additional, Lengger, Christoph, additional, Leuchtenberger, Stefanie, additional, Marschall, Susan, additional, Oestereicher, Manuela A., additional, Rathkolb, Birgit, additional, Sanz-Moreno, Adrián, additional, Seisenberger, Claudia, additional, Spielmann, Nadine, additional, Stoeger, Claudia, additional, Kumar, Vivek, additional, Keskivali, Piia, additional, King, Ruairidh, additional, Haselimashhadi, Hamed, additional, Bezginov, Alexandr, additional, Norris, Clare, additional, Taylor, Sarah, additional, Pimm, Dale, additional, Kelsey, Lois, additional, Berberovic, Zorana, additional, Qu, Dawei, additional, D'Souza, Abigail, additional, Bradaschia, Vivian, additional, Eskandarian, Mohammed, additional, Shang, Xueyuan, additional, Duffin, Kyle, additional, Roberton, Kyle, additional, Xu, Catherine, additional, Baguinat, Gloria, additional, Laurin, Valerie, additional, Lan, Qing, additional, Sleep, Gillian, additional, Lintott, Lauri, additional, Gertsenstein, Marina, additional, Tondat, Sandra, additional, Cruz, Maribelle, additional, Miller, David, additional, Sorg, Tania, additional, Riet, Fabrice, additional, Tolentino, Heather, additional, Tolentino, Todd, additional, Schuchbauer, Mike, additional, Hockenbury, Nichole, additional, Beeman, Karrie, additional, Pedroia, Sheryl, additional, Salazar, Jason, additional, Heffner, Mollie, additional, Hsu, Joanne, additional, Fletcher, Colin, additional, Vanzanten, Maya, additional, Golini, Elisabetta, additional, Seavitt, John R., additional, Lanza, Denise G., additional, Lorenzo, Isabel, additional, Gaspero, Angelina, additional, Rios, Amanda, additional, White, Jacqueline K., additional, McKerlie, Colin, additional, Nutter, Lauryl M.J., additional, Vukobradovic, Igor, additional, Veeraragavan, Surabi, additional, Yuva, Lisa, additional, Heaney, Jason D., additional, Dickinson, Mary E., additional, Meziane, Hamid, additional, Hérault, Yann, additional, Wells, Sara, additional, Lloyd, K.C.Kent, additional, Bower, Lynette, additional, Lanoue, Louise, additional, Clary, Dave, additional, Zimprich, Annemarie, additional, Gailus-Durner, Valerie, additional, Fuchs, Helmut, additional, Brown, Steve D.M., additional, Chesler, Elissa J., additional, Wurst, Wolfgang, additional, Hrabě de Angelis, Martin, additional, and Hölter, Sabine M., additional
Published: 2024
Full Text: View/download PDF

14. COPB2 loss of function causes a coatopathy with osteoporosis and developmental delay

Author: Marom, Ronit, Burrage, Lindsay C., Venditti, Rossella, Clément, Aurélie, Blanco-Sánchez, Bernardo, Jain, Mahim, Scott, Daryl A., Rosenfeld, Jill A., Sutton, V. Reid, Shinawi, Marwan, Mirzaa, Ghayda, DeVile, Catherine, Roberts, Rowenna, Calder, Alistair D., Allgrove, Jeremy, Grafe, Ingo, Lanza, Denise G., Li, Xiaohui, Joeng, Kyu Sang, Lee, Yi-Chien, Song, I-Wen, Sliepka, Joseph M., Batkovskyte, Dominyka, Washington, Megan, Dawson, Brian C., Jin, Zixue, Jiang, Ming-Ming, Chen, Shan, Chen, Yuqing, Tran, Alyssa A., Emrick, Lisa T., Murdock, David R., Hanchard, Neil A., Zapata, Gladys E., Mehta, Nitesh R., Weis, Mary Ann, Scott, Abbey A., Tremp, Brenna A., Phillips, Jennifer B., Wegner, Jeremy, Taylor-Miller, Tashunka, Gibbs, Richard A., Muzny, Donna M., Jhangiani, Shalini N., Hicks, John, Stottmann, Rolf W., Dickinson, Mary E., Seavitt, John R., Heaney, Jason D., Eyre, David R., Westerfield, Monte, De Matteis, Maria Antonietta, and Lee, Brendan
Published: 2021
Full Text: View/download PDF

15. Identification of genes required for eye development by high-throughput screening of mouse knockouts

Author: Moore, Bret A, Leonard, Brian C, Sebbag, Lionel, Edwards, Sydney G, Cooper, Ann, Imai, Denise M, Straiton, Ewan, Santos, Luis, Reilly, Christopher, Griffey, Stephen M, Bower, Lynette, Clary, David, Mason, Jeremy, Roux, Michel J, Meziane, Hamid, Herault, Yann, McKerlie, Colin, Flenniken, Ann M, Nutter, Lauryl MJ, Berberovic, Zorana, Owen, Celeste, Newbigging, Susan, Adissu, Hibret, Eskandarian, Mohammed, Hsu, Chih-Wei, Kalaga, Sowmya, Udensi, Uchechukwu, Asomugha, Chinwe, Bohat, Ritu, Gallegos, Juan J, Seavitt, John R, Heaney, Jason D, Beaudet, Arthur L, Dickinson, Mary E, Justice, Monica J, Philip, Vivek, Kumar, Vivek, Svenson, Karen L, Braun, Robert E, Wells, Sara, Cater, Heather, Stewart, Michelle, Clementson-Mobbs, Sharon, Joynson, Russell, Gao, Xiang, Suzuki, Tomohiro, Wakana, Shigeharu, Smedley, Damian, Seong, JK, Tocchini-Valentini, Glauco, Moore, Mark, Fletcher, Colin, Karp, Natasha, Ramirez-Solis, Ramiro, White, Jacqueline K, de Angelis, Martin Hrabe, Wurst, Wolfgang, Thomasy, Sara M, Flicek, Paul, Parkinson, Helen, Brown, Steve DM, Meehan, Terrence F, Nishina, Patsy M, Murray, Stephen A, Krebs, Mark P, Mallon, Ann-Marie, Lloyd, KC Kent, Murphy, Christopher J, and Moshiri, Ala
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Ophthalmology and Optometry, Eye Disease and Disorders of Vision, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Eye, International Mouse Phenotyping Consortium, Biological sciences, Biomedical and clinical sciences
Abstract: Despite advances in next generation sequencing technologies, determining the genetic basis of ocular disease remains a major challenge due to the limited access and prohibitive cost of human forward genetics. Thus, less than 4,000 genes currently have available phenotype information for any organ system. Here we report the ophthalmic findings from the International Mouse Phenotyping Consortium, a large-scale functional genetic screen with the goal of generating and phenotyping a null mutant for every mouse gene. Of 4364 genes evaluated, 347 were identified to influence ocular phenotypes, 75% of which are entirely novel in ocular pathology. This discovery greatly increases the current number of genes known to contribute to ophthalmic disease, and it is likely that many of the genes will subsequently prove to be important in human ocular development and disease.
Published: 2018

16. Correction: Corrigendum: High-throughput discovery of novel developmental phenotypes

Author: Dickinson, Mary E, Flenniken, Ann M, Ji, Xiao, Teboul, Lydia, Wong, Michael D, White, Jacqueline K, Meehan, Terrence F, Weninger, Wolfgang J, Westerberg, Henrik, Adissu, Hibret, Baker, Candice N, Bower, Lynette, Brown, James M, Caddle, L Brianna, Chiani, Francesco, Clary, Dave, Cleak, James, Daly, Mark J, Denegre, James M, Doe, Brendan, Dolan, Mary E, Edie Helmut Fuchs, Sarah M, Gailus-Durner, Valerie, Galli, Antonella, Gambadoro, Alessia, Gallegos, Juan, Guo, Shiying, Horner, Neil R, Hsu, Chih-Wei, Johnson, Sara J, Kalaga, Sowmya, Keith, Lance C, Lanoue, Louise, Lawson, Thomas N, Lek, Monkol, Mark, Manuel, Marschall, Susan, Mason, Jeremy, McElwee, Melissa L, Nutter, Susan Newbigging Lauryl MJ, Peterson, Kevin A, Ramirez-Solis, Ramiro, Rowland, Douglas J, Ryder, Edward, Samocha, Kaitlin E, Seavitt, John R, Selloum, Mohammed, Szoke-Kovacs, Zsombor, Tamura, Masaru, Trainor, Amanda G, Tudose, Ilinca, Wakana, Shigeharu, Warren, Jonathan, Wendling, Olivia, West, David B, Wong, Leeyean, Yoshiki, Atsushi, Wurst, Wolfgang, MacArthur, Daniel G, Tocchini-Valentini, Glauco P, Gao, Xiang, Flicek, Paul, Bradley, Allan, Skarnes, William C, Justice, Monica J, Parkinson, Helen E, Moore, Mark, Wells, Sara, Braun, Robert E, Svenson, Karen L, de Angelis, Martin Hrabe, Herault, Yann, Mohun, Tim, Mallon, Ann-Marie, Henkelman, R Mark, Brown, Steve DM, Adams, David J, Lloyd, KC Kent, McKerlie, Colin, Beaudet, Arthur L, and Murray, Maja Bućan Stephen A
Subjects: International Mouse Phenotyping Consortium, General Science & Technology
Abstract: This corrects the article DOI: 10.1038/nature19356.
Published: 2017

17. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.

Author: Meehan, Terrence F, Conte, Nathalie, West, David B, Jacobsen, Julius O, Mason, Jeremy, Warren, Jonathan, Chen, Chao-Kung, Tudose, Ilinca, Relac, Mike, Matthews, Peter, Karp, Natasha, Santos, Luis, Fiegel, Tanja, Ring, Natalie, Westerberg, Henrik, Greenaway, Simon, Sneddon, Duncan, Morgan, Hugh, Codner, Gemma F, Stewart, Michelle E, Brown, James, Horner, Neil, International Mouse Phenotyping Consortium, Haendel, Melissa, Washington, Nicole, Mungall, Christopher J, Reynolds, Corey L, Gallegos, Juan, Gailus-Durner, Valerie, Sorg, Tania, Pavlovic, Guillaume, Bower, Lynette R, Moore, Mark, Morse, Iva, Gao, Xiang, Tocchini-Valentini, Glauco P, Obata, Yuichi, Cho, Soo Young, Seong, Je Kyung, Seavitt, John, Beaudet, Arthur L, Dickinson, Mary E, Herault, Yann, Wurst, Wolfgang, de Angelis, Martin Hrabe, Lloyd, KC Kent, Flenniken, Ann M, Nutter, Lauryl MJ, Newbigging, Susan, McKerlie, Colin, Justice, Monica J, Murray, Stephen A, Svenson, Karen L, Braun, Robert E, White, Jacqueline K, Bradley, Allan, Flicek, Paul, Wells, Sara, Skarnes, William C, Adams, David J, Parkinson, Helen, Mallon, Ann-Marie, Brown, Steve DM, and Smedley, Damian
Subjects: International Mouse Phenotyping Consortium, Animals, Mice, Knockout, Humans, Mice, Genetic Diseases, Inborn, Disease Models, Animal, Genetic Predisposition to Disease, Phenotype, Female, Male, Gene Knockout Techniques, Knockout, Genetic Diseases, Inborn, Disease Models, Animal, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract: Although next-generation sequencing has revolutionized the ability to associate variants with human diseases, diagnostic rates and development of new therapies are still limited by a lack of knowledge of the functions and pathobiological mechanisms of most genes. To address this challenge, the International Mouse Phenotyping Consortium is creating a genome- and phenome-wide catalog of gene function by characterizing new knockout-mouse strains across diverse biological systems through a broad set of standardized phenotyping tests. All mice will be readily available to the biomedical community. Analyzing the first 3,328 genes identified models for 360 diseases, including the first models, to our knowledge, for type C Bernard-Soulier, Bardet-Biedl-5 and Gordon Holmes syndromes. 90% of our phenotype annotations were novel, providing functional evidence for 1,092 genes and candidates in genetically uncharacterized diseases including arrhythmogenic right ventricular dysplasia 3. Finally, we describe our role in variant functional validation with The 100,000 Genomes Project and others.
Published: 2017

18. A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

Author: Bowl, Michael R, Simon, Michelle M, Ingham, Neil J, Greenaway, Simon, Santos, Luis, Cater, Heather, Taylor, Sarah, Mason, Jeremy, Kurbatova, Natalja, Pearson, Selina, Bower, Lynette R, Clary, Dave A, Meziane, Hamid, Reilly, Patrick, Minowa, Osamu, Kelsey, Lois, The International Mouse Phenotyping Consortium, Tocchini-Valentini, Glauco P, Gao, Xiang, Bradley, Allan, Skarnes, William C, Moore, Mark, Beaudet, Arthur L, Justice, Monica J, Seavitt, John, Dickinson, Mary E, Wurst, Wolfgang, de Angelis, Martin Hrabe, Herault, Yann, Wakana, Shigeharu, Nutter, Lauryl MJ, Flenniken, Ann M, McKerlie, Colin, Murray, Stephen A, Svenson, Karen L, Braun, Robert E, West, David B, Lloyd, KC Kent, Adams, David J, White, Jacqui, Karp, Natasha, Flicek, Paul, Smedley, Damian, Meehan, Terrence F, Parkinson, Helen E, Teboul, Lydia M, Wells, Sara, Steel, Karen P, Mallon, Ann-Marie, and Brown, Steve DM
Subjects: Biological Sciences, Biomedical and Clinical Sciences, Genetics, Allied Health and Rehabilitation Science, Clinical Sciences, Health Sciences, Neurosciences, Hearing Loss, Clinical Research, Human Genome, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Ear, Neurological, Animals, Datasets as Topic, Genetic Testing, Hearing Tests, Mice, Mice, Knockout, Phenotype, Protein Interaction Maps, International Mouse Phenotyping Consortium
Abstract: The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function.The full extent of the genetic basis for hearing impairment is unknown. Here, as part of the International Mouse Phenotyping Consortium, the authors perform a hearing loss screen in 3006 mouse knockout strains and identify 52 new candidate genes for genetic hearing loss.
Published: 2017

19. Prevalence of sexual dimorphism in mammalian phenotypic traits

Author: Karp, Natasha A, Mason, Jeremy, Beaudet, Arthur L, Benjamini, Yoav, Bower, Lynette, Braun, Robert E, Brown, Steve DM, Chesler, Elissa J, Dickinson, Mary E, Flenniken, Ann M, Fuchs, Helmut, Angelis, Martin Hrabe de, Gao, Xiang, Guo, Shiying, Greenaway, Simon, Heller, Ruth, Herault, Yann, Justice, Monica J, Kurbatova, Natalja, Lelliott, Christopher J, Lloyd, KC Kent, Mallon, Ann-Marie, Mank, Judith E, Masuya, Hiroshi, McKerlie, Colin, Meehan, Terrence F, Mott, Richard F, Murray, Stephen A, Parkinson, Helen, Ramirez-Solis, Ramiro, Santos, Luis, Seavitt, John R, Smedley, Damian, Sorg, Tania, Speak, Anneliese O, Steel, Karen P, Svenson, Karen L, Wakana, Shigeharu, West, David, Wells, Sara, Westerberg, Henrik, Yaacoby, Shay, and White, Jacqueline K
Subjects: Biological Psychology, Biological Sciences, Biomedical and Clinical Sciences, Psychology, Women's Health, Genetics, Estrogen, 2.1 Biological and endogenous factors, Infection, Generic health relevance, Animals, Body Weight, Female, Genes, Modifier, Genotype, Mammals, Mice, Phenotype, Quantitative Trait, Heritable, Sex Characteristics, International Mouse Phenotyping Consortium
Abstract: The role of sex in biomedical studies has often been overlooked, despite evidence of sexually dimorphic effects in some biological studies. Here, we used high-throughput phenotype data from 14,250 wildtype and 40,192 mutant mice (representing 2,186 knockout lines), analysed for up to 234 traits, and found a large proportion of mammalian traits both in wildtype and mutants are influenced by sex. This result has implications for interpreting disease phenotypes in animal models and humans.
Published: 2017

20. High-throughput discovery of novel developmental phenotypes.

Author: Dickinson, Mary E, Flenniken, Ann M, Ji, Xiao, Teboul, Lydia, Wong, Michael D, White, Jacqueline K, Meehan, Terrence F, Weninger, Wolfgang J, Westerberg, Henrik, Adissu, Hibret, Baker, Candice N, Bower, Lynette, Brown, James M, Caddle, L Brianna, Chiani, Francesco, Clary, Dave, Cleak, James, Daly, Mark J, Denegre, James M, Doe, Brendan, Dolan, Mary E, Edie, Sarah M, Fuchs, Helmut, Gailus-Durner, Valerie, Galli, Antonella, Gambadoro, Alessia, Gallegos, Juan, Guo, Shiying, Horner, Neil R, Hsu, Chih-Wei, Johnson, Sara J, Kalaga, Sowmya, Keith, Lance C, Lanoue, Louise, Lawson, Thomas N, Lek, Monkol, Mark, Manuel, Marschall, Susan, Mason, Jeremy, McElwee, Melissa L, Newbigging, Susan, Nutter, Lauryl MJ, Peterson, Kevin A, Ramirez-Solis, Ramiro, Rowland, Douglas J, Ryder, Edward, Samocha, Kaitlin E, Seavitt, John R, Selloum, Mohammed, Szoke-Kovacs, Zsombor, Tamura, Masaru, Trainor, Amanda G, Tudose, Ilinca, Wakana, Shigeharu, Warren, Jonathan, Wendling, Olivia, West, David B, Wong, Leeyean, Yoshiki, Atsushi, International Mouse Phenotyping Consortium, Jackson Laboratory, Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), Charles River Laboratories, MRC Harwell, Toronto Centre for Phenogenomics, Wellcome Trust Sanger Institute, RIKEN BioResource Center, MacArthur, Daniel G, Tocchini-Valentini, Glauco P, Gao, Xiang, Flicek, Paul, Bradley, Allan, Skarnes, William C, Justice, Monica J, Parkinson, Helen E, Moore, Mark, Wells, Sara, Braun, Robert E, Svenson, Karen L, de Angelis, Martin Hrabe, Herault, Yann, Mohun, Tim, Mallon, Ann-Marie, Henkelman, R Mark, Brown, Steve DM, Adams, David J, Lloyd, KC Kent, McKerlie, Colin, Beaudet, Arthur L, Bućan, Maja, and Murray, Stephen A
Subjects: International Mouse Phenotyping Consortium, Jackson Laboratory, Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris, Charles River Laboratories, MRC Harwell, Toronto Centre for Phenogenomics, Wellcome Trust Sanger Institute, RIKEN BioResource Center, Animals, Mice, Inbred C57BL, Mice, Knockout, Humans, Mice, Disease, Imaging, Three-Dimensional, Conserved Sequence, Sequence Homology, Phenotype, Penetrance, Mutation, Polymorphism, Single Nucleotide, Genes, Essential, Genes, Lethal, Embryo, Mammalian, Genome-Wide Association Study, High-Throughput Screening Assays, Biotechnology, Human Genome, Pediatric, Congenital Structural Anomalies, Genetics, 2.1 Biological and endogenous factors, General Science & Technology
Abstract: Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.
Published: 2016

21. Bi-allelic Variants in TONSL Cause SPONASTRIME Dysplasia and a Spectrum of Skeletal Dysplasia Phenotypes

Author: Adams, David R., Aday, Aaron, Alejandro, Mercedes E., Allard, Patrick, Ashley, Euan A., Azamian, Mahshid S., Bacino, Carlos A., Baker, Eva, Balasubramanyam, Ashok, Barseghyan, Hayk, Batzli, Gabriel F., Beggs, Alan H., Behnam, Babak, Bellen, Hugo J., Bernstein, Jonathan A., Berry, Gerard T., Bican, Anna, Bick, David P., Birch, Camille L., Bonner, Devon, Boone, Braden E., Bostwick, Bret L., Briere, Lauren C., Brokamp, Elly, Brown, Donna M., Brush, Matthew, Burke, Elizabeth A., Burrage, Lindsay C., Butte, Manish J., Chen, Shan, Clark, Gary D., Coakley, Terra R., Cogan, Joy D., Colley, Heather A., Cooper, Cynthia M., Cope, Heidi, Craigen, William J., D’Souza, Precilla, Davids, Mariska, Davidson, Jean M., Dayal, Jyoti G., Dell’Angelica, Esteban C., Dhar, Shweta U., Dipple, Katrina M., Donnell-Fink, Laurel A., Dorrani, Naghmeh, Dorset, Daniel C., Douine, Emilie D., Draper, David D., Dries, Annika M., Duncan, Laura, Eckstein, David J., Emrick, Lisa T., Eng, Christine M., Enns, Gregory M., Eskin, Ascia, Esteves, Cecilia, Estwick, Tyra, Fernandez, Liliana, Ferreira, Carlos, Fieg, Elizabeth L., Fisher, Paul G., Fogel, Brent L., Friedman, Noah D., Gahl, William A., Glanton, Emily, Godfrey, Rena A., Goldman, Alica M., Goldstein, David B., Gould, Sarah E., Gourdine, Jean-Philippe F., Groden, Catherine A., Gropman, Andrea L., Haendel, Melissa, Hamid, Rizwan, Hanchard, Neil A., High, Frances, Holm, Ingrid A., Hom, Jason, Howerton, Ellen M., Huang, Yong, Jamal, Fariha, Jiang, Yong-hui, Johnston, Jean M., Jones, Angela L., Karaviti, Lefkothea, Koeller, David M., Kohane, Isaac S., Kohler, Jennefer N., Krasnewich, Donna M., Korrick, Susan, Koziura, Mary, Krier, Joel B., Kyle, Jennifer E., Lalani, Seema R., Lau, C. Christopher, Lazar, Jozef, LeBlanc, Kimberly, Lee, Brendan H., Lee, Hane, Levy, Shawn E., Lewis, Richard A., Lincoln, Sharyn A., Loo, Sandra K., Loscalzo, Joseph, Maas, Richard L., Macnamara, Ellen F., MacRae, Calum A., Maduro, Valerie V., Majcherska, Marta M., Malicdan, May Christine V., Mamounas, Laura A., Manolio, Teri A., Markello, Thomas C., Marom, Ronit, Martin, Martin G., Martínez-Agosto, Julian A., Marwaha, Shruti, May, Thomas, McConkie-Rosell, Allyn, McCormack, Colleen E., McCray, Alexa T., Merker, Jason D., Metz, Thomas O., Might, Matthew, Moretti, Paolo M., Morimoto, Marie, Mulvihill, John J., Murdock, David R., Murphy, Jennifer L., Muzny, Donna M., Nehrebecky, Michele E., Nelson, Stan F., Newberry, J. Scott, Newman, John H., Nicholas, Sarah K., Novacic, Donna, Orange, Jordan S., Orengo, James P., Pallais, J. Carl, Palmer, Christina G.S., Papp, Jeanette C., Parker, Neil H., Pena, Loren D.M., Phillips, John A., III, Posey, Jennifer E., Postlethwait, John H., Potocki, Lorraine, Pusey, Barbara N., Renteria, Genecee, Reuter, Chloe M., Rives, Lynette, Robertson, Amy K., Rodan, Lance H., Rosenfeld, Jill A., Sampson, Jacinda B., Samson, Susan L., Schoch, Kelly, Scott, Daryl A., Shakachite, Lisa, Sharma, Prashant, Shashi, Vandana, Signer, Rebecca, Silverman, Edwin K., Sinsheimer, Janet S., Smith, Kevin S., Spillmann, Rebecca C., Stoler, Joan M., Stong, Nicholas, Sullivan, Jennifer A., Sweetser, David A., Tan, Queenie K.-G., Tifft, Cynthia J., Toro, Camilo, Tran, Alyssa A., Urv, Tiina K., Vilain, Eric, Vogel, Tiphanie P., Waggott, Daryl M., Wahl, Colleen E., Walley, Nicole M., Walsh, Chris A., Walker, Melissa, Wan, Jijun, Wangler, Michael F., Ward, Patricia A., Waters, Katrina M., Webb-Robertson, Bobbie-Jo M., Westerfield, Monte, Wheeler, Matthew T., Wise, Anastasia L., Wolfe, Lynne A., Worthey, Elizabeth A., Yamamoto, Shinya, Yang, John, Yang, Yaping, Yoon, Amanda J., Yu, Guoyun, Zastrow, Diane B., Zhao, Chunli, Zheng, Allison, Reynolds, John J., Baratang, Nissan Vida, Phillips, Jennifer B., Wegner, Jeremy, McFarquhar, Ashley, Higgs, Martin R., Christiansen, Audrey E., Lanza, Denise G., Seavitt, John R., Jain, Mahim, Li, Xiaohui, Parry, David A., Raman, Vandana, Chitayat, David, Chinn, Ivan K., Bertuch, Alison A., Schlesinger, Alan E., Earl, Dawn, Bamshad, Michael, Savarirayan, Ravi, Doddapaneni, Harsha, Muzny, Donna, Jhangiani, Shalini N., Gibbs, Richard A., Bi, Weimin, Emrick, Lisa, Postlethwait, John, Dickinson, Mary E., Beaudet, Arthur L., Ranza, Emmanuelle, Huber, Celine, Cormier-Daire, Valérie, Shen, Wei, Mao, Rong, Heaney, Jason D., Bertola, Débora, Yamamoto, Guilherme L., Baratela, Wagner A.R., Butler, Merlin G., Ali, Asim, Adeli, Mehdi, Cohn, Daniel H., Krakow, Deborah, Jackson, Andrew P., Lees, Melissa, Offiah, Amaka C., Carlston, Colleen M., Carey, John C., Stewart, Grant S., Campeau, Philippe M., and Lee, Brendan
Published: 2019
Full Text: View/download PDF

22. Rapid and Integrative Discovery of Retina Regulatory Molecules

Author: Albrecht, Nicholas E., Alevy, Jonathan, Jiang, Danye, Burger, Courtney A., Liu, Brian I., Li, Fenge, Wang, Julia, Kim, Seon-Young, Hsu, Chih-Wei, Kalaga, Sowmya, Udensi, Uchechukwu, Asomugha, Chinwe, Bohat, Ritu, Gaspero, Angelina, Justice, Monica J., Westenskow, Peter D., Yamamoto, Shinya, Seavitt, John R., Beaudet, Arthur L., Dickinson, Mary E., and Samuel, Melanie A.
Published: 2018
Full Text: View/download PDF

23. An oocyte‐specific Cas9‐expressing mouse for germline CRISPR/Cas9‐mediated genome editing.

Author: Lanza, Denise G., Mao, Jianqiang, Lorenzo, Isabel, Liao, Lan, Seavitt, John R., Ljungberg, M. Cecilia, Simpson, Elizabeth M., DeMayo, Francesco J., and Heaney, Jason D.
Published: 2024
Full Text: View/download PDF

24. Loss of Functionally Redundant p38 Isoforms in T Cells Enhances Regulatory T Cell Induction

Author: Hayakawa, Morisada, Hayakawa, Hiroko, Petrova, Tsvetana, Ritprajak, Patcharee, Sutavani, Ruhcha V., Jiménez-Andrade, Guillermina Yanek, Sano, Yasuyo, Choo, Min-Kyung, Seavitt, John, Venigalla, Ram K.C., Otsu, Kinya, Georgopoulos, Katia, Arthur, J. Simon C., and Park, Jin Mo
Published: 2017
Full Text: View/download PDF

25. Delayed skeletal development and IGF-1 deficiency in a mouse model of lysinuric protein intolerance

Author: Stroup, Bridget M., primary, Li, Xiaohui, additional, Ho, Sara, additional, Zhouyao, Haonan, additional, Chen, Yuqing, additional, Ani, Safa, additional, Dawson, Brian, additional, Jin, Zixue, additional, Marom, Ronit, additional, Jiang, Ming-Ming, additional, Lorenzo, Isabel, additional, Rosen, Daniel, additional, Lanza, Denise, additional, Aceves, Nathalie, additional, Koh, Sara, additional, Seavitt, John R., additional, Heaney, Jason D., additional, Lee, Brendan, additional, and Burrage, Lindsay C., additional
Published: 2023
Full Text: View/download PDF

26. P173: Precision animal modeling and VUS-resolution in a novel AXIN2-related disorder

Author: Burrage, Lindsay, Lanza, Denise, Marcogliese, Paul, Lu, Di, Logan Hsu, Chih-Wei, Aceves, Nathalie, Gonzalez, Matthew, Christiansen, Audrey, Rasmussen, Tara, Gaspero, Angelina, Seavitt, John, Dickinson, Mary, Shayota, Brian, Pachter, Stephanie, Day-Salvatore, Debra-Lynn, Kanca, Oguz, Wangler, Michael, Potocki, Lorraine, Rosenfeld, Jill, Lee, Brendan, Yamamoto, Shinya, Bellen, Hugo, and Heaney, Jason
Published: 2024
Full Text: View/download PDF

27. Three-dimensional microCT imaging of mouse development from early post-implantation to early postnatal stages

Author: Hsu, Chih-Wei, Wong, Leeyean, Rasmussen, Tara L., Kalaga, Sowmya, McElwee, Melissa L., Keith, Lance C., Bohat, Ritu, Seavitt, John R., Beaudet, Arthur L., and Dickinson, Mary E.
Published: 2016
Full Text: View/download PDF

28. Comparative analysis of single-stranded DNA donors to generate conditional null mouse alleles

Author: Lanza, Denise G., Gaspero, Angelina, Lorenzo, Isabel, Liao, Lan, Zheng, Ping, Wang, Ying, Deng, Yu, Cheng, Chonghui, Zhang, Chuansheng, Seavitt, John R., DeMayo, Francesco J., Xu, Jianming, Dickinson, Mary E., Beaudet, Arthur L., and Heaney, Jason D.
Published: 2018
Full Text: View/download PDF

29. The Role of the Ikaros Gene Family in Lymphocyte Development

Author: Gómez-del Arco, Pablo, Naito, Taku, Seavitt, John, Yoshida, Toshimi, Williams, Christine, Georgopoulos, Katia, Iuchi, Shiro, editor, and Kuldell, Natalie, editor
Published: 2005
Full Text: View/download PDF

30. Corrigendum: High-throughput discovery of novel developmental phenotypes

Author: Dickinson, Mary E., Flenniken, Ann M., Ji, Xiao, Teboul, Lydia, Wong, Michael D., White, Jacqueline K., Meehan, Terrence F., Weninger, Wolfgang J., Westerberg, Henrik, Adissu, Hibret, Baker, Candice N., Bower, Lynette, Brown, James M., Caddle, Brianna L., Chiani, Francesco, Clary, Dave, Cleak, James, Daly, Mark J., Denegre, James M., Doe, Brendan, Dolan, Mary E., Helmut Fuchs, Sarah M. Edie, Gailus-Durner, Valerie, Galli, Antonella, Gambadoro, Alessia, Gallegos, Juan, Guo, Shiying, Horner, Neil R., Hsu, Chih-Wei, Johnson, Sara J., Kalaga, Sowmya, Keith, Lance C., Lanoue, Louise, Lawson, Thomas N., Lek, Monkol, Mark, Manuel, Marschall, Susan, Mason, Jeremy, McElwee, Melissa L., Nutter, Susan Newbigging Lauryl M. J., Peterson, Kevin A., Ramirez-Solis, Ramiro, Rowland, Douglas J., Ryder, Edward, Samocha, Kaitlin E., Seavitt, John R., Selloum, Mohammed, Szoke-Kovacs, Zsombor, Tamura, Masaru, Trainor, Amanda G., Tudose, Ilinca, Wakana, Shigeharu, Warren, Jonathan, Wendling, Olivia, West, David B., Wong, Leeyean, Yoshiki, Atsushi, Wurst, Wolfgang, MacArthur, Daniel G., Tocchini-Valentini, Glauco P., Gao, Xiang, Flicek, Paul, Bradley, Allan, Skarnes, William C., Justice, Monica J., Parkinson, Helen E., Moore, Mark, Wells, Sara, Braun, Robert E., Svenson, Karen L., de Angelis, Martin Hrabe, Herault, Yann, Mohun, Tim, Mallon, Ann-Marie, Henkelman, Mark R., Brown, Steve D. M., Adams, David J., Lloyd, Kent K.C., McKerlie, Colin, Beaudet, Arthur L., and Murray, Maja Bućan Stephen A.
Published: 2017
Full Text: View/download PDF

31. Untargeted Metabolomics of Slc13a5 Deficiency Reveal Critical Liver–Brain Axis for Lipid Homeostasis

Author: Milosavljevic, Sofia, primary, Glinton, Kevin E., additional, Li, Xiqi, additional, Medeiros, Cláudia, additional, Gillespie, Patrick, additional, Seavitt, John R., additional, Graham, Brett H., additional, and Elsea, Sarah H., additional
Published: 2022
Full Text: View/download PDF

32. DELAYED SKELETAL DEVELOPMENT IN A MOUSE MODEL OF GLOBAL DEFICIENCY

Author: Stroup, Bridget M., primary, Marom, Ronit, additional, Heaney, Jason D., additional, Li, Xiaohui, additional, Ani, Safa, additional, Chen, Yuqing, additional, Green, Jennie Rose, additional, Christiansen, Audrey, additional, Dickinson, Mary E., additional, Seavitt, John R., additional, Lee, Brendan, additional, and Burrage, Lindsay C., additional
Published: 2022
Full Text: View/download PDF

33. eP090: Precision medicine modelling for undiagnosed and rare disease

Author: Burrage, Lindsay, primary, Rosenfeld, Jill, additional, Yamamoto, Shinya, additional, Wangler, Michael, additional, Bellen, Hugo, additional, Lanza, Denise, additional, Roth, Matthew, additional, Darshoori, Ramin Zahedi, additional, Seavitt, John R., additional, Dickinson, Mary, additional, Lee, Brendan, additional, Milosavljevic, Aleksandar, additional, and Heaney, Jason, additional
Published: 2022
Full Text: View/download PDF

34. Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes

Author: Vo, Peter, Imai-Leonard, Denise M., Yang, Benjamin, Briere, Andrew, Shao, Andy, Casanova, M. Isabel, Adams, David, Amano, Takanori, Amarie, Oana, Berberovic, Zorana, Bower, Lynette, Braun, Robert, Brown, Steve, Burrill, Samantha, Cho, Soo Young, Clementson-Mobbs, Sharon, D’Souza, Abigail, Dickinson, Mary, Eskandarian, Mohammad, Flenniken, Ann M., Fuchs, Helmut, Gailus-Durner, Valerie, Heaney, Jason, Hérault, Yann, Angelis, Martin Hrabe de, Hsu, Chih-Wei, Jin, Shundan, Joynson, Russell, Kang, Yeon Kyung, Kim, Haerim, Masuya, Hiroshi, Meziane, Hamid, Murray, Steve, Nam, Ki-Hoan, Noh, Hyuna, Nutter, Lauryl M. J., Palkova, Marcela, Prochazka, Jan, Raishbrook, Miles Joseph, Riet, Fabrice, Ryan, Jennifer, Salazar, Jason, Seavey, Zachery, Seavitt, John Richard, Sedlacek, Radislav, Selloum, Mohammed, Seo, Kyoung Yul, Seong, Je Kyung, Shin, Hae-Sol, Shiroishi, Toshihiko, Stewart, Michelle, Svenson, Karen, Tamura, Masaru, Tolentino, Heather, Udensi, Uchechukwu, Wells, Sara, White, Jacqueline, Willett, Amelia, Wotton, Janine, Wurst, Wolfgang, Yoshiki, Atsushi, Lanoue, Louise, Lloyd, K. C. Kent, Leonard, Brian C., Roux, Michel J., McKerlie, Colin, and Moshiri, Ala
Published: 2025
Full Text: View/download PDF

35. Whole genome analysis for 163 guide RNAs in Cas9 edited mice reveals minimal off-target activity

Author: Peterson, Kevin A., primary, Khalouei, Sam, additional, Wood, Joshua A., additional, Lanza, Denise G., additional, Lintott, Lauri G., additional, Willis, Brandon J., additional, Seavitt, John R., additional, Hanafi, Nour, additional, Braun, Robert E., additional, Dickinson, Mary E., additional, White, Jacqueline K., additional, Lloyd, K.C. Kent, additional, Heaney, Jason D., additional, Murray, Stephen A., additional, Ramani, Arun, additional, and Nutter, Lauryl M.J., additional
Published: 2021
Full Text: View/download PDF

36. The occurrence of tarsal injuries in male mice of C57BL/6N substrains in multiple international mouse facilities

Author: Herbert, Eleanor, primary, Stewart, Michelle, additional, Hutchison, Marie, additional, Flenniken, Ann M., additional, Qu, Dawei, additional, Nutter, Lauryl M. J., additional, McKerlie, Colin, additional, Hobson, Liane, additional, Kick, Brenda, additional, Lyons, Bonnie, additional, Wiegand, Jean-Paul, additional, Doty, Rosalinda, additional, Aguilar-Pimentel, Juan Antonio, additional, Hrabe de Angelis, Martin, additional, Dickinson, Mary, additional, Seavitt, John, additional, White, Jacqueline K., additional, Scudamore, Cheryl L., additional, and Wells, Sara, additional
Published: 2020
Full Text: View/download PDF

37. A global Slc7a7 knockout mouse model demonstrates characteristic phenotypes of human lysinuric protein intolerance

Author: Stroup, Bridget M, primary, Marom, Ronit, additional, Li, Xiaohui, additional, Hsu, Chih-Wei, additional, Chang, Cheng-Yen, additional, Truong, Luan D, additional, Dawson, Brian, additional, Grafe, Ingo, additional, Chen, Yuqing, additional, Jiang, Ming-Ming, additional, Lanza, Denise, additional, Green, Jennie Rose, additional, Sun, Qin, additional, Barrish, J P, additional, Ani, Safa, additional, Christiansen, Audrey E, additional, Seavitt, John R, additional, Dickinson, Mary E, additional, Kheradmand, Farrah, additional, Heaney, Jason D, additional, Lee, Brendan, additional, and Burrage, Lindsay C, additional
Published: 2020
Full Text: View/download PDF

38. The Chromatin Remodeler Mi-2β Is Required for CD4 Expression and T Cell Development

Author: Williams, Christine J, Naito, Taku, Arco, Pablo Gómez-del, Seavitt, John R, Cashman, Susan M, De Souza, Beverly, Qi, Xiaoqing, Keables, Piper, Von Andrian, Ulrich H, and Georgopoulos, Katia
Published: 2004
Full Text: View/download PDF

39. CD45

Author: Seavitt, John, primary and Thomas, Matthew L., additional
Published: 1998
Full Text: View/download PDF

40. Regulation of T-cell Antigen Receptors signaling by the Membrane Trafficking of CD45

Author: Thomas, Matthew L., Johnson, Ken, Seavitt, John, Hasegawa, Kiminori, Roach, Tamara, He, Xiao, Brown, Eric, and Dustin, Mike
Published: 1999

41. DELAYED SKELETAL DEVELOPMENT IN A MOUSE MODEL OF GLOBAL SLC7A7 DEFICIENCY

Author: Stroup, Bridget M., Marom, Ronit, Heaney, Jason D., Li, Xiaohui, Ani, Safa, Chen, Yuqing, Green, Jennie Rose, Christiansen, Audrey, Dickinson, Mary E., Seavitt, John R., Lee, Brendan, and Burrage, Lindsay C.
Published: 2022
Full Text: View/download PDF

42. Soft windowing application to improve analysis of high-throughput phenotyping data

Author: Haselimashhadi, Hamed, primary, Mason, Jeremy C, additional, Munoz-Fuentes, Violeta, additional, López-Gómez, Federico, additional, Babalola, Kolawole, additional, Acar, Elif F, additional, Kumar, Vivek, additional, White, Jacqui, additional, Flenniken, Ann M, additional, King, Ruairidh, additional, Straiton, Ewan, additional, Seavitt, John Richard, additional, Gaspero, Angelina, additional, Garza, Arturo, additional, Christianson, Audrey E, additional, Hsu, Chih-Wei, additional, Reynolds, Corey L, additional, Lanza, Denise G, additional, Lorenzo, Isabel, additional, Green, Jennie R, additional, Gallegos, Juan J, additional, Bohat, Ritu, additional, Samaco, Rodney C, additional, Veeraragavan, Surabi, additional, Kim, Jong Kyoung, additional, Miller, Gregor, additional, Fuchs, Helmult, additional, Garrett, Lillian, additional, Becker, Lore, additional, Kang, Yeon Kyung, additional, Clary, David, additional, Cho, Soo Young, additional, Tamura, Masaru, additional, Tanaka, Nobuhiko, additional, Soo, Kyung Dong, additional, Bezginov, Alexandr, additional, About, Ghina Bou, additional, Champy, Marie-France, additional, Vasseur, Laurent, additional, Leblanc, Sophie, additional, Meziane, Hamid, additional, Selloum, Mohammed, additional, Reilly, Patrick T, additional, Spielmann, Nadine, additional, Maier, Holger, additional, Gailus-Durner, Valerie, additional, Sorg, Tania, additional, Hiroshi, Masuya, additional, Yuichi, Obata, additional, Heaney, Jason D, additional, Dickinson, Mary E, additional, Wolfgang, Wurst, additional, Tocchini-Valentini, Glauco P, additional, Lloyd, Kevin C Kent, additional, McKerlie, Colin, additional, Seong, Je Kyung, additional, Yann, Herault, additional, de Angelis, Martin Hrabé, additional, Brown, Steve D M, additional, Smedley, Damian, additional, Flicek, Paul, additional, Mallon, Ann-Marie, additional, Parkinson, Helen, additional, and Meehan, Terrence F, additional
Published: 2019
Full Text: View/download PDF

43. Unconventional Potentiation of Gene Expression by Ikaros

Author: Koipally, Joseph, Heller, Elizabeth J., Seavitt, John R., and Georgopoulos, Katia
Published: 2002
Full Text: View/download PDF

44. Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features

Author: Afawi, Zaid, Balling, Rudi, Barisic, Nina, Baulac, Stéphanie, Craiu, Dana, De Jonghe, Peter, Guerrero-Lopez, Rosa, Guerrini, Renzo, Helbig, Ingo, Hjalgrim, Helle, Jähn, Johanna, Klein, Karl Martin, Leguern, Eric, Lerche, Holger, Marini, Carla, Muhle, Hiltrud, Rosenow, Felix, Serratosa, José, Sterbová, Katalin, Suls, Arvid, Moller, Rikke S., Striano, Pasquale, Weber, Yvonne, Zara, Federico, Santiago-Sim, Teresa, Burrage, Lindsay C., Ebstein, Frédéric, Tokita, Mari J., Miller, Marcus, Bi, Weimin, Braxton, Alicia A., Rosenfeld, Jill A., Shahrour, Maher, Lehmann, Andrea, Cogné, Benjamin, Küry, Sébastien, Besnard, Thomas, Isidor, Bertrand, Bézieau, Stéphane, Hazart, Isabelle, Nagakura, Honey, Immken, LaDonna L., Littlejohn, Rebecca O., Roeder, Elizabeth, Kara, Bulent, Hardies, Katia, Weckhuysen, Sarah, May, Patrick, Lemke, Johannes R., Elpeleg, Orly, Abu-Libdeh, Bassam, James, Kiely N., Silhavy, Jennifer L., Issa, Mahmoud Y., Zaki, Maha S., Gleeson, Joseph G., Seavitt, John R., Dickinson, Mary E., Ljungberg, M. Cecilia, Wells, Sara, Johnson, Sara J., Teboul, Lydia, Eng, Christine M., Yang, Yaping, Kloetzel, Peter-Michael, Heaney, Jason D., and Walkiewicz, Magdalena A.
Published: 2017
Full Text: View/download PDF

45. Additional file 3: of Comparative analysis of single-stranded DNA donors to generate conditional null mouse alleles

Author: Lanza, Denise, Gaspero, Angelina, Lorenzo, Isabel, Liao, Lan, Zheng, Ping, Wang, Ying, Deng, Yu, Chonghui Cheng, Chuansheng Zhang, Seavitt, John, DeMayo, Francesco, Jianming Xu, Dickinson, Mary, Beaudet, Arthur, and Heaney, Jason
Abstract: Figure S1. Aâ D. Individual conditional KO symmetric and asymmetric ssODN and lssDNA targeting attempts. (A) Symmetric homology arm design attempts for the 20 genes attempted. (B) Paired comparison of the symmetric and asymmetric homology arm design attempts for Il1rl1 and Eif2s2. The red circle circumscribing the total number of mice genotyped indicates an asymmetric design attempt. (C) Asymmetric homology arm design attempts for an additional eight genes. (D) lssDNA-mediated attempts for four genes, which included Eif2s2. (PDF 309 kb)
Published: 2018
Full Text: View/download PDF

46. Additional file 2: of Comparative analysis of single-stranded DNA donors to generate conditional null mouse alleles

Author: Lanza, Denise, Gaspero, Angelina, Lorenzo, Isabel, Liao, Lan, Zheng, Ping, Wang, Ying, Deng, Yu, Chonghui Cheng, Chuansheng Zhang, Seavitt, John, DeMayo, Francesco, Jianming Xu, Dickinson, Mary, Beaudet, Arthur, and Heaney, Jason
Abstract: Table S2. Microinjection information for all 32 paired, ssODN donor and the 4 lssDNA donor microinjections, including injection concentrations for Cas9, sgRNAs (each), and donor DNAs. Column headings: Embryo, represents the number of embryos injected for each targeting attempt; Recip, the number of recipient moms utilized per targeting attempt; Tfx, the number of surviving embryos transferred into recipient females; F0 born, the number of F0 pups born for each targeting attempt; PE, percent efficiency – the number of F0 pups born divided by the number of embryos transferred; Genotyped, the number of F0 pups that survived to genotyping at 2 weeks of age; Wild-type, the number of F0 pups genotyped without any evidence of genome editing; NHEJ event, the number of F0 pups genotyped in which only indel alleles were observed; Single HDR, the number of F0 pups genotyped with a single HDR event with or without additional indel events; Null Allele, the number of F0 pups genotyped with a null allele, which may also have a single HDR and/or NHEJ indel event; 5 + 3 + N, the number of F0 pups genotyped with both 5′ and 3′ loxP sites and a null allele; 2 loxP, the number of F0 pups genotyped with both 5′ and 3′ loxP sites, irrespective of the presence of any additional alleles. Data for the breeding of 2 LoxP founders is presented in beige shading; N1 cis, the number of 2 LoxP founders that transmitted in cis; N1 trans, the number of 2 LoxP founders that transmitted in trans; Not bred, the number of 2 LoxP founders not bred. (PDF 235 kb)
Published: 2018
Full Text: View/download PDF

47. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation · the IMPC consortium

Author: Muñoz-Fuentes, Violeta, Cacheiro, Pilar, Meehan, Terrence, Aguilar-Pimentel, Juan Antonio, Brown, Steve, Flenniken, Ann, Flicek, Paul, Galli, Antonella, Mashhadi, Hamed Haseli, Hrabě De Angelis, Martin, Kim, Jong Kyoung, Lloyd, K C Kent, McKerlie, Colin, Morgan, Hugh, Murray, Stephen, Nutter, Lauryl, Reilly, Patrick, Seavitt, John, Seong, Je Kyung, Simon, Michelle, Wardle-Jones, Hannah, Mallon, Ann-Marie, Smedley, Damian, Parkinson, Helen, Queen Mary University of London (QMUL), German Research Center for Environmental Health - Helmholtz Center München (GmbH), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, The Wellcome Trust Sanger Institute [Cambridge], Institute for Experimental Genetics, GSF - National Research Center for Environment and Health, Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Medical Research Counc, and European Bioinformatics Institute
Subjects: Wolf, Mouse, Knockout, Cheetah, Essential genes, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Endangered species, Loss-of-function, Polar bear, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Panda, Phenotype, IMPC, Non-model species
Abstract: International audience; The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.
Published: 2018
Full Text: View/download PDF

48. Additional file 1: of Comparative analysis of single-stranded DNA donors to generate conditional null mouse alleles

Author: Lanza, Denise, Gaspero, Angelina, Lorenzo, Isabel, Liao, Lan, Zheng, Ping, Wang, Ying, Deng, Yu, Chonghui Cheng, Chuansheng Zhang, Seavitt, John, DeMayo, Francesco, Jianming Xu, Dickinson, Mary, Beaudet, Arthur, and Heaney, Jason
Abstract: Table S1. Design information for all genes targeted, separated by length and homology arm design. Web links are provided to NCBI and Ensembl for the annotation of each gene and exon or exons targeted, and separate web links are provided to the WTSI Genome Editing website for the selected sgRNA information. Donor sequences for each gene targeted are also listed. (PDF 115 kb)
Published: 2018
Full Text: View/download PDF

49. Identification of genetic elements in metabolism by high-throughput mouse phenotyping

Author: Rozman, Jan, Rathkolb, Birgit, Meehan, Terrence F, Codner, Gemma F, Fiegel, Tanja, Ring, Natalie, Westerberg, Henrik, Greenaway, Simon, Sneddon, Duncan, Morgan, Hugh, Loeffler, Jorik, Stewart, Michelle E, Ramirez-Solis, Ramiro, Mason, Jeremy, Bradley, Allan, Skarnes, William C, Steel, Karen P, Maguire, Simon A, Dench, Joshua, Lafont, David, Vancollie, Valerie E, Pearson, Selina A, Gates, Amy S, Sanderson, Mark, Haselimashhadi, Hamed, Shannon, Carl, Anthony, Lauren F E, Sumowski, Maksymilian T, McLaren, Robbie S B, Doe, Brendan, Wardle-Jones, Hannah, Griffiths, Mark N D, Galli, Antonella, Swiatkowska, Agnieszka, Isherwood, Christopher M, Consortium, IMPC, Speak, Anneliese O, Cambridge, Emma L, Wilson, Heather M, Caetano, Susana S, Maguire, Anna Karin B, Adams, David J, Bottomley, Joanna, Ryder, Ed, Gleeson, Diane, Pouilly, Laurent, Hough, Tertius, Rousseau, Stephane, Auburtin, Aurélie, Reilly, Patrick, Ayadi, Abdel, Selloum, Mohammed, Wood, Joshua A, Clary, Dave, Havel, Peter, Tolentino, Todd, Tolentino, Heather, Mallon, Ann-Marie, Schuchbauer, Mike, Pedroia, Sheryl, Trainor, Amanda, Djan, Esi, Pham, Milton, Huynh, Alison, De Vera, Vincent, Seavitt, John, Gallegos, Juan, Garza, Arturo, Wells, Sara, Mangin, Elise, Senderstrom, Joel, Lazo, Iride, Mowrey, Kate, Bohat, Ritu, Samaco, Rodney, Veeraragavan, Surabi, Beeton, Christine, Kalaga, Sowmya, Kelsey, Lois, Santos, Luis, Vukobradovic, Igor, Berberovic, Zorana, Owen, Celeste, Qu, Dawei, Guo, Ruolin, Newbigging, Susan, Morikawa, Lily, Law, Napoleon, Shang, Xueyuan, Feugas, Patricia, Lelliott, Christopher J, Wang, Yanchun, Eskandarian, Mohammad, Zhu, Yingchun, Penton, Patricia, Laurin, Valerie, Clarke, Shannon, Lan, Qing, Sleep, Gillian, Creighton, Amie, Jacob, Elsa, White, Jacqueline K, Danisment, Ozge, Gertsenstein, Marina, Pereira, Monica, MacMaster, Suzanne, Tondat, Sandra, Carroll, Tracy, Cabezas, Jorge, Hunter, Jane, Clark, Greg, Bubshait, Mohammed, Oestereicher, Manuela A, Sorg, Tania, Miller, David, Sohel, Khondoker, Adissu, Hibret, Ganguly, Milan, Bezginov, Alexandr, Chiani, Francesco, Di Pietro, Chiara, Di Segni, Gianfranco, Ermakova, Olga, Ferrara, Filomena, Champy, Marie-France, Fruscoloni, Paolo, Gambadoro, Aalessia, Gastaldi, Serena, Golini, Elisabetta, La Sala, Gina, Mandillo, Silvia, Marazziti, Daniela, Massimi, Marzia, Matteoni, Rafaele, Orsini, Tiziana, Bower, Lynette R, Pasquini, Miriam, Raspa, Marcello, Rauch, Aline, Rossi, Gianfranco, Rossi, Nicoletta, Putti, Sabrina, Scavizzi, Ferdinando, Tocchini-Valentini, Giuseppe D, Wakana, Shigeharu, Suzuki, Tomohiro, Reynolds, Corey L, Tamura, Masaru, Kaneda, Hideki, Furuse, Tamio, Kobayashi, Kimio, Miura, Ikuo, Yamada, Ikuko, Obata, Yuichi, Yoshiki, Atsushi, Ayabe, Shinya, Chambers, J Nicole, Flenniken, Ann M, Chalupsky, Karel, Seisenberger, Claudia, Bürger, Antje, Beig, Joachim, Kühn, Ralf, Hörlein, Andreas, Schick, Joel, Oritz, Oskar, Giesert, Florian, Graw, Jochen, Murray, Stephen A, Ollert, Markus, Schmidt-Weber, Carsten, Stoeger, Tobias, Önder Yildirim, Ali, Eickelberg, Oliver, Klopstock, Thomas, Busch, Dirk H, Bekeredjian, Raffi, Zimmer, Andreas, Jacobsen, Jules O, Nutter, Lauryl M J, Smedley, Damian, Dickinson, Mary E, Benso, Frank, Morse, Iva, Kim, Hyoung-Chin, Lee, Ho, Cho, Soo Young, Svenson, Karen L, West, David, Tocchini-Valentini, Glauco P, Schütt, Christine, Beaudet, Arthur L, Bosch, Fatima, Braun, Robert B, Dobbie, Michael S, Gao, Xiang, Herault, Yann, Moshiri, Ala, Moore, Bret A, Kent Lloyd, K. C., McKerlie, Colin, Ravindranath, Aakash Chavan, Masuya, Hiroshi, Tanaka, Nobuhiko, Flicek, Paul, Parkinson, Helen E, Sedlacek, Radislav, Seong, Je Kyung, Wang, Chi-Kuang Leo, Moore, Mark, Brown, Steve D, Tschöp, Matthias H, Leuchtenberger, Stefanie, Wurst, Wolfgang, Klingenspor, Martin, Wolf, Eckhard, Beckers, Johannes, Machicao, Fausto, Peter, Andreas, Staiger, Harald, Häring, Hans-Ulrich, Grallert, Harald, Campillos, Monica, Sharma, Sapna, Maier, Holger, Fuchs, Helmut, Gailus-Durner, Valerie, Werner, Thomas, Hrabe de Angelis, Martin, Aguilar-Pimentel, Antonio, Becker, Lore, Treise, Irina, Moreth, Kristin, Garrett, Lillian, Kistler, Martin, Hölter, Sabine M, Zimprich, Annemarie, Marschall, Susan, Amarie, Oana V, Calzada-Wack, Julia, Neff, Frauke, Brachthäuser, Laura, Lengger, Christoph, Stoeger, Claudia, Zapf, Lilly, Willershäuser, Monja, Cho, Yi-Li, da Silva-Buttkus, Patricia, Kraiger, Markus J, Mayer-Kuckuk, Philipp, Gampe, Karen Kristine, Wu, Moya, Conte, Nathalie, Warren, Jonathan, Chen, Chao-Kung, Tudose, Ilinca, Brommage, Robert, Relac, Mike, Matthews, Peter, Cater, Heather L, Natukunda, Helen P, Cleak, James, Teboul, Lydia M, Clementson-Mobbs, Sharon, Szoke-Kovacs, Zsombor, Walling, Alison P, Johnson, Sara J, Rozman, Jan [0000-0002-8035-8904], Kistler, Martin [0000-0003-0116-7761], Mason, Jeremy [0000-0002-2796-5123], Lelliott, Christopher J [0000-0001-8087-4530], Herault, Yann [0000-0001-7049-6900], Kent Lloyd, KC [0000-0002-5318-4144], McKerlie, Colin [0000-0002-2232-0967], Flicek, Paul [0000-0002-3897-7955], Maier, Holger [0000-0003-2514-8290], Fuchs, Helmut [0000-0002-5143-2677], Hrabe de Angelis, Martin [0000-0002-7898-2353], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Blood Glucose, Candidate gene, Cancer Research, Basal Metabolism/genetics, Gene regulatory network, Obesity/genetics, genetics [Metabolic Diseases], General Physics and Astronomy, Genome-wide association study, Genome, Mice, genetics [Obesity], Triglycerides/metabolism, 2.1 Biological and endogenous factors, Gene Regulatory Networks, Aetiology, lcsh:Science, metabolism [Blood Glucose], Mice, Knockout, Multidisciplinary, genetics [Basal Metabolism], Phenotype, Area Under Curve, Diabetes Mellitus, Type 2/genetics, ddc:500, Technology Platforms, Type 2, metabolism [Triglycerides], Knockout, Science, Computational biology, Biology, genetics [Diabetes Mellitus, Type 2], General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Oxygen Consumption, Metabolic Diseases, Body Weight/genetics, Diabetes Mellitus, Genetics, Animals, Humans, Metabolic Diseases/genetics, Obesity, Gene, Gene knockout, Triglycerides, Oxygen Consumption/genetics, Blood Glucose/metabolism, genetics [Body Weight], Human Genome, Body Weight, Promoter, General Chemistry, genetics [Oxygen Consumption], High-Throughput Screening Assays, 030104 developmental biology, Diabetes Mellitus, Type 2, IMPC Consortium, lcsh:Q, Basal Metabolism, Genome-Wide Association Study
Abstract: Metabolic diseases are a worldwide problem but the underlying genetic factors and their relevance to metabolic disease remain incompletely understood. Genome-wide research is needed to characterize so-far unannotated mammalian metabolic genes. Here, we generate and analyze metabolic phenotypic data of 2016 knockout mouse strains under the aegis of the International Mouse Phenotyping Consortium (IMPC) and find 974 gene knockouts with strong metabolic phenotypes. 429 of those had no previous link to metabolism and 51 genes remain functionally completely unannotated. We compared human orthologues of these uncharacterized genes in five GWAS consortia and indeed 23 candidate genes are associated with metabolic disease. We further identify common regulatory elements in promoters of candidate genes. As each regulatory element is composed of several transcription factor binding sites, our data reveal an extensive metabolic phenotype-associated network of co-regulated genes. Our systematic mouse phenotype analysis thus paves the way for full functional annotation of the genome., The genetic basis of metabolic diseases is incompletely understood. Here, by high-throughput phenotyping of 2,016 knockout mouse strains, Rozman and colleagues identify candidate metabolic genes, many of which are associated with unexplored regulatory gene networks and metabolic traits in human GWAS.
Published: 2018
Full Text: View/download PDF

50. Corrigendum: High-throughput discovery of novel developmental phenotypes

Author: Dickinson, Mary E, Flenniken, Ann M, Ji, Xiao, Teboul, Lydia, Wong, Michael D, White, Jacqueline K, Meehan, Terrence F, Weninger, Wolfgang J, Westerberg, Henrik, Adissu, Hibret, Baker, Candice N, Bower, Lynette, Brown, James M, Caddle, L Brianna, Chiani, Francesco, Clary, Dave, Cleak, James, Daly, Mark J, Denegre, James M, Doe, Brendan, Dolan, Mary E, Edie Helmut Fuchs, Sarah M, Gailus-Durner, Valerie, Galli, Antonella, Gambadoro, Alessia, Gallegos, Juan, Guo, Shiying, Horner, Neil R, Hsu, Chih-Wei, Johnson, Sara J, Kalaga, Sowmya, Keith, Lance C, Lanoue, Louise, Lawson, Thomas N, Lek, Monkol, Mark, Manuel, Marschall, Susan, Mason, Jeremy, McElwee, Melissa L, Nutter, Susan Newbigging Lauryl MJ, Peterson, Kevin A, Ramirez-Solis, Ramiro, Rowland, Douglas J, Ryder, Edward, Samocha, Kaitlin E, Seavitt, John R, Selloum, Mohammed, Szoke-Kovacs, Zsombor, Tamura, Masaru, Trainor, Amanda G, Tudose, Ilinca, Wakana, Shigeharu, Warren, Jonathan, Wendling, Olivia, West, David B, Wong, Leeyean, Yoshiki, Atsushi, International Mouse Phenotyping Consortium, Wurst, Wolfgang, MacArthur, Daniel G, Tocchini-Valentini, Glauco P, Gao, Xiang, Flicek, Paul, Bradley, Allan, Skarnes, William C, Justice, Monica J, Parkinson, Helen E, Moore, Mark, Wells, Sara, Braun, Robert E, Svenson, Karen L, de Angelis, Martin Hrabe, Herault, Yann, Mohun, Tim, Mallon, Ann-Marie, Henkelman, R Mark, Brown, Steve DM, Adams, David J, Lloyd, KC Kent, McKerlie, Colin, Beaudet, Arthur L, and Murray, Maja Bućan Stephen A
Subjects: General Science & Technology, International Mouse Phenotyping Consortium
Abstract: This corrects the article DOI: 10.1038/nature19356.
Published: 2017

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

208 results on '"Seavitt, John"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources