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2. High-throughput discovery of novel developmental phenotypes

Author

McKay, Matthew, Urban, Barbara, Lund, Caroline, Froeter, Erin, LaCasse, Taylor, Mehalow, Adrienne, Gordon, Emily, Donahue, Leah Rae, Taft, Robert, Kutney, Peter, Dion, Stephanie, Goodwin, Leslie, Kales, Susan, Urban, Rachel, Palmer, Kristina, Pertuy, Fabien, Bitz, Deborah, Weber, Bruno, Goetz-Reiner, Patrice, Jacobs, Hughes, Le Marchand, Elise, El Amri, Amal, El Fertak, Leila, Ennah, Hamid, Ali-Hadji, Dalila, Ayadi, Abdel, Wattenhofer-Donze, Marie, Jacquot, Sylvie, André, Philippe, Birling, Marie-Christine, Pavlovic, Guillaume, Sorg, Tania, Morse, Iva, Benso, Frank, Stewart, Michelle E, Copley, Carol, Harrison, Jackie, Joynson, Samantha, Guo, Ruolin, Qu, Dawei, Spring, Shoshana, Yu, Lisa, Ellegood, Jacob, Morikawa, Lily, Shang, Xueyuan, Feugas, Pat, Creighton, Amie, Castellanos Penton, Patricia, Danisment, Ozge, Griggs, Nicola, Tudor, Catherine L, Green, Angela L, Icoresi Mazzeo, Cecilia, Siragher, Emma, Lillistone, Charlotte, Tuck, Elizabeth, Gleeson, Diane, Sethi, Debarati, Bayzetinova, Tanya, Burvill, Jonathan, Habib, Bishoy, Weavers, Lauren, Maswood, Ryea, Miklejewska, Evelina, Woods, Michael, Grau, Evelyn, Newman, Stuart, Sinclair, Caroline, Brown, Ellen, Ayabe, Shinya, Iwama, Mizuho, and Murakami, Ayumi

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Animals, Conserved Sequence, Disease, Embryo, Mammalian, Genes, Essential, Genes, Lethal, Genome-Wide Association Study, High-Throughput Screening Assays, Humans, Imaging, Three-Dimensional, Mice, Mice, Inbred C57BL, Mice, Knockout, Mutation, Penetrance, Phenotype, Polymorphism, Single Nucleotide, Sequence Homology, 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, 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

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

Author

Birling, Marie-Christine, Yoshiki, Atsushi, Chiani, Francesco, Kaloff, Cornelia, Hörlein, Andreas, Teichmann, Sandy, Tasdemir, Adriane, Krause, Heidi, German, Dorota, Könitzer, Anne, Weber, Sarah, Beig, Joachim, McKay, Matthew, Chin, Hsian-Jean Genie, Bedigian, Richard, Dion, Stephanie, Kutny, Peter, Kelmenson, Jennifer, Perry, Emily, Nguyen-Bresinsky, Dong, Seluke, Audrie, Leach, Timothy, Perkins, Sara, Slater, Amanda, Christou, Skevoulla, Petit, Michaela, Urban, Rachel, Kales, Susan, DaCosta, Michael, McFarland, Michael, Palazola, Rick, Peterson, Kevin A, Svenson, Karen, Braun, Robert E, Taft, Robert, Codner, Gemma F, Rhue, Mark, Garay, Jose, Clary, Dave, Araiza, Renee, Grimsrud, Kristin, Bower, Lynette, Anchell, Nicole L, Jager, Kayla M, Young, Diana L, Dao, Phuong T, DeMayo, Francesco J, Gardiner, Wendy, Bell, Toni, Kenyon, Janet, Stewart, Michelle E, Lynch, Denise, Loeffler, Jorik, Caulder, Adam, Hillier, Rosie, Quwailid, Mohamed M, Zaman, Rumana, Dickinson, Mary E, Santos, Luis, Obata, Yuichi, Iwama, Mizuho, Nakata, Hatsumi, Hashimoto, Tomomi, Kadota, Masayo, Masuya, Hiroshi, Tanaka, Nobuhiko, Miura, Ikuo, Yamada, Ikuko, Doe, Brendan, Furuse, Tamio, Selloum, Mohammed, Jacquot, Sylvie, Ayadi, Abdel, Ali-Hadji, Dalila, Charles, Philippe, Le Marchand, Elise, El Amri, Amal, Kujath, Christelle, Fougerolle, Jean-Victor, Donahue, Leah Rae, Mellul, Peggy, Legeay, Sandrine, Vasseur, Laurent, Moro, Anne-Isabelle, Lorentz, Romain, Schaeffer, Laurence, Dreyer, Dominique, Erbs, Valérie, Eisenmann, Benjamin, Rossi, Giovanni, Fray, Martin D, Luppi, Laurence, Mertz, Annelyse, Jeanblanc, Amélie, Grau, Evelyn, Sinclair, Caroline, Brown, Ellen, Kundi, Helen, Madich, Alla, Woods, Mike, Pearson, Laila, Gambadoro, Alessia, Mayhew, Danielle, Griggs, Nicola, Houghton, Richard, Bussell, James, Ingle, Catherine, Valentini, Sara, Gleeson, Diane, Sethi, Debarati, Bayzetinova, Tanya, Burvill, Jonathan, Adams, David J, Gao, Xiang, Habib, Bishoy, Weavers, Lauren, Maswood, Ryea, Miklejewska, Evelina, Cook, Ross, Platte, Radka, Price, Stacey, Vyas, Sapna, Collinson, Adam, Hardy, Matt, Gertsenstein, Marina, Dalvi, Priya, Iyer, Vivek, West, Tony, Thomas, Mark, Mujica, Alejandro, Sins, Elodie, Barrett, Daniel, Dobbie, Michael, Grobler, Anne, Loots, Glaudina, Gomez-Segura, Alba, Hayeshi, Rose, Scholtz, Liezl-Marie, Bester, Cor, Pheiffer, Wihan, Venter, Kobus, Bosch, Fatima, Goodwin, Leslie O, Heaney, Jason D, Hérault, Yann, de Angelis, Martin Hrabě, Jiang, Si-Tse, Justice, Monica J, Kasparek, Petr, Ayabe, Shinya, King, Ruairidh E, Kühn, Ralf, Lee, Ho, Lee, Youngik, Liu, Zhiwei, Lloyd, K C Kent, Lorenzo, Isabel, Mallon, Ann-Marie, McKerlie, Colin, Meehan, Terrence F, Beaudet, Arthur L, Fuentes, Violeta Munoz, Newman, Stuart, Nutter, Lauryl M J, Oh, Goo Taeg, Pavlovic, Guillaume, Ramirez-Solis, Ramiro, Rosen, Barry, Ryder, Edward J, Santos, Luis A, Schick, Joel, Bottomley, Joanna, 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, Bradley, Allan, Wardle-Jones, Hannah, Wattenhofer-Donzé, Marie, Wells, Sara, Wiles, Michael V, Willis, Brandon J, Wood, Joshua A, Wurst, Wolfgang, Xu, Ying, Consortium, International Mouse Phenotyping, Teboul, Lydia, Brown, Steve D M, Murray, Stephen A, Gallegos, Juan J, Green, Jennie R, Bohat, Ritu, Zimmel, Katie, Pereira, Monica, MacMaster, Suzanne, Tondat, Sandra, Wei, Linda, Carroll, Tracy, Bürger, Antje, Cabezas, Jorge, Fan-Lan, Qing, Jacob, Elsa, Creighton, Amie, Castellanos-Penton, Patricia, Danisment, Ozge, Clarke, Shannon, Joeng, Joanna, Kelly, Deborah, To, Christine, Bushell, Wendy, van Bruggen, Rebekah, Gailus-Durner, Valerie, Fuchs, Helmut, Marschall, Susan, Dunst, Stefanie, Romberger, Markus, Rey, Bernhard, Fessele, Sabine, Gormanns, Philipp, Friedel, Roland, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), and Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Cancer Research, Genotype, Knockout, International Cooperation, [SDV]Life Sciences [q-bio], Mutant, Mutagenesis (molecular biology technique), cytology [Mouse Embryonic Stem Cells], Mouse Mutant Strains, Biology, Genome, Medical and Health Sciences, Article, 03 medical and health sciences, Mice, 0302 clinical medicine, Research community, ddc:570, Genetics, Animals, Allele, Gene, Genetic Association Studies, 030304 developmental biology, Mice, Knockout, 0303 health sciences, Internet, metabolism [Mouse Embryonic Stem Cells], Information Dissemination, mutant mouse IMPC, Mouse Embryonic Stem Cells, Biological Sciences, Null allele, Embryonic stem cell, Phenotype, Mutagenesis, Montertondo Mouse Production, Technology Platforms, International Mouse Phenotyping Consortium, Function (biology), 030217 neurology & neurosurgery, Gene Deletion, Developmental Biology
Abstract

The International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for over 5,000 genes from targeted embryonic stem cells on the C57BL/6N genetic background. This includes 2,850 null alleles for which no equivalent mutant mouse line exists, 2,987 novel conditional-ready alleles, and 4,433 novel reporter alleles. This nearly triples the number of genes with reporter alleles and almost doubles the number of conditional alleles available to the scientific community. When combined with more than 30 years of community effort, the total mutant allele mouse resource covers more than half of the genome. The extensively validated collection is archived and distributed through public repositories, facilitating availability to the worldwide biomedical research community, and expanding our understanding of gene function and human disease.

Published
2021
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4. 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 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, McKay, Matthew, Urban, Barbara, Lund, Caroline, Froeter, Erin, LaCasse, Taylor, Mehalow, Adrienne, Gordon, Emily, Donahue, Leah Rae, Taft, Robert, Kutney, Peter, Dion, Stephanie, Goodwin, Leslie, Kales, Susan, Urban, Rachel, Palmer, Kristina, Pertuy, Fabien, Bitz, Deborah, Weber, Bruno, Goetz-Reiner, Patrice, Jacobs, Hughes, Le Marchand, Elise, El Amri, Amal, El Fertak, Leila, Ennah, Hamid, Ali-Hadji, Dalila, Ayadi, Abdel, Wattenhofer-Donze, Marie, Jacquot, Sylvie, Andr, Philippe, Birling, Marie-Christine, Pavlovic, Guillaume, Sorg, Tania, Morse, Iva, Benso, Frank, Stewart, Michelle E., Copley, Carol, Harrison, Jackie, Joynson, Samantha, Guo, Ruolin, Qu, Dawei, Spring, Shoshana, Yu, Lisa, Ellegood, Jacob, Morikawa, Lily, Shang, Xueyuan, Feugas, Pat, Creighton, Amie, Castellanos Penton, Patricia, Danisment, Ozge, Griggs, Nicola, Tudor, Catherine L., Green, Angela L., Icoresi Mazzeo, Cecilia, Siragher, Emma, Lillistone, Charlotte, Tuck, Elizabeth, Gleeson, Diane, Sethi, Debarati, Bayzetinova, Tanya, Burvill, Jonathan, Habib, Bishoy, Weavers, Lauren, Maswood, Ryea, Miklejewska, Evelina, Woods, Michael, Grau, Evelyn, Newman, Stuart, Sinclair, Caroline, Brown, Ellen, Ayabe, Shinya, Iwama, Mizuho, Murakami, Ayumi, 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 D. M., Adams, David J., Lloyd, K. C. Kent, McKerlie, Colin, Beaudet, Arthur L., Buan, Maja, and Murray, Stephen A.

Subjects
Research, Methods, Phenotypes -- Research, Genetic research, High-throughput screening (Biochemical assaying) -- Methods
Abstract

Author(s): Mary E. Dickinson [1]; Ann M. Flenniken [2, 3]; Xiao Ji [4]; Lydia Teboul [5]; Michael D. Wong [2, 6]; Jacqueline K. White [7]; Terrence F. Meehan [8]; Wolfgang [...], 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
Full Text
View/download PDF

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