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1. Saturation genome editing of BAP1 functionally classifies somatic and germline variants

Author

Waters, Andrew J., Brendler-Spaeth, Timothy, Smith, Danielle, Offord, Victoria, Tan, Hong Kee, Zhao, Yajie, Obolenski, Sofia, Nielsen, Maartje, van Doorn, Remco, Murphy, Jo-Ellen, Gupta, Prashant, Rowlands, Charlie F., Hanson, Helen, Delage, Erwan, Thomas, Mark, Radford, Elizabeth J., Gerety, Sebastian S., Turnbull, Clare, Perry, John R. B., Hurles, Matthew E., and Adams, David J.

Published
2024
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7. Genome-wide screening reveals the genetic basis of mammalian embryonic eye development

Author

Chee, Justine M, Lanoue, Louise, Clary, Dave, Higgins, Kendall, Bower, Lynette, Flenniken, Ann, Guo, Ruolin, Adams, David J, Bosch, Fatima, Braun, Robert E, Brown, Steve DM, Chin, H-J Genie, Dickinson, Mary E, Hsu, Chih-Wei, Dobbie, Michael, Gao, Xiang, Galande, Sanjeev, Grobler, Anne, Heaney, Jason D, Herault, Yann, de Angelis, Martin Hrabe, Mammano, Fabio, Nutter, Lauryl MJ, Parkinson, Helen, Qin, Chuan, Shiroishi, Toshi, Sedlacek, Radislav, Seong, J-K, Xu, Ying, Brooks, Brian, McKerlie, Colin, Lloyd, KC Kent, Westerberg, Henrik, and Moshiri, Ala

Subjects
Biological Sciences, Genetics, Congenital Structural Anomalies, Rare Diseases, Human Genome, Eye Disease and Disorders of Vision, Pediatric, 2.1 Biological and endogenous factors, Eye, Humans, Mice, Animals, Eye Abnormalities, Anophthalmos, Microphthalmos, Coloboma, Mice, Knockout, Embryonic Development, Phenotype, Mammals, MAC spectrum, Eye development, Mouse, IMPC, Serine-glycine biosynthesis, CPLANE, International Mouse Phenotyping Consortium, Developmental Biology
Abstract

BackgroundMicrophthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome.ResultsQuery of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation.ConclusionsUsing genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.

Published
2023

8. Transposon Mutagenesis Reveals RBMS3 Silencing as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis

Author

Vaishnavi, Aria, Juan, Joseph, Jacob, Maebh, Stehn, Christopher, Gardner, Eric E, Scherzer, Michael T, Schuman, Sophia, van Veen, J Edward, Murphy, Brandon, Hackett, Christopher S, Dupuy, Adam J, Chmura, Steve A, van der Weyden, Louise, Newberg, Justin Y, Liu, Annie, Mann, Karen, Rust, Alistair G, Weiss, William A, Kinsey, Conan G, Adams, David J, Grossmann, Allie, Mann, Michael B, and McMahon, Martin

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Lung, Rare Diseases, Genetics, Lung Cancer, Cancer, Biotechnology, Aetiology, 2.1 Biological and endogenous factors, Animals, Humans, Mice, Adenocarcinoma of Lung, Carcinoma, Non-Small-Cell Lung, Cell Proliferation, Lung Neoplasms, Mutagenesis, Proto-Oncogene Proteins B-raf, RNA-Binding Proteins, Trans-Activators, Wnt Signaling Pathway, Carcinogenesis, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Mutationally activated BRAF is detected in approximately 7% of human lung adenocarcinomas, with BRAFT1799A serving as a predictive biomarker for treatment of patients with FDA-approved inhibitors of BRAFV600E oncoprotein signaling. In genetically engineered mouse (GEM) models, expression of BRAFV600E in the lung epithelium initiates growth of benign lung tumors that, without additional genetic alterations, rarely progress to malignant lung adenocarcinoma. To identify genes that cooperate with BRAFV600E for malignant progression, we used Sleeping Beauty-mediated transposon mutagenesis, which dramatically accelerated the emergence of lethal lung cancers. Among the genes identified was Rbms3, which encodes an RNA-binding protein previously implicated as a putative tumor suppressor. Silencing of RBMS3 via CRISPR/Cas9 gene editing promoted growth of BRAFV600E lung organoids and promoted development of malignant lung cancers with a distinct micropapillary architecture in BRAFV600E and EGFRL858R GEM models. BRAFV600E/RBMS3Null lung tumors displayed elevated expression of Ctnnb1, Ccnd1, Axin2, Lgr5, and c-Myc mRNAs, suggesting that RBMS3 silencing elevates signaling through the WNT/β-catenin signaling axis. Although RBMS3 silencing rendered BRAFV600E-driven lung tumors resistant to the effects of dabrafenib plus trametinib, the tumors were sensitive to inhibition of porcupine, an acyltransferase of WNT ligands necessary for their secretion. Analysis of The Cancer Genome Atlas patient samples revealed that chromosome 3p24, which encompasses RBMS3, is frequently lost in non-small cell lung cancer and correlates with poor prognosis. Collectively, these data reveal the role of RBMS3 as a lung cancer suppressor and suggest that RBMS3 silencing may contribute to malignant NSCLC progression.SignificanceLoss of RBMS3 cooperates with BRAFV600E to induce lung tumorigenesis, providing a deeper understanding of the molecular mechanisms underlying mutant BRAF-driven lung cancer and potential strategies to more effectively target this disease.

Published
2022

9. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Author

Islam, SM Ashiqul, Díaz-Gay, Marcos, Wu, Yang, Barnes, Mark, Vangara, Raviteja, Bergstrom, Erik N, He, Yudou, Vella, Mike, Wang, Jingwei, Teague, Jon W, Clapham, Peter, Moody, Sarah, Senkin, Sergey, Li, Yun Rose, Riva, Laura, Zhang, Tongwu, Gruber, Andreas J, Steele, Christopher D, Otlu, Burçak, Khandekar, Azhar, Abbasi, Ammal, Humphreys, Laura, Syulyukina, Natalia, Brady, Samuel W, Alexandrov, Boian S, Pillay, Nischalan, Zhang, Jinghui, Adams, David J, Martincorena, Iñigo, Wedge, David C, Landi, Maria Teresa, Brennan, Paul, Stratton, Michael R, Rozen, Steven G, and Alexandrov, Ludmil B

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Tobacco Smoke and Health, Human Genome, Cancer, Prevention, Tobacco, Good Health and Well Being, cancer genomics, genomics, mutagenesis, mutational signatures
Abstract

Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.

Published
2022

11. Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation

Author

Radford, Elizabeth J., Tan, Hong-Kee, Andersson, Malin H. L., Stephenson, James D., Gardner, Eugene J., Ironfield, Holly, Waters, Andrew J., Gitterman, Daniel, Lindsay, Sarah, Abascal, Federico, Martincorena, Iñigo, Kolesnik-Taylor, Anna, Ng-Cordell, Elise, Firth, Helen V., Baker, Kate, Perry, John R. B., Adams, David J., Gerety, Sebastian S., and Hurles, Matthew E.

Published
2023
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12. Knockout or inhibition of USP30 protects dopaminergic neurons in a Parkinson’s disease mouse model

Author

Fang, Tracy-Shi Zhang, Sun, Yu, Pearce, Andrew C., Eleuteri, Simona, Kemp, Mark, Luckhurst, Christopher A., Williams, Rachel, Mills, Ross, Almond, Sarah, Burzynski, Laura, Márkus, Nóra M., Lelliott, Christopher J., Karp, Natasha A., Adams, David J., Jackson, Stephen P., Zhao, Jin-Feng, Ganley, Ian G., Thompson, Paul W., Balmus, Gabriel, and Simon, David K.

Published
2023
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13. Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer

Author

Wong, Kim, Abascal, Federico, Ludwig, Latasha, Aupperle-Lellbach, Heike, Grassinger, Julia, Wright, Colin W., Allison, Simon J., Pinder, Emma, Phillips, Roger M., Romero, Laura P., Gal, Arnon, Roady, Patrick J., Pires, Isabel, Guscetti, Franco, Munday, John S., Peleteiro, Maria C., Pinto, Carlos A., Carvalho, Tânia, Cota, João, Du Plessis, Elizabeth C., Constantino-Casas, Fernando, Plog, Stephanie, Moe, Lars, de Brot, Simone, Bemelmans, Ingrid, Amorim, Renée Laufer, Georgy, Smitha R., Prada, Justina, del Pozo, Jorge, Heimann, Marianne, de Carvalho Nunes, Louisiane, Simola, Outi, Pazzi, Paolo, Steyl, Johan, Ubukata, Rodrigo, Vajdovich, Peter, Priestnall, Simon L., Suárez-Bonnet, Alejandro, Roperto, Franco, Millanta, Francesca, Palmieri, Chiara, Ortiz, Ana L., Barros, Claudio S. L., Gava, Aldo, Söderström, Minna E., O’Donnell, Marie, Klopfleisch, Robert, Manrique-Rincón, Andrea, Martincorena, Inigo, Ferreira, Ingrid, Arends, Mark J., Wood, Geoffrey A., Adams, David J., and van der Weyden, Louise

Published
2023
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16. Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes

Author

Higgins, Kendall, Moore, Bret A, Berberovic, Zorana, Adissu, Hibret A, Eskandarian, Mohammad, Flenniken, Ann M, Shao, Andy, Imai, Denise M, Clary, Dave, Lanoue, Louise, Newbigging, Susan, Nutter, Lauryl MJ, Adams, David J, Bosch, Fatima, Braun, Robert E, Brown, Steve DM, Dickinson, Mary E, Dobbie, Michael, Flicek, Paul, Gao, Xiang, Galande, Sanjeev, Grobler, Anne, Heaney, Jason D, Herault, Yann, de Angelis, Martin Hrabe, Chin, Hsian-Jean Genie, Mammano, Fabio, Qin, Chuan, Shiroishi, Toshihiko, Sedlacek, Radislav, Seong, J-K, Xu, Ying, Lloyd, KC Kent, McKerlie, Colin, and Moshiri, Ala

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Biotechnology, Rare Diseases, 2.1 Biological and endogenous factors, Mice, Animals, Mice, Knockout, Ciliopathies, Gene Knockout Techniques, Cilia, Databases, Factual, Nerve Tissue Proteins, Cell Cycle Proteins, IMPC Consortium
Abstract

We searched a database of single-gene knockout (KO) mice produced by the International Mouse Phenotyping Consortium (IMPC) to identify candidate ciliopathy genes. We first screened for phenotypes in mouse lines with both ocular and renal or reproductive trait abnormalities. The STRING protein interaction tool was used to identify interactions between known cilia gene products and those encoded by the genes in individual knockout mouse strains in order to generate a list of "candidate ciliopathy genes." From this list, 32 genes encoded proteins predicted to interact with known ciliopathy proteins. Of these, 25 had no previously described roles in ciliary pathobiology. Histological and morphological evidence of phenotypes found in ciliopathies in knockout mouse lines are presented as examples (genes Abi2, Wdr62, Ap4e1, Dync1li1, and Prkab1). Phenotyping data and descriptions generated on IMPC mouse line are useful for mechanistic studies, target discovery, rare disease diagnosis, and preclinical therapeutic development trials. Here we demonstrate the effective use of the IMPC phenotype data to uncover genes with no previous role in ciliary biology, which may be clinically relevant for identification of novel disease genes implicated in ciliopathies.

Published
2022

17. Melanoma models for the next generation of therapies

Author

Patton, E Elizabeth, Mueller, Kristen L, Adams, David J, Anandasabapathy, Niroshana, Aplin, Andrew E, Bertolotto, Corine, Bosenberg, Marcus, Ceol, Craig J, Burd, Christin E, Chi, Ping, Herlyn, Meenhard, Holmen, Sheri L, Karreth, Florian A, Kaufman, Charles K, Khan, Shaheen, Kobold, Sebastian, Leucci, Eleonora, Levy, Carmit, Lombard, David B, Lund, Amanda W, Marie, Kerrie L, Marine, Jean-Christophe, Marais, Richard, McMahon, Martin, Robles-Espinoza, Carla Daniela, Ronai, Ze'ev A, Samuels, Yardena, Soengas, Maria S, Villanueva, Jessie, Weeraratna, Ashani T, White, Richard M, Yeh, Iwei, Zhu, Jiyue, Zon, Leonard I, Hurlbert, Marc S, and Merlino, Glenn

Subjects
Clinical Research, Cancer, Climate-Related Exposures and Conditions, 5.1 Pharmaceuticals, 5.2 Cellular and gene therapies, Development of treatments and therapeutic interventions, Animals, Disease Models, Animal, Humans, Immunity, Immunotherapy, Melanoma, Skin Neoplasms, Tumor Microenvironment, animal models, drug discovery, immunotherapy, melanoma, targeted therapy, therapeutics, tumor microenvironment, Neurosciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

There is a lack of appropriate melanoma models that can be used to evaluate the efficacy of novel therapeutic modalities. Here, we discuss the current state of the art of melanoma models including genetically engineered mouse, patient-derived xenograft, zebrafish, and ex vivo and in vitro models. We also identify five major challenges that can be addressed using such models, including metastasis and tumor dormancy, drug resistance, the melanoma immune response, and the impact of aging and environmental exposures on melanoma progression and drug resistance. Additionally, we discuss the opportunity for building models for rare subtypes of melanomas, which represent an unmet critical need. Finally, we identify key recommendations for melanoma models that may improve accuracy of preclinical testing and predict efficacy in clinical trials, to help usher in the next generation of melanoma therapies.

Published
2021

18. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.

Author

Dentro, Stefan C, Leshchiner, Ignaty, Haase, Kerstin, Tarabichi, Maxime, Wintersinger, Jeff, Deshwar, Amit G, Yu, Kaixian, Rubanova, Yulia, Macintyre, Geoff, Demeulemeester, Jonas, Vázquez-García, Ignacio, Kleinheinz, Kortine, Livitz, Dimitri G, Malikic, Salem, Donmez, Nilgun, Sengupta, Subhajit, Anur, Pavana, Jolly, Clemency, Cmero, Marek, Rosebrock, Daniel, Schumacher, Steven E, Fan, Yu, Fittall, Matthew, Drews, Ruben M, Yao, Xiaotong, Watkins, Thomas BK, Lee, Juhee, Schlesner, Matthias, Zhu, Hongtu, Adams, David J, McGranahan, Nicholas, Swanton, Charles, Getz, Gad, Boutros, Paul C, Imielinski, Marcin, Beroukhim, Rameen, Sahinalp, S Cenk, Ji, Yuan, Peifer, Martin, Martincorena, Inigo, Markowetz, Florian, Mustonen, Ville, Yuan, Ke, Gerstung, Moritz, Spellman, Paul T, Wang, Wenyi, Morris, Quaid D, Wedge, David C, Van Loo, Peter, and PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium

Subjects
PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium, branching evolution, cancer driver genes, cancer evolution, intra-tumor heterogeneity, pan-cancer genomics, subclonal reconstruction, tumor phylogeny, whole-genome sequencing, Genetics, Cancer, Human Genome, 2.1 Biological and endogenous factors, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.

Published
2021

19. 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, 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

20. Epitope spreading toward wild-type melanocyte-lineage antigens rescues suboptimal immune checkpoint blockade responses

Author

Lo, Jennifer A, Kawakubo, Masayoshi, Juneja, Vikram R, Su, Mack Y, Erlich, Tal H, LaFleur, Martin W, Kemeny, Lajos V, Rashid, Mamunur, Malehmir, Mohsen, Rabi, S Alireza, Raghavan, Rumya, Allouche, Jennifer, Kasumova, Gyulnara, Frederick, Dennie T, Pauken, Kristen E, Weng, Qing Yu, Pereira da Silva, Marcelo, Xu, Yu, van der Sande, Anita AJ, Silkworth, Whitney, Roider, Elisabeth, Browne, Edward P, Lieb, David J, Wang, Belinda, Garraway, Levi A, Wu, Catherine J, Flaherty, Keith T, Brinckerhoff, Constance E, Mullins, David W, Adams, David J, Hacohen, Nir, Hoang, Mai P, Boland, Genevieve M, Freeman, Gordon J, Sharpe, Arlene H, Manstein, Dieter, and Fisher, David E

Subjects
Cancer, Animals, Antigens, Neoplasm, Epitopes, Humans, Immune Checkpoint Inhibitors, Melanocytes, Melanoma, Mice, Biological Sciences, Medical and Health Sciences
Abstract

Although immune checkpoint inhibitors (ICIs), such as anti-programmed cell death protein-1 (PD-1), can deliver durable antitumor effects, most patients with cancer fail to respond. Recent studies suggest that ICI efficacy correlates with a higher load of tumor-specific neoantigens and development of vitiligo in patients with melanoma. Here, we report that patients with low melanoma neoantigen burdens who responded to ICI had tumors with higher expression of pigmentation-related genes. Moreover, expansion of peripheral blood CD8+ T cell populations specific for melanocyte antigens was observed only in patients who responded to anti-PD-1 therapy, suggesting that ICI can promote breakdown of tolerance toward tumor-lineage self-antigens. In a mouse model of poorly immunogenic melanomas, spreading of epitope recognition toward wild-type melanocyte antigens was associated with markedly improved anti-PD-1 efficacy in two independent approaches: introduction of neoantigens by ultraviolet (UV) B radiation mutagenesis or the therapeutic combination of ablative fractional photothermolysis plus imiquimod. Complete responses against UV mutation-bearing tumors after anti-PD-1 resulted in protection from subsequent engraftment of melanomas lacking any shared neoantigens, as well as pancreatic adenocarcinomas forcibly overexpressing melanocyte-lineage antigens. Our data demonstrate that somatic mutations are sufficient to provoke strong antitumor responses after checkpoint blockade, but long-term responses are not restricted to these putative neoantigens. Epitope spreading toward T cell recognition of wild-type tumor-lineage self-antigens represents a common pathway for successful response to ICI, which can be evoked in neoantigen-deficient tumors by combination therapy with ablative fractional photothermolysis and imiquimod.

Published
2021

23. Contributors

Author

Accorsi–Mendonça, Daniela, primary, Adams, David J., additional, Allen, Andrew M., additional, Alvarenga, Marlies, additional, Ardell, Jeffrey L., additional, Arnold, Amy C., additional, Ashton, Jesse L., additional, Badrov, Mark B., additional, Ballantyne, Brennan A., additional, Bardsley, Emma N., additional, Barez-Lopez, Soledad, additional, Barman, Susan M., additional, Barrett, Carolyn J., additional, Bauer, Deborah, additional, Bell, Christopher, additional, Ben-Tal, Alona, additional, Benarroch, Eduardo E., additional, Biaggioni, Italo, additional, Brandl, Katharina, additional, Brooks, Virginia L., additional, Brown, Amy E., additional, Browning, Kirsteen N., additional, Bryarly, Meredith, additional, Camargo, Livia L., additional, Camilleri, Michael, additional, Campbell, Preston J., additional, Caron, Marc G., additional, Carter, Jason R., additional, Chapleau, Mark W., additional, Charkoudian, Nisha, additional, Chelimsky, Gisela, additional, Chelimsky, Thomas C., additional, Chompoopong, Pitcha, additional, Claydon, Victoria E., additional, Clément, Gilles, additional, Convertino, Victor A., additional, Coon, Elizabeth A., additional, Cortelli, Pietro, additional, Davis, Stephen N., additional, Diedrich, André, additional, DiPette, Donald J., additional, Diz, Debra I., additional, Drake, Marcus J., additional, Eisenhofer, Graeme, additional, Elefteriou, Florent, additional, Elijovich, Fernando, additional, Elmenhorst, Eva-Maria, additional, English, Brett A., additional, Esler, Murray, additional, Esler, Rosemary, additional, Fadel, Paul J., additional, Fahrenholz, John M., additional, Fanciulli, Alessandra, additional, Fang, John Y., additional, Fealey, Robert D., additional, Ferreira, Nathanne S., additional, Filogonio, Renato, additional, Fink, Gregory D., additional, Fisher, James P., additional, Floras, John S., additional, Fountain, Samuel J., additional, Fu, Qi, additional, Fudim, Marat, additional, Furlan, Raffaello, additional, Gamboa, Alfredo, additional, Garland, Emily M., additional, Gibbons, Christopher H., additional, Giritharan, Andrew, additional, Goldstein, David S., additional, Golombék, Diego A., additional, Gomez-Sanchez, Elise P., additional, Gomez-Sanchez, Celso E., additional, Graham, Robert M., additional, Grassi, Guido, additional, Greenlund, Ian M., additional, Grubb, Blair P., additional, Guekht, Alla, additional, Guild, Sarah-Jane, additional, Guo, Ling, additional, Gurevich, Vsevolod V., additional, Habermann, Ralf, additional, Hadaya, Joseph, additional, Hahn, Maureen K., additional, Hanna, Peter, additional, Henderson, Luke A., additional, Herring, Neil, additional, Hilz, Max J., additional, Hunter, Peter, additional, Hyland, Keith, additional, Hyland, Lauren A., additional, Jackson, Edwin Kerry, additional, Jacob, Giris, additional, Jänig, Wilfrid, additional, Japundžić-Žigon, Nina, additional, Jones, Carrie K., additional, Joos, Karen M., additional, Jordan, Jens, additional, Joyce, William, additional, Kaidonis, Xenia, additional, Kaufmann, Horacio, additional, Kaye, David, additional, Khan Minhas, Abdul Mannan, additional, Kim, Joyce S., additional, Kitta, Takeya, additional, Kline, David D., additional, Konecny, Thomas, additional, Koons, Natalie J., additional, Kumar, Ambrish, additional, Laffer, Cheryl L., additional, Lagrange, Andre H., additional, Laiken, Nora, additional, Lambert, Gavin, additional, Lambert, Elisabeth, additional, Lamotte, Guillaume, additional, Lenders, Jacques W.M., additional, Levine, Benjamin D., additional, Leys, Fabian, additional, Limper, Ulrich, additional, Lin, Mabelle, additional, Listik, Eduardo, additional, Longmuir, Reid, additional, Low, David A., additional, Low, Phillip A., additional, Luther, James M., additional, Macefield, Vaughan G., additional, Machado, Benedito H., additional, Madel, Maria-Bernadette, additional, Martelli, Davide, additional, Mathias, Christopher J., additional, Mauermann, Michelle L., additional, McAllen, Robin M., additional, McBryde, Fiona D., additional, McKeon, Andrew, additional, McKinley, Michael J., additional, Menuet, Clément, additional, Milam, Douglas F., additional, Mohl, Marion C., additional, Montgomery, Johanna M., additional, Moraes, Davi J.A., additional, Morrison, Shaun F., additional, Murphy, David, additional, Nichols, Charles D., additional, Niewiński, Piotr, additional, Norcliffe-Kaufmann, Lucy, additional, Okamoto, Luis E., additional, Osanlouy, Mahyar, additional, Osborn, John W., additional, Oubaid, Viktor, additional, Palma, Jose-Alberto, additional, Pamporaki, Christina, additional, Parsons, Brian A., additional, Paterson, David J., additional, Paton, Julian F.R., additional, Peltier, Amanda C., additional, Pensato, Umberto, additional, Peterson, Sean M., additional, Phibbs, Fenna T., additional, Pierangeli, Giulia, additional, Potts, Jay D., additional, Rabinstein, Alejandro A., additional, Raizada, Mohan K., additional, Raj, Satish R., additional, Rand, Casey M., additional, Reichmann, Heinz, additional, Robertson, Calum, additional, Robertson, Rose Marie, additional, Robinson, Michael B., additional, Ruzieh, Mohammed, additional, Sandroni, Paola, additional, Sato, Takayuki, additional, Schiffrin, Ernesto L., additional, Schlaich, Markus, additional, Schondorf, Ronald, additional, Schultz, Harold D., additional, Scott, Michael M., additional, Seravalle, Gino, additional, Shannon, John R., additional, Sheikh, Abu Baker, additional, Shibao, Cyndya A., additional, Shivkumar, Kalyanam, additional, Shouman, Kamal, additional, Siepmann, Timo, additional, Singer, Wolfgang, additional, Soltani, Elias, additional, Somers, Virend, additional, Sridharan, Aadhavi, additional, Stefanova, Nadia, additional, Stewart, Julian, additional, Stiles, Lauren E., additional, Sunagawa, Kenji, additional, Tank, Jens, additional, Thijs, Roland D., additional, Tomek, Jakub, additional, Touyz, Rhian M., additional, Tracy, Jennifer A., additional, Travagli, R. Alberto, additional, Undem, Bradley J., additional, Urs, Nikhil, additional, Vernino, Steven, additional, Vianna, Lauro C., additional, Vigo, Daniel E., additional, Vizzard, Margaret A., additional, Wahba, Amr, additional, Waheed, Waqar, additional, Wang, Han-Jun, additional, Wang, Tobias, additional, Wang, Qin, additional, Wang, Ruihao, additional, Weese-Mayer, Debra E., additional, Wenning, Gregor K., additional, Wieling, Wouter, additional, Williams, Kevin W., additional, Winzer-Serhan, Ursula H., additional, Wood, Scott, additional, Yap, Kai Lee, additional, Yoshimura, Naoki, additional, Zavalin, Kirill A., additional, Zhuravlev, Dmitry, additional, Zoccal, Daniel B., additional, and Zubcevic, Jasenka, additional

Published
2023
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24. The Deep Genome Project

Author

Lloyd, KC Kent, Adams, David J, Baynam, Gareth, Beaudet, Arthur L, Bosch, Fatima, Boycott, Kym M, Braun, Robert E, Caulfield, Mark, Cohn, Ronald, Dickinson, Mary E, Dobbie, Michael S, Flenniken, Ann M, Flicek, Paul, Galande, Sanjeev, Gao, Xiang, Grobler, Anne, Heaney, Jason D, Herault, Yann, de Angelis, Martin Hrabě, Lupski, James R, Lyonnet, Stanislas, Mallon, Ann-Marie, Mammano, Fabio, MacRae, Calum A, McInnes, Roderick, McKerlie, Colin, Meehan, Terrence F, Murray, Stephen A, Nutter, Lauryl MJ, Obata, Yuichi, Parkinson, Helen, Pepper, Michael S, Sedlacek, Radislav, Seong, Je Kyung, Shiroishi, Toshihiko, Smedley, Damian, Tocchini-Valentini, Glauco, Valle, David, Wang, Chi-Kuang Leo, Wells, Sara, White, Jacqueline, Wurst, Wolfgang, Xu, Ying, and Brown, Steve DM

Subjects
Animals, Genes, Genome, Humans, Mice, Mutation, Phenotype, Proteins, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Published
2020

25. The mutational signature profile of known and suspected human carcinogens in mice

Author

Riva, Laura, Pandiri, Arun R, Li, Yun Rose, Droop, Alastair, Hewinson, James, Quail, Michael A, Iyer, Vivek, Shepherd, Rebecca, Herbert, Ronald A, Campbell, Peter J, Sills, Robert C, Alexandrov, Ludmil B, Balmain, Allan, and Adams, David J

Subjects
Cancer, Human Genome, Rare Diseases, Genetics, 2.2 Factors relating to the physical environment, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Animals, Carcinogenesis, Carcinogens, DNA Mutational Analysis, Environmental Pollutants, Female, Genome, Humans, Male, Mice, Mutation, Mutation Rate, Propane, Species Specificity, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Epidemiological studies have identified many environmental agents that appear to significantly increase cancer risk in human populations. By analyzing tumor genomes from mice chronically exposed to 1 of 20 known or suspected human carcinogens, we reveal that most agents do not generate distinct mutational signatures or increase mutation burden, with most mutations, including driver mutations, resulting from tissue-specific endogenous processes. We identify signatures resulting from exposure to cobalt and vinylidene chloride and link distinct human signatures (SBS19 and SBS42) with 1,2,3-trichloropropane, a haloalkane and pollutant of drinking water, and find these and other signatures in human tumor genomes. We define the cross-species genomic landscape of tumors induced by an important compendium of agents with relevance to human health.

Published
2020

28. 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, Biotechnology, Human Genome, Prevention, 2.1 Biological and endogenous factors, Aetiology, 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

31. IFI207, a young and fast‐evolving protein, controls retroviral replication via the STING pathway

Author

Moran, Eileen A., primary, Salas-Briceno, Karen, additional, Zhao, Wenming, additional, Enya, Takuji, additional, Aguilera, Alexya N., additional, Acosta, Ivan, additional, Alonzo, Francis, additional, Kiani, Dara, additional, Behnsen, Judith, additional, Alvarez, Catalina, additional, Keane, Thomas M., additional, Adams, David J., additional, Lilue, Jingtao, additional, and Ross, Susan R., additional

Published
2024
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32. NUDCD3 deficiency disrupts V(D)J recombination to cause SCID and Omenn syndrome

Author

Chen, Rui, primary, Lukianova, Elena, additional, van der Loeff, Ina Schim, additional, Spegarova, Jarmila Stremenova, additional, Willet, Joseph D.P., additional, James, Kieran D., additional, Ryder, Edward J., additional, Griffin, Helen, additional, IJspeert, Hanna, additional, Gajbhiye, Akshada, additional, Lamoliatte, Frederic, additional, Marin-Rubio, Jose L., additional, Woodbine, Lisa, additional, Lemos, Henrique, additional, Swan, David J., additional, Pintar, Valeria, additional, Sayes, Kamal, additional, Ruiz-Morales, Elias R., additional, Eastham, Simon, additional, Dixon, David, additional, Prete, Martin, additional, Prigmore, Elena, additional, Jeggo, Penny, additional, Boyes, Joan, additional, Mellor, Andrew, additional, Huang, Lei, additional, van der Burg, Mirjam, additional, Engelhardt, Karin R., additional, Stray-Pedersen, Asbjørg, additional, Erichsen, Hans Christian, additional, Gennery, Andrew R., additional, Trost, Matthias, additional, Adams, David J., additional, Anderson, Graham, additional, Lorenc, Anna, additional, Trynka, Gosia, additional, and Hambleton, Sophie, additional

Published
2024
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33. Distinct molecular and functional properties of human induced-proprioceptor and low-threshold mechanoreceptor neurons

Author

Hulme, Amy J, primary, Finol-Urdaneta, Rocio K, additional, McArthur, Jeffrey R, additional, Marzano, Nicholas R, additional, Maksour, Simon, additional, Thind, Amarinder Singh, additional, Guo, Yang, additional, Kaul, Dominic, additional, Maddock, Marnie, additional, Friedrich, Oliver, additional, Martinac, Boris, additional, Adams, David J., additional, and Dottori, Mirella, additional

Published
2024
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35. IFI207, a young and fast-evolving protein, controls retroviral replication via the STING pathway

Author

Moran, Eileen A, primary, Salas-Briceno, Karen, additional, Zhao, Wenming, additional, Enya, Takuji, additional, Aguilera, Alexya, additional, Acosta, Ivan, additional, Alonzo, Francis, additional, Kiani, Dara, additional, Behnsen, Judith, additional, Alvarez, Catalina, additional, Keane, Thomas, additional, Adams, David J, additional, Lilue, Jingtao, additional, and Ross, Susan R., additional

Published
2024
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37. Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets.

Author

Newell, Felicity, Kong, Yan, Wilmott, James S, Johansson, Peter A, Ferguson, Peter M, Cui, Chuanliang, Li, Zhongwu, Kazakoff, Stephen H, Burke, Hazel, Dodds, Tristan J, Patch, Ann-Marie, Nones, Katia, Tembe, Varsha, Shang, Ping, van der Weyden, Louise, Wong, Kim, Holmes, Oliver, Lo, Serigne, Leonard, Conrad, Wood, Scott, Xu, Qinying, Rawson, Robert V, Mukhopadhyay, Pamela, Dummer, Reinhard, Levesque, Mitchell P, Jönsson, Göran, Wang, Xuan, Yeh, Iwei, Wu, Hong, Joseph, Nancy, Bastian, Boris C, Long, Georgina V, Spillane, Andrew J, Shannon, Kerwin F, Thompson, John F, Saw, Robyn PM, Adams, David J, Si, Lu, Pearson, John V, Hayward, Nicholas K, Waddell, Nicola, Mann, Graham J, Guo, Jun, and Scolyer, Richard A

Subjects
Melanocytes, Humans, Melanoma, Telomerase, Signal Transduction, Point Mutation, Female, Male, Cyclin-Dependent Kinase 4, Proto-Oncogene Proteins c-mdm2, DNA Copy Number Variations, Biomarkers, Tumor, Whole Genome Sequencing, Biomarkers, Tumor
Abstract

Knowledge of key drivers and therapeutic targets in mucosal melanoma is limited due to the paucity of comprehensive mutation data on this rare tumor type. To better understand the genomic landscape of mucosal melanoma, here we describe whole genome sequencing analysis of 67 tumors and validation of driver gene mutations by exome sequencing of 45 tumors. Tumors have a low point mutation burden and high numbers of structural variants, including recurrent structural rearrangements targeting TERT, CDK4 and MDM2. Significantly mutated genes are NRAS, BRAF, NF1, KIT, SF3B1, TP53, SPRED1, ATRX, HLA-A and CHD8. SF3B1 mutations occur more commonly in female genital and anorectal melanomas and CTNNB1 mutations implicate a role for WNT signaling defects in the genesis of some mucosal melanomas. TERT aberrations and ATRX mutations are associated with alterations in telomere length. Mutation profiles of the majority of mucosal melanomas suggest potential susceptibility to CDK4/6 and/or MEK inhibitors.

Published
2019

38. Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma.

Author

Wong, Kim, van der Weyden, Louise, Schott, Courtney R, Foote, Alastair, Constantino-Casas, Fernando, Smith, Sionagh, Dobson, Jane M, Murchison, Elizabeth P, Wu, Hong, Yeh, Iwei, Fullen, Douglas R, Joseph, Nancy, Bastian, Boris C, Patel, Rajiv M, Martincorena, Inigo, Robles-Espinoza, Carla Daniela, Iyer, Vivek, Kuijjer, Marieke L, Arends, Mark J, Brenn, Thomas, Harms, Paul W, Wood, Geoffrey A, and Adams, David J

Subjects
Mucous Membrane, Animals, Dogs, Horses, Humans, Melanoma, Mouth Neoplasms, Skin Neoplasms, Neoplasm Recurrence, Local, GTP Phosphohydrolases, Protein-Serine-Threonine Kinases, Cell Cycle Proteins, Microtubule-Associated Proteins, Cadherins, Membrane Proteins, Neoplasm Proteins, Tumor Suppressor Proteins, BRCA1 Protein, BRCA2 Protein, Species Specificity, Gene Expression Regulation, Neoplastic, Germ-Line Mutation, Tumor Suppressor Protein p53, PTEN Phosphohydrolase, Proto-Oncogene Proteins c-mdm2, Receptor-Like Protein Tyrosine Phosphatases, Class 3, DNA Copy Number Variations, Carcinogenesis, Gene Expression Regulation, Neoplastic, Neoplasm Recurrence, Local, Receptor-Like Protein Tyrosine Phosphatases, Class 3
Abstract

Mucosal melanoma is a rare and poorly characterized subtype of human melanoma. Here we perform a cross-species analysis by sequencing tumor-germline pairs from 46 primary human muscosal, 65 primary canine oral and 28 primary equine melanoma cases from mucosal sites. Analysis of these data reveals recurrently mutated driver genes shared between species such as NRAS, FAT4, PTPRJ, TP53 and PTEN, and pathogenic germline alleles of BRCA1, BRCA2 and TP53. We identify a UV mutation signature in a small number of samples, including human cases from the lip and nasal mucosa. A cross-species comparative analysis of recurrent copy number alterations identifies several candidate drivers including MDM2, B2M, KNSTRN and BUB1B. Comparison of somatic mutations in recurrences and metastases to those in the primary tumor suggests pervasive intra-tumor heterogeneity. Collectively, these studies suggest a convergence of some genetic changes in mucosal melanomas between species but also distinctly different paths to tumorigenesis.

Published
2019

39. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

Author

Lilue, Jingtao, Doran, Anthony G, Fiddes, Ian T, Abrudan, Monica, Armstrong, Joel, Bennett, Ruth, Chow, William, Collins, Joanna, Collins, Stephan, Czechanski, Anne, Danecek, Petr, Diekhans, Mark, Dolle, Dirk-Dominik, Dunn, Matt, Durbin, Richard, Earl, Dent, Ferguson-Smith, Anne, Flicek, Paul, Flint, Jonathan, Frankish, Adam, Fu, Beiyuan, Gerstein, Mark, Gilbert, James, Goodstadt, Leo, Harrow, Jennifer, Howe, Kerstin, Ibarra-Soria, Ximena, Kolmogorov, Mikhail, Lelliott, Chris J, Logan, Darren W, Loveland, Jane, Mathews, Clayton E, Mott, Richard, Muir, Paul, Nachtweide, Stefanie, Navarro, Fabio CP, Odom, Duncan T, Park, Naomi, Pelan, Sarah, Pham, Son K, Quail, Mike, Reinholdt, Laura, Romoth, Lars, Shirley, Lesley, Sisu, Cristina, Sjoberg-Herrera, Marcela, Stanke, Mario, Steward, Charles, Thomas, Mark, Threadgold, Glen, Thybert, David, Torrance, James, Wong, Kim, Wood, Jonathan, Yalcin, Binnaz, Yang, Fengtang, Adams, David J, Paten, Benedict, and Keane, Thomas M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Animals, Animals, Laboratory, Chromosome Mapping, Genetic Loci, Genome, Haplotypes, Mice, Mice, Inbred BALB C, Mice, Inbred C3H, Mice, Inbred C57BL, Mice, Inbred CBA, Mice, Inbred DBA, Mice, Inbred NOD, Mice, Inbred Strains, Molecular Sequence Annotation, Phylogeny, Polymorphism, Single Nucleotide, Species Specificity, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.

Published
2018

40. CRLF3 plays a key role in the final stage of platelet genesis and is a potential therapeutic target for thrombocythemia

Author

Bennett, Cavan, Lawrence, Moyra, Guerrero, Jose A., Stritt, Simon, Waller, Amie K., Yan, Yahui, Mifsud, Richard W., Ballester-Beltrán, Jose, Baig, Ayesha, Mueller, Annett, Mayer, Louisa, Warland, James, Penkett, Christopher J., Akbari, Parsa, Moreau, Thomas, Evans, Amanda L., Mookerjee, Souradip, Hoffman, Gary J., Saeb-Parsy, Kourosh, Adams, David J., Couzens, Amber L., Bender, Markus, Erber, Wendy N., Nieswandt, Bernhard, Read, Randy J., and Ghevaert, Cedric

Published
2022
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41. Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes

Author

Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie, Fonseca, Nuno A., Wongchenko, Matthew, Yan, Yibing, Lauss, Martin, Jönsson, Göran B., Newton-Bishop, Julia, Parkinson, Christine, Middleton, Mark R., Bishop, D. Timothy, McDonald, Sarah, Stefanos, Nikki, Tadross, John, Vergara, Ismael A., Lo, Serigne, Newell, Felicity, Wilmott, James S., Thompson, John F., Long, Georgina V., Scolyer, Richard A., Corrie, Pippa, Adams, David J., Brazma, Alvis, and Rabbie, Roy

Published
2022
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47. The clinicopathologic spectrum and genomic landscape of de-/trans-differentiated melanoma

Author

Ferreira, Ingrid, Droop, Alastair, Edwards, Olivia, Wong, Kim, Harle, Victoria, Habeeb, Omar, Gharpuray-Pandit, Deepa, Houghton, Joseph, Wiedemeyer, Katharina, Mentzel, Thomas, Billings, Steven D., Ko, Jennifer S., Füzesi, Laszlo, Mulholland, Kathleen, Prusac, Ivana Kuzmic, Liegl-Atzwanger, Bernadette, de Saint Aubain, Nicolas, Caldwell, Helen, Riva, Laura, van der Weyden, Louise, Arends, Mark J., Brenn, Thomas, and Adams, David J.

Published
2021
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48. 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

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