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101. Real-time genomics for One Health

Author: Urban, Lara, Perlas, Albert, Francino, Olga, Martí-Carreras, Joan, Muga, Brenda A., Mwangi, Jenniffer W., Boykin Okalebo, Laura, Stanton, Jo-Ann L., Black, Amanda, Waipara, Nick, Fontsere, Claudia, Eccles, David, Urel, Harika, Reska, Tim, Morales, Hernán E., Palmada-Flores, Marc, Marques-Bonet, Tomas, Watsa, Mrinalini, Libke, Zane, Erkenswick, Gideon, van Oosterhout, Cock, Urban, Lara, Perlas, Albert, Francino, Olga, Martí-Carreras, Joan, Muga, Brenda A., Mwangi, Jenniffer W., Boykin Okalebo, Laura, Stanton, Jo-Ann L., Black, Amanda, Waipara, Nick, Fontsere, Claudia, Eccles, David, Urel, Harika, Reska, Tim, Morales, Hernán E., Palmada-Flores, Marc, Marques-Bonet, Tomas, Watsa, Mrinalini, Libke, Zane, Erkenswick, Gideon, and van Oosterhout, Cock
Abstract: The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself – from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.
Published: 2023

102. Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs

Author: Alvarez-Estape, Marina, Pawar, Harvinder, Fontsere, Claudia, Trujillo, Amber E., Gunson, Jessica L., Bergl, Richard A., Bermejo, Magdalena, Linder, Joshua M., McFarland, Kelley, Oates, John F., Sunderland-Groves, Jacqueline L., Orkin, Joseph, Higham, James P., Viaud-Martinez, Karine A., Lizano, Esther, Marques-Bonet, Tomas, Alvarez-Estape, Marina, Pawar, Harvinder, Fontsere, Claudia, Trujillo, Amber E., Gunson, Jessica L., Bergl, Richard A., Bermejo, Magdalena, Linder, Joshua M., McFarland, Kelley, Oates, John F., Sunderland-Groves, Jacqueline L., Orkin, Joseph, Higham, James P., Viaud-Martinez, Karine A., Lizano, Esther, and Marques-Bonet, Tomas
Abstract: The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. In this study, we expand the number of whole genomes available for wild western gorillas, generating 41 new genomes (25 belonging to Cross River gorillas) using single shed hairs collected from gorilla nests. By combining these genomes with publicly available wild gorilla genomes, we confirm that Cross River gorillas form three population clusters. We also found little variation in genome-wide heterozygosity among them. Our analyses reveal long runs of homozygosity (>10 Mb), indicating recent inbreeding in Cross River gorillas. This is similar to that seen in mountain gorillas but with a much more recent bottleneck. We also detect past gene flow between two Cross River sites, Afi Mountain Wildlife Sanctuary and the Mbe Mountains. Furthermore, we observe past allele sharing between Cross River gorillas and the northern western lowland gorilla sites, as well as with the eastern gorilla species. This is the first study using single shed hairs from a wild species for whole genome sequencing to date. Taken together, our results highlight the importance of implementing conservation measures to increase connectivity among Cross River gorilla sites.
Published: 2023

103. A global catalog of whole-genome diversity from 233 primate species

Author: Kuderna, Lukas F.K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai How, Marques Bonet, Tomas, Kuderna, Lukas F.K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai How, and Marques Bonet, Tomas
Abstract: The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research., The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
Published: 2023

104. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author: Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.
Abstract: Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.
Published: 2023
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105. Chimpanzee genomic diversity reveals ancient admixture with bonobos

Author: de Manuel, Marc, Kuhlwilm, Martin, Frandsen, Peter, Sousa, Vitor C., Desai, Tariq, Prado-Martinez, Javier, Hernandez-Rodriguez, Jessica, Dupanloup, Isabelle, Lao, Oscar, Hallast, Pille, Schmidt, Joshua M., Heredia-Genestar, José María, Benazzo, Andrea, Barbujani, Guido, Peter, Benjamin M., Kuderna, Lukas F. K., Casals, Ferran, Angedakin, Samuel, Arandjelovic, Mimi, Boesch, Christophe, Kühl, Hjalmar, Vigilant, Linda, Langergraber, Kevin, Novembre, John, Gut, Marta, Gut, Ivo, Navarro, Arcadi, Carlsen, Frauds, Andres, Aida M., Siegismund, Hans. R., Scally, Aylwyn, Excoffier, Laurent, Tyler-Smith, Chris, Castellano, Sergi, Xue, Yali, Hvilsom, Christina, and Marques-Bonet, Tomas
Published: 2016

106. Whole mitochondrial genomes illuminate ancient intercontinental dispersals of grey wolves (Canis lupus)

Author: Koblmüller, Stephan, Vilá, Carles, Lorente-Galdos, Belen, Dabad, Marc, Ramirez, Oscar, Marques-Bonet, Tomas, Wayne, Robert K., and Leonard, Jennifer A.
Published: 2016

107. Evolutionary constraint and innovation across hundreds of placental mammals

Author: Christmas, Matthew J., Kaplow, Irene M., Genereux, Diane P., Dong, Michael X., Hughes, Graham M., Li, Xue, Sullivan, Patrick F., Hindle, Allyson G., Andrews, Gregory, Armstrong, Joel C., Bianchi, Matteo, Breit, Ana M., Diekhans, Mark, Fanter, Cornelia, Foley, Nicole M., Goodman, Daniel B., Goodman, Linda, Keough, Kathleen C., Kirilenko, Bogdan, Kowalczyk, Amanda, Lawless, Colleen, Lind, Abigail L., Meadows, Jennifer R. S., Moreira, Lucas R., Redlich, Ruby W., Ryan, Louise, Swofford, Ross, Valenzuela, Alejandro, Wagner, Franziska, Wallerman, Ola, Brown, Ashley R., Damas, Joana, Fan, Kaili, Gatesy, John, Grimshaw, Jenna, Johnson, Jeremy, Kozyrev, Sergey V., Lawler, Alyssa J., Marinescu, Voichita D., Morrill, Kathleen M., Osmanski, Austin, Paulat, Nicole S., Phan, BaDoi N., Reilly, Steven K., Schäffer, Daniel E., Steiner, Cynthia, Supple, Megan A., Wilder, Aryn P., Wirthlin, Morgan E., Xue, James R., Birren, Bruce W., Gazal, Steven, Hubley, Robert M., Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Meyer, Wynn K., Nweeia, Martin, Sabeti, Pardis C., Shapiro, Beth, Smit, Arian F. A., Springer, Mark S., Teeling, Emma C., Weng, Zhiping, Hiller, Michael, Levesque, Danielle L., Lewin, Harris A., Murphy, William J., Navarro, Arcadi, Paten, Benedict, Pollard, Katherine S., Ray, David A., Ruf, Irina, Ryder, Oliver A., Pfenning, Andreas R., Lindblad-Toh, Kerstin, and Karlsson, Elinor K.
Subjects: Article
Abstract: Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth’s vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.
Published: 2023

108. Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations

Author: Lorente-Galdos, Belen, Lao, Oscar, Serra-Vidal, Gerard, Santpere, Gabriel, Kuderna, Lukas F. K., Arauna, Lara R., Fadhlaoui-Zid, Karima, Pimenoff, Ville N., Soodyall, Himla, Zalloua, Pierre, Marques-Bonet, Tomas, and Comas, David
Published: 2019
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109. Genomes reveal marked differences in the adaptive evolution between orangutan species

Author: Mattle-Greminger, Maja P., Bilgin Sonay, Tugce, Nater, Alexander, Pybus, Marc, Desai, Tariq, de Valles, Guillem, Casals, Ferran, Scally, Aylwyn, Bertranpetit, Jaume, Marques-Bonet, Tomas, van Schaik, Carel P., Anisimova, Maria, and Krützen, Michael
Published: 2018
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110. The molecular evolution of spermatogenesis across mammals

Author: Murat, Florent, primary, Mbengue, Noe, additional, Winge, Sofia Boeg, additional, Trefzer, Timo, additional, Leushkin, Evgeny, additional, Sepp, Mari, additional, Cardoso-Moreira, Margarida, additional, Schmidt, Julia, additional, Schneider, Celine, additional, Mößinger, Katharina, additional, Brüning, Thoomke, additional, Lamanna, Francesco, additional, Belles, Meritxell Riera, additional, Conrad, Christian, additional, Kondova, Ivanela, additional, Bontrop, Ronald, additional, Behr, Rüdiger, additional, Khaitovich, Philipp, additional, Pääbo, Svante, additional, Marques-Bonet, Tomas, additional, Grützner, Frank, additional, Almstrup, Kristian, additional, Schierup, Mikkel Heide, additional, and Kaessmann, Henrik, additional
Published: 2022
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111. Ghost admixture in eastern gorillas

Author: Pawar, Harvinder, primary, Cuadros, Sebastian, additional, de Manuel, Marc, additional, van der Valk, Tom, additional, Lobon, Irene, additional, Alvarez-Estape, Marina, additional, Haber, Marc, additional, Dolgova, Olga, additional, Han, Sojung, additional, Ayub, Qasim, additional, Bautista, Ruben, additional, Kelley, Joanna L., additional, Cornejo, Omar E., additional, Lao, Oscar, additional, Andrés, Aida M., additional, Guschanski, Katerina, additional, Ssebide, Benard, additional, Cranfield, Mike, additional, Tyler-Smith, Chris, additional, Xue, Yali, additional, Prado-Martinez, Javier, additional, Marques-Bonet, Tomas, additional, and Kuhlwilm, Martin, additional
Published: 2022
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112. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr)

Author: Riaño, Gabriel, primary, Fontsere, Claudia, additional, de Manuel, Marc, additional, Talavera, Adrián, additional, Burriel-Carranza, Bernat, additional, Tejero-Cicuéndez, Héctor, additional, AlGethami, Raed Hamoud M., additional, Shobrak, Mohammed, additional, Marques-Bonet, Tomas, additional, and Carranza, Salvador, additional
Published: 2022
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113. The population genomic legacy of the second plague pandemic

Author: Gopalakrishnan, Shyam, primary, Ebenesersdóttir, S. Sunna, additional, Lundstrøm, Inge K.C., additional, Turner-Walker, Gordon, additional, Moore, Kristjan H.S., additional, Luisi, Pierre, additional, Margaryan, Ashot, additional, Martin, Michael D., additional, Ellegaard, Martin Rene, additional, Magnússon, Ólafur þ., additional, Sigurðsson, Ásgeir, additional, Snorradóttir, Steinunn, additional, Magnúsdóttir, Droplaug N., additional, Laffoon, Jason E., additional, van Dorp, Lucy, additional, Liu, Xiaodong, additional, Moltke, Ida, additional, Ávila-Arcos, María C., additional, Schraiber, Joshua G., additional, Rasmussen, Simon, additional, Juan, David, additional, Gelabert, Pere, additional, de-Dios, Toni, additional, Fotakis, Anna K., additional, Iraeta-Orbegozo, Miren, additional, Vågene, Åshild J., additional, Denham, Sean Dexter, additional, Christophersen, Axel, additional, Stenøien, Hans K., additional, Vieira, Filipe G., additional, Liu, Shanlin, additional, Günther, Torsten, additional, Kivisild, Toomas, additional, Moseng, Ole Georg, additional, Skar, Birgitte, additional, Cheung, Christina, additional, Sandoval-Velasco, Marcela, additional, Wales, Nathan, additional, Schroeder, Hannes, additional, Campos, Paula F., additional, Guðmundsdóttir, Valdís B., additional, Sicheritz-Ponten, Thomas, additional, Petersen, Bent, additional, Halgunset, Jostein, additional, Gilbert, Edmund, additional, Cavalleri, Gianpiero L., additional, Hovig, Eivind, additional, Kockum, Ingrid, additional, Olsson, Tomas, additional, Alfredsson, Lars, additional, Hansen, Thomas F., additional, Werge, Thomas, additional, Willerslev, Eske, additional, Balloux, Francois, additional, Marques-Bonet, Tomas, additional, Lalueza-Fox, Carles, additional, Nielsen, Rasmus, additional, Stefánsson, Kári, additional, Helgason, Agnar, additional, and Gilbert, M. Thomas P., additional
Published: 2022
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114. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Author: Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, 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Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yao, Xiaotong, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yoon, Sung-Soo, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zamora, Jorge, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Cheng-Zhong, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
Published: 2023
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115. Combined burden and functional impact tests for cancer driver discovery using DriverPower

Author: Shuai, Shimin, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Barenboim, Jonathan, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Paczkowska, Marta, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reimand, Jüri, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, Claes, Wadi, Lina, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wheeler, David A, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, von Mering, Christian, Gallinger, Steven, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, 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Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Han, Leng, Hanna, George B, Hansmann, Martin, Harismendy, Olivier, Harliwong, Ivon, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, 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Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yao, Xiaotong, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yoon, Sung-Soo, Yousif, Fouad, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zamora, Jorge, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Cheng-Zhong, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Junjun, Zhang, Xiuqing, Zhang, Zemin, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, and Veer, L van’t
Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
Published: 2023
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116. Integrative pathway enrichment analysis of multivariate omics data

Author: Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pich, Oriol, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sabarinathan, Radhakrishnan, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, 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Vijver, Marc J, and Veer, L van’t
Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
Published: 2023
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117. Pathway and network analysis of more than 2500 whole cancer genomes

Author: Reyna, Matthew A, Haan, David, Paczkowska, Marta, Verbeke, Lieven PC, Vazquez, Miguel, Kahraman, Abdullah, Pulido-Tamayo, Sergio, Barenboim, Jonathan, Wadi, Lina, Dhingra, Priyanka, Shrestha, Raunak, Getz, Gad, Lawrence, Michael S, Pedersen, Jakob Skou, Rubin, Mark A, Wheeler, David A, Brunak, Søren, Izarzugaza, Jose MG, Khurana, Ekta, Marchal, Kathleen, von Mering, Christian, Sahinalp, S Cenk, Valencia, Alfonso, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Guo, Qianyun, Gut, Ivo G, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, 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Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
Published: 2023
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118. Divergent mutational processes distinguish hypoxic and normoxic tumours

Author: Bhandari, Vinayak, Li, Constance H, Bristow, Robert G, Boutros, Paul C, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, 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Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
Published: 2023
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119. Genomic footprints of activated telomere maintenance mechanisms in cancer

Author: Sieverling, Lina, Hong, Chen, Koser, Sandra D, Ginsbach, Philip, Kleinheinz, Kortine, Hutter, Barbara, Braun, Delia M, Cortés-Ciriano, Isidro, Xi, Ruibin, Kabbe, Rolf, Park, Peter J, Eils, Roland, Schlesner, Matthias, Akdemir, Kadir C, Alvarez, Eva G, Baez-Ortega, Adrian, Beroukhim, Rameen, Boutros, Paul C, Bowtell, David DL, Brors, Benedikt, Burns, Kathleen H, Campbell, Peter J, Chan, Kin, Chen, Ken, Dueso-Barroso, Ana, Dunford, Andrew J, Edwards, Paul A, Estivill, Xavier, Etemadmoghadam, Dariush, Feuerbach, Lars, Fink, J Lynn, Frenkel-Morgenstern, Milana, Garsed, Dale W, Gerstein, Mark, Gordenin, Dmitry A, Haan, David, Haber, James E, Hess, Julian M, Imielinski, Marcin, Jones, David TW, Ju, Young Seok, Kazanov, Marat D, Klimczak, Leszek J, Koh, Youngil, Korbel, Jan O, Kumar, Kiran, Lee, Eunjung Alice, Lee, Jake June-Koo, Li, Yilong, Lynch, Andy G, Macintyre, Geoff, Markowetz, Florian, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Meyerson, Matthew, Miyano, Satoru, Nakagawa, Hidewaki, Navarro, Fabio CP, Ossowski, Stephan, Pearson, John V, Puiggròs, Montserrat, Rippe, Karsten, Roberts, Nicola D, Roberts, Steven A, Rodriguez-Martin, Bernardo, Schumacher, Steven E, Scully, Ralph, Shackleton, Mark, Sidiropoulos, Nikos, Stewart, Chip, Torrents, David, MC Tubio, Jose, Villasante, Izar, Waddell, Nicola, Wala, Jeremiah A, Weischenfeldt, Joachim, Yang, Lixing, Yao, Xiaotong, Yoon, Sung-Soo, Zamora, Jorge, Zhang, Cheng-Zhong, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, 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Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Field, Matthew A, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Friedman, William, Frigola, Joan, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey 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Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Pardeep, Kumar, Sushant, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lawrence, Michael S, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Hee Jin, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H, Li, 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Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Derek W, Wright, Mark H, Wu, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
Subjects: Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract: Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
Published: 2023
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120. MHC class I diversity in chimpanzees and bonobos

Author: Maibach, Vincent, Hans, Jörg B., Hvilsom, Christina, Marques-Bonet, Tomas, and Vigilant, Linda
Published: 2017
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121. Author Correction: The dental proteome of Homo antecessor

Author: Welker, Frido, Ramos-Madrigal, Jazmín, Gutenbrunner, Petra, Mackie, Meaghan, Tiwary, Shivani, Jersie-Christensen, Rosa Rakownikow, Chiva, Cristina, Dickinson, Marc R., Kuhlwilm, Martin, de Manuel, Marc, Gelabert, Pere, Martinón-Torres, María, Margvelashvili, Ann, Arsuaga, Juan Luis, Carbonell, Eudald, Marques-Bonet, Tomas, Penkman, Kirsty, Sabidó, Eduard, Cox, Jürgen, Olsen, Jesper V., Lordkipanidze, David, Racimo, Fernando, Lalueza-Fox, Carles, de Castro, José María Bermúdez, Willerslev, Eske, and Cappellini, Enrico
Published: 2020
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122. Ancient gene flow from early modern humans into Eastern Neanderthals

Author: Kuhlwilm, Martin, Gronau, Ilan, Hubisz, Melissa J., de Filippo, Cesare, Prado-Martinez, Javier, Kircher, Martin, Fu, Qiaomei, Burbano, Hernan A., Lalueza-Fox, Carles, de la Rasilla, Marco, Rosas, Antonio, Rudan, Pavao, Brajkovic, Dejana, Kucan, Zeljko, Gusic, Ivan, Marques-Bonet, Tomas, Andres, Aida M., Viola, Bence, Paabo, Svante, Meyer, Matthias, Siepel, Adam, and Castellano, Sergi
Subjects: Neanderthals -- Genetic aspects -- Research, Genomes -- Natural history -- Research, Gene flow -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought., Based on the fossil record, Neanderthals diverged from modern humans at least 430,000 years ago (1), and the analysis of a Neanderthal genome from a cave in the Altai Mountains [...]
Published: 2016
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123. Recovering the genomes hidden in museum wet collections

Author: Ruiz‐Gartzia, Irune, primary, Lizano, Esther, additional, Marques‐Bonet, Tomas, additional, and Kelley, Joanna L., additional
Published: 2022
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124. Rates and patterns of great ape retrotransposition

Author: Great Ape Genome Project, Hormozdiari, Fereydoun, Konkel, Miriam K., Prado-Martinez, Javier, Chiatante, Giorgia, Herraez, Irene Hernando, Walker, Jerilyn A., Nelson, Benjamin, Alkan, Can, Sudmant, Peter H., Huddleston, John, Catacchio, Claudia R., Ko, Arthur, Malig, Maika, Baker, Carl, Marques-Bonet, Tomas, Ventura, Mario, Batzer, Mark A., and Eichler, Evan E.
Published: 2013

125. The Earth BioGenome Project 2020: Starting the clock

Author: Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, and Zhang, Guojie
Published: 2022

126. Standards recommendations for the Earth BioGenome Project

Author: Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen
Abstract: A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
Published: 2022

127. Initiation of the Primate Genome Project

Author: Wu, Dong-Dong, Qi, Xiao-Guang, Yu, Li, Li, Ming, Liu, Zhi-Jin, Yoder, Anne D., Roos, Christian, Hayakawa, Takashi, Rogers, Jeffrey, Marques-Bonet, Tomas, Su, Bing, Yao, Yong-Gang, Zhang, Ya-Ping, Zhang, Guojie, Wu, Dong-Dong, Qi, Xiao-Guang, Yu, Li, Li, Ming, Liu, Zhi-Jin, Yoder, Anne D., Roos, Christian, Hayakawa, Takashi, Rogers, Jeffrey, Marques-Bonet, Tomas, Su, Bing, Yao, Yong-Gang, Zhang, Ya-Ping, and Zhang, Guojie
Published: 2022

128. Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

Author: Janiak, Mareike, Silva, Felipe E., Beck, Robin, de Vries, Dorien, Kuderna, Lukas F.K., Torosin, Nicole, Melin, Amanda D., Marques-Bonet, Tomas, Goodhead, Ian, Messias, Mariluce, da Silva, Maria N.F., Sampaio, Iracilda, Farias, Izeni Pires, Rossi, Rogerio, de Melo, Fabiano R., Valsecchi, João, Hrbek, Tomas, Boubli, Jean, Janiak, Mareike, Silva, Felipe E., Beck, Robin, de Vries, Dorien, Kuderna, Lukas F.K., Torosin, Nicole, Melin, Amanda D., Marques-Bonet, Tomas, Goodhead, Ian, Messias, Mariluce, da Silva, Maria N.F., Sampaio, Iracilda, Farias, Izeni Pires, Rossi, Rogerio, de Melo, Fabiano R., Valsecchi, João, Hrbek, Tomas, and Boubli, Jean
Abstract: Altres ajuts: CERCA Programme/Generalitat de Catalunya, Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high-quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long-standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade-specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.
Published: 2022

129. Insights from the rescue and breeding management of Cuvier's gazelle (Gazella cuvieri) through whole-genome sequencing

Author: Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas, Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Moreno, Eulalia, Lizano, Esther, Alvarez-Estape, Marina, Fontsere, Claudia, Serres-Armero, Aitor, Kuderna, Lukas, Dobrynin, Pavel, Guidara, Héla, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Moreno, Eulalia, and Lizano, Esther
Abstract: Captive breeding programmes represent the most intensive type of ex situ population management for threatened species. One example is the Cuvier's gazelle programme that started in 1975 with only four founding individuals, and after more than four decades of management in captivity, a reintroduction effort was undertaken in Tunisia in 2016, to establish a population in an area historically included within its range. Here, we aim to determine the genetic consequences of this reintroduction event by assessing the genetic diversity of the founder stock as well as of their descendants. We present the first whole-genome sequencing dataset of 30 Cuvier's gazelles including captive-bred animals, animals born in Tunisia after a reintroduction and individuals from a genetically unrelated Moroccan population. Our analyses revealed no difference between the founder and the offspring cohorts in genome-wide heterozygosity and inbreeding levels, and in the amount and length of runs of homozygosity. The captive but unmanaged Moroccan gazelles have the lowest genetic diversity of all genomes analysed. Our findings demonstrate that the Cuvier's gazelle captive breeding programme can serve as source populations for future reintroductions of this species. We believe that this study can serve as a starting point for global applications of genomics to the conservation plan of this species.
Published: 2022

130. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

Author: Palmada-Flores, Marc, Orkin, Joseph, Haase, Bettina, Mountcastle, Jacquelyn, Bertelsen, Mads, Fedrigo, Olivier, Kuderna, Lukas, Jarvis, Erich D., Marques-Bonet, Tomas, Palmada-Flores, Marc, Orkin, Joseph, Haase, Bettina, Mountcastle, Jacquelyn, Bertelsen, Mads, Fedrigo, Olivier, Kuderna, Lukas, Jarvis, Erich D., and Marques-Bonet, Tomas
Abstract: Altres ajuts: "la Caixa" Foundation (ID 100010434), Background: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in the popular media. Unfortunately, a recent population decline has resulted in the census population decreasing to <2,500 individuals in the wild, and the species's classification as an endangered species by the IUCN. As is the case for most strepsirrhine primates, only a limited amount of genomic research has been conducted on L. catta, in part owing to the lack of genomic resources. Results: We generated a new high-quality reference genome assembly for L. catta (mLemCat1) that conforms to the standards of the Vertebrate Genomes Project. This new long-read assembly is composed of Pacific Biosciences continuous long reads (CLR data), Optical Mapping Bionano reads, Arima HiC data, and 10X linked reads. The contiguity and completeness of the assembly are extremely high, with scaffold and contig N50 values of 90.982 and 10.570 Mb, respectively. Additionally, when compared to other high-quality primate assemblies, L. catta has the lowest reported number of Alu elements, which results predominantly from a lack of AluS and AluY elements. Conclusions: mLemCat1 is an excellent genomic resource not only for the ring-tailed lemur community, but also for other members of the Lemuridae family, and is the first very long read assembly for a strepsirrhine.
Published: 2022

131. The population genomic legacy of the second plague pandemic

Author: Gopalakrishnan, Shyam, Ebenesersdottir, S. Sunna, Lundström, Inge K. C., Turner-Walker, Gordon, Moore, Kristjan H. S., Luisi, Pierre, Margaryan, Ashot, Martin, Michael D., Ellegaard, Martin Rene, Magnusson, Olafur P., Sigurosson, Asgeir, Snorradottir, Steinunn, Magnusdottir, Droplaug N., Laffoon, Jason E., van Dorp, Lucy, Liu, Xiaodong, Moltke, Ida, Avila-Arcos, Maria C., Schraiber, Joshua G., Rasmussen, Simon, Juan, David, Gelabert, Pere, de-Dios, Toni, Fotakis, Anna K., Iraeta-Orbegozo, Miren, Vågene, Åshild J., Denham, Sean Dexter, Christophersen, Axel, Stenøien, Hans K., Vieira, Filipe G., Liu, Shanlin, Günther, Torsten, Kivisild, Toomas, Moseng, Ole Georg, Skar, Birgitte, Cheung, Christina, Sandoval-Velasco, Marcela, Wales, Nathan, Schroeder, Hannes, Campos, Paula F., Guomundsdottir, Valdis B., Sicheritz-Ponten, Thomas, Peterson, Bent, Halgunset, Jostein, Gilbert, Edmund, Cavalleri, Gianpiero L., Hovig, Eivind, Kockum, Ingrid, Olsson, Tomas, Alfredsson, Lars, Hansen, Thomas F., Werge, Thomas, Willerslev, Eske, Balloux, Francois, Marques-Bonet, Tomas, Lalueza-Fox, Carles, Nielsen, Rasmus, Stefansson, Kari, Holgason, Agnar, Gilbert, M. Thomas P., Gopalakrishnan, Shyam, Ebenesersdottir, S. Sunna, Lundström, Inge K. C., Turner-Walker, Gordon, Moore, Kristjan H. S., Luisi, Pierre, Margaryan, Ashot, Martin, Michael D., Ellegaard, Martin Rene, Magnusson, Olafur P., Sigurosson, Asgeir, Snorradottir, Steinunn, Magnusdottir, Droplaug N., Laffoon, Jason E., van Dorp, Lucy, Liu, Xiaodong, Moltke, Ida, Avila-Arcos, Maria C., Schraiber, Joshua G., Rasmussen, Simon, Juan, David, Gelabert, Pere, de-Dios, Toni, Fotakis, Anna K., Iraeta-Orbegozo, Miren, Vågene, Åshild J., Denham, Sean Dexter, Christophersen, Axel, Stenøien, Hans K., Vieira, Filipe G., Liu, Shanlin, Günther, Torsten, Kivisild, Toomas, Moseng, Ole Georg, Skar, Birgitte, Cheung, Christina, Sandoval-Velasco, Marcela, Wales, Nathan, Schroeder, Hannes, Campos, Paula F., Guomundsdottir, Valdis B., Sicheritz-Ponten, Thomas, Peterson, Bent, Halgunset, Jostein, Gilbert, Edmund, Cavalleri, Gianpiero L., Hovig, Eivind, Kockum, Ingrid, Olsson, Tomas, Alfredsson, Lars, Hansen, Thomas F., Werge, Thomas, Willerslev, Eske, Balloux, Francois, Marques-Bonet, Tomas, Lalueza-Fox, Carles, Nielsen, Rasmus, Stefansson, Kari, Holgason, Agnar, and Gilbert, M. Thomas P.
Abstract: Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.
Published: 2022
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132. Standards recommendations for the Earth BioGenome Project.

Author: Lawniczak, Mara KN, Lawniczak, Mara KN, Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M, Baker, William J, Belov, Katherine, Blaxter, Mark L, Marques Bonet, Tomas, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Crawford, Andrew J, Davey, Robert P, Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J, Howe, Kerstin, Jarvis, Erich D, Johnson, Warren E, Johnson, Rebecca N, Kersey, Paul J, Liu, Xin, Lopez, Jose Victor, Myers, Eugene W, Pettersson, Olga Vinnere, Phillippy, Adam M, Poelchau, Monica F, Pruitt, Kim D, Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A, Soltis, Pamela S, Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L, Zhang, Guojie, Zhang, He, Lewin, Harris A, Richards, Stephen, Lawniczak, Mara KN, Lawniczak, Mara KN, Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M, Baker, William J, Belov, Katherine, Blaxter, Mark L, Marques Bonet, Tomas, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Crawford, Andrew J, Davey, Robert P, Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J, Howe, Kerstin, Jarvis, Erich D, Johnson, Warren E, Johnson, Rebecca N, Kersey, Paul J, Liu, Xin, Lopez, Jose Victor, Myers, Eugene W, Pettersson, Olga Vinnere, Phillippy, Adam M, Poelchau, Monica F, Pruitt, Kim D, Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A, Soltis, Pamela S, Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L, Zhang, Guojie, Zhang, He, Lewin, Harris A, and Richards, Stephen
Abstract: A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
Published: 2022

133. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr)

Author: Riaño, Gabriel, Fontsere, Claudia, de Manuel, Marc, Talavera, Adrián, Burriel-Carranza, Bernat, Tejero-Cicuéndez, Héctor, AlGethami, Raed Hamoud M., Shobrak, Mohammed, Marques-Bonet, Tomas, Carranza, Salvador, Riaño, Gabriel, Fontsere, Claudia, de Manuel, Marc, Talavera, Adrián, Burriel-Carranza, Bernat, Tejero-Cicuéndez, Héctor, AlGethami, Raed Hamoud M., Shobrak, Mohammed, Marques-Bonet, Tomas, and Carranza, Salvador
Abstract: Low genetic variation and high levels of inbreeding are usually a consequence of recent population declines in endangered species. From a conservation point of view, it is essential to genetically screen endangered populations to help assess their vulnerability to extinction and to properly create informed management actions towards their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies inhabiting a wide range of habitats. Yet, genomic data is still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two specimens of Arabian leopard and assembled the most complete genomic dataset for leopards to date, including genomic data for all current subspecies. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades, one including the only African subspecies and a second one including all seven subspecies of Asian leopards. Interestingly, the Arabian leopard represents a well-differentiated lineage sister to the rest of Asian subspecies. The demographic history, genomic diversity, Runs of Homozygosity (RoHs), and mutational load in the Arabian leopard indicate a prolonged population decline, which has led to an increase in inbreeding and RoHs, with consequent purging of deleterious mutations. Our study represents the first attempt to genetically inform captive breeding programs for this Critically Endangered subspecies. Still, more genomes, particularly from wild individuals, are needed to fully characterise the genetic makeup of this singular and iconic subspecies.
Published: 2022

134. The Earth BioGenome Project 2020:Starting the clock

Author: Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., and Zhang, Guojie
Published: 2022

135. The genome of melon (Cucumis melo L.)

Author: Garcia-Mas, Jordi, Benjak, Andrej, Sanseverino, Walter, Bourgeois, Michael, Mir, Gisela, González, Víctor M., Hénaff, Elizabeth, Câmara, Francisco, Cozzuto, Luca, Lowy, Ernesto, Alioto, Tyler, Capella-Gutiérrez, Salvador, Blanca, Jose, Cañizares, Joaquín, Ziarsolo, Pello, Gonzalez-Ibeas, Daniel, Rodríguez-Moreno, Luis, Droege, Marcus, Du, Lei, Alvarez-Tejado, Miguel, Lorente-Galdos, Belen, Melé, Marta, Yang, Luming, Weng, Yiqun, Navarro, Arcadi, Marques-Bonet, Tomas, Aranda, Miguel A., Nuez, Fernando, Picó, Belén, Gabaldón, Toni, Roma, Guglielmo, Guigó, Roderic, Casacuberta, Josep M., Arús, Pere, and Puigdomènech, Pere
Published: 2012

136. Author Correction: Ancient admixture from an extinct ape lineage into bonobos

Author: Kuhlwilm, Martin, Han, Sojung, Sousa, Vitor C., Excoffier, Laurent, and Marques-Bonet, Tomas
Published: 2019
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137. Author Correction: Direct estimation of mutations in great apes reconciles phylogenetic dating

Author: Besenbacher, Søren, Hvilsom, Christina, Marques-Bonet, Tomas, Mailund, Thomas, and Schierup, Mikkel Heide
Published: 2019
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138. Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes

Author: Lobon, Irene, primary, Solís-Moruno, Manuel, additional, Juan, David, additional, Muhaisen, Ashraf, additional, Abascal, Federico, additional, Esteller-Cucala, Paula, additional, García-Pérez, Raquel, additional, Martí, Maria Josep, additional, Tolosa, Eduardo, additional, Ávila, Jesús, additional, Rahbari, Raheleh, additional, Marques-Bonet, Tomas, additional, Casals, Ferran, additional, and Soriano, Eduardo, additional
Published: 2022
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139. Insights from the rescue and breeding management of Cuvier’s gazelle ( Gazella cuvieri ) through whole‐genome sequencing

Author: Alvarez‐Estape, Marina, primary, Fontsere, Claudia, additional, Serres‐Armero, Aitor, additional, Kuderna, Lukas F. K., additional, Dobrynin, Pavel, additional, Guidara, Héla, additional, Pukazhenthi, Budhan S., additional, Koepfli, Klaus‐Peter, additional, Marques‐Bonet, Tomas, additional, Moreno, Eulalia, additional, and Lizano, Esther, additional
Published: 2022
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140. A Draft Sequence of the Neandertal Genome

Author: Green, Richard E., Krause, Johannes, Briggs, Adrian W., Marcic, Tomislav, Stenzel, Udo, Kircher, Martin, Patterson, Nick, Li, Heng, Zhai, Weiwei, Fritz, Markus Hsi-Yang, Hansen, Nancy F., Durand, Eric Y., Malaspinas, Anna-Sapfo, Jensen, Jeffrey D., Marques-Bonet, Tomas, Alkan, Can, Prüfer, kay, Meyer, Matthias, Burbano, Hernán A., Good, Jeffrey M., Schultz, Rigo, Aximu-Petri, Ayinuer, Butthof, Anne, Höber, Barbara, Höffner, Barbara, Siegemund, Madlen, Weihmann, Antje, Nusbaum, Chad, Lander, Eric S., Russ, Carsten, Novod, Nathaniel, Affourtit, Jason, Egholm, Michael, Verna, Christine, Rudan, Pavao, Brajkovic, Dejana, Kucan, Zeljko, Gusic, Ivan, Doronichev, Vladimir B., Golovanova, Liubov V., Lalueza-Fox, Carles, de la Rasilla, Marco, Fortea, Javier, Rosas, Antonio, Schmitz, Ralf W., Johnson, Philip L F., Eichler, Evan E., Falush, Daniel, Birney, Ewan, Mullikin, James, Slatkin, Montgomery, Nielsen, Rasmus, Kelso, Janet, Lachmann, Michael, Reich, David, and Pääbo, Svante
Published: 2010

141. Standards recommendations for the Earth BioGenome Project

Author: Lawniczak, Mara K. N., primary, Durbin, Richard, additional, Flicek, Paul, additional, Lindblad-Toh, Kerstin, additional, Wei, Xiaofeng, additional, Archibald, John M., additional, Baker, William J., additional, Belov, Katherine, additional, Blaxter, Mark L., additional, Marques Bonet, Tomas, additional, Childers, Anna K., additional, Coddington, Jonathan A., additional, Crandall, Keith A., additional, Crawford, Andrew J., additional, Davey, Robert P., additional, Di Palma, Federica, additional, Fang, Qi, additional, Haerty, Wilfried, additional, Hall, Neil, additional, Hoff, Katharina J., additional, Howe, Kerstin, additional, Jarvis, Erich D., additional, Johnson, Warren E., additional, Johnson, Rebecca N., additional, Kersey, Paul J., additional, Liu, Xin, additional, Lopez, Jose Victor, additional, Myers, Eugene W., additional, Pettersson, Olga Vinnere, additional, Phillippy, Adam M., additional, Poelchau, Monica F., additional, Pruitt, Kim D., additional, Rhie, Arang, additional, Castilla-Rubio, Juan Carlos, additional, Sahu, Sunil Kumar, additional, Salmon, Nicholas A., additional, Soltis, Pamela S., additional, Swarbreck, David, additional, Thibaud-Nissen, Françoise, additional, Wang, Sibo, additional, Wegrzyn, Jill L., additional, Zhang, Guojie, additional, Zhang, He, additional, Lewin, Harris A., additional, and Richards, Stephen, additional
Published: 2022
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142. The Earth BioGenome Project 2020: Starting the clock

Author: Lewin, Harris A., primary, Richards, Stephen, additional, Lieberman Aiden, Erez, additional, Allende, Miguel L., additional, Archibald, John M., additional, Bálint, Miklós, additional, Barker, Katharine B., additional, Baumgartner, Bridget, additional, Belov, Katherine, additional, Bertorelle, Giorgio, additional, Blaxter, Mark L., additional, Cai, Jing, additional, Caperello, Nicolette D., additional, Carlson, Keith, additional, Castilla-Rubio, Juan Carlos, additional, Chaw, Shu-Miaw, additional, Chen, Lei, additional, Childers, Anna K., additional, Coddington, Jonathan A., additional, Conde, Dalia A., additional, Corominas, Montserrat, additional, Crandall, Keith A., additional, Crawford, Andrew J., additional, DiPalma, Federica, additional, Durbin, Richard, additional, Ebenezer, ThankGod E., additional, Edwards, Scott V., additional, Fedrigo, Olivier, additional, Flicek, Paul, additional, Formenti, Giulio, additional, Gibbs, Richard A., additional, Gilbert, M. Thomas P., additional, Goldstein, Melissa M., additional, Graves, Jennifer Marshall, additional, Greely, Henry T., additional, Grigoriev, Igor V., additional, Hackett, Kevin J., additional, Hall, Neil, additional, Haussler, David, additional, Helgen, Kristofer M., additional, Hogg, Carolyn J., additional, Isobe, Sachiko, additional, Jakobsen, Kjetill Sigurd, additional, Janke, Axel, additional, Jarvis, Erich D., additional, Johnson, Warren E., additional, Jones, Steven J. M., additional, Karlsson, Elinor K., additional, Kersey, Paul J., additional, Kim, Jin-Hyoung, additional, Kress, W. John, additional, Kuraku, Shigehiro, additional, Lawniczak, Mara K. N., additional, Leebens-Mack, James H., additional, Li, Xueyan, additional, Lindblad-Toh, Kerstin, additional, Liu, Xin, additional, Lopez, Jose V., additional, Marques-Bonet, Tomas, additional, Mazard, Sophie, additional, Mazet, Jonna A. K., additional, Mazzoni, Camila J., additional, Myers, Eugene W., additional, O’Neill, Rachel J., additional, Paez, Sadye, additional, Park, Hyun, additional, Robinson, Gene E., additional, Roquet, Cristina, additional, Ryder, Oliver A., additional, Sabir, Jamal S. M., additional, Shaffer, H. Bradley, additional, Shank, Timothy M., additional, Sherkow, Jacob S., additional, Soltis, Pamela S., additional, Tang, Boping, additional, Tedersoo, Leho, additional, Uliano-Silva, Marcela, additional, Wang, Kun, additional, Wei, Xiaofeng, additional, Wetzer, Regina, additional, Wilson, Julia L., additional, Xu, Xun, additional, Yang, Huanming, additional, Yoder, Anne D., additional, and Zhang, Guojie, additional
Published: 2022
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143. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author: Bentley, Blair P., primary, Carrasco-Valenzuela, Tomás, additional, Ramos, Elisa K. S., additional, Pawar, Harvinder, additional, Arantes, Larissa Souza, additional, Alexander, Alana, additional, Banerjee, Shreya M., additional, Masterson, Patrick, additional, Kuhlwilm, Martin, additional, Pippel, Martin, additional, Mountcastle, Jacquelyn, additional, Haase, Bettina, additional, Uliano-Silva, Marcela, additional, Formenti, Giulio, additional, Howe, Kerstin, additional, Chow, William, additional, Tracey, Alan, additional, Sims, Ying, additional, Pelan, Sarah, additional, Wood, Jonathan, additional, Yetsko, Kelsey, additional, Perrault, Justin R., additional, Stewart, Kelly, additional, Benson, Scott R., additional, Levy, Yaniv, additional, Todd, Erica V., additional, Shaffer, H. Bradley, additional, Scott, Peter, additional, Henen, Brian T., additional, Murphy, Robert W., additional, Mohr, David W., additional, Scott, Alan F., additional, Duffy, David J., additional, Gemmell, Neil J., additional, Suh, Alexander, additional, Winkler, Sylke, additional, Thibaud-Nissen, Françoise, additional, Nery, Mariana F., additional, Marques-Bonet, Tomas, additional, Antunes, Agostinho, additional, Tikochinski, Yaron, additional, Dutton, Peter H., additional, Fedrigo, Olivier, additional, Myers, Eugene W., additional, Jarvis, Erich D., additional, Mazzoni, Camila J., additional, and Komoroske, Lisa M., additional
Published: 2022
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144. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

Author: Palmada-Flores, Marc, primary, Orkin, Joseph D, additional, Haase, Bettina, additional, Mountcastle, Jacquelyn, additional, Bertelsen, Mads F, additional, Fedrigo, Olivier, additional, Kuderna, Lukas F K, additional, Jarvis, Erich D, additional, and Marques-Bonet, Tomas, additional
Published: 2022
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145. Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Author: Ferrandez-Peral, Luis, primary, Zhan, Xiaoyu, additional, Alvarez-Estape, Marina, additional, Chiva, Cristina, additional, Esteller-Cucala, Paula, additional, Garcia-Perez, Raquel, additional, Julia, Eva, additional, Lizano, Esther, additional, Fornas, Oscar, additional, Sabido, Eduard, additional, Li, Qiye, additional, Marques-Bonet, Tomas, additional, Juan, David, additional, and Zhang, Guojie, additional
Published: 2021
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146. The molecular evolution of spermatogenesis across mammals

Author: Murat, Florent, primary, Mbengue, Noe, additional, Winge, Sofia Boeg, additional, Trefzer, Timo, additional, Leushkin, Evgeny, additional, Sepp, Mari, additional, Cardoso-Moreira, Margarida, additional, Schmidt, Julia, additional, Schneider, Celine, additional, Mößinger, Katharina, additional, Brüning, Thoomke, additional, Lamanna, Francesco, additional, Belles, Meritxell Riera, additional, Conrad, Christian, additional, Kondova, Ivanela, additional, Bontrop, Ronald, additional, Behr, Rüdiger, additional, Khaitovich, Philipp, additional, Pääbo, Svante, additional, Marques-Bonet, Tomas, additional, Grützner, Frank, additional, Almstrup, Kristian, additional, Schierup, Mikkel Heide, additional, and Kaessmann, Henrik, additional
Published: 2021
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147. Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

Author: de-Dios, Toni, primary, Fontsere, Claudia, additional, Renom, Pere, additional, Stiller, Josefin, additional, Llovera, Laia, additional, Uliano-Silva, Marcela, additional, Sanchez-Gracia, Alejandro, additional, Wright, Charlotte, additional, Lizano, Esther, additional, Navarro, Arcadi, additional, Civit, Sergi, additional, Robbins, Robert K, additional, Blaxter, Mark, additional, Marques-Bonet, Tomas, additional, Vila, Roger, additional, and Lalueza-Fox, Carles, additional
Published: 2021
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148. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

Author: Olalde, Inigo, Allentoft, Morten E., Sanchez-Quinto, Federico, Santpere, Gabriel, Chiang, Charleston W.K., DeGiorgio, Michael, Prado-Martinez, Javier, Rodriguez, Juan Antonio, Rasmussen, Simon, Quilez, Javier, Ramirez, Oscar, Marigorta, Urko M., Fernandez-Callejo, Marcos, Prada, Maria Encina, Encinas, Julio Manuel Vidal, Nielsen, Rasmus, Netea, Mihai G., Novembre, John, Sturm, Richard A., Sabeti, Pardis, Marques-Bonet, Tomas, Navarro, Arcadi, Willerslev, Eske, and Lalueza-Fox, Carles
Subjects: Nucleotide sequencing -- Research, DNA sequencing -- Research, Skin color -- Genetic aspects, Allelomorphism -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe (1-3). The adoption of farming, stock breeding and [...]
Published: 2014

149. Elephant shark genome provides unique insights into gnathostome evolution

Author: Venkatesh, Byrappa, Lee, Alison P., Ravi, Vydianathan, Maurya, Ashish K., Lian, Michelle M., Swann, Jeremy B., Ohta, Yuko, Flajnik, Martin F., Sutoh, Yoichi, Kasahara, Masanori, Hoon, Shawn, Gangu, Vamshidhar, Roy, Scott W., Irimia, Manuel, Korzh, Vladimir, Kondrychyn, Igor, Lim, Zhi Wei, Tay, Boon-Hui, Tohari, Sumanty, Kong, Kiat Whye, Ho, Shufen, Lorente-Galdos, Belen, Quilez, Javier, Marques-Bonet, Tomas, Raney, Brian J., Ingham, Philip W., Tay, Alice, Hillier, LaDeana W., Minx, Patrick, Boehm, Thomas, Wilson, Richard K., Brenner, Sydney, and Warren, Wesley C.
Subjects: Nucleotide sequencing -- Methods, Immune system -- Genetic aspects, DNA sequencing -- Methods, Genomes -- Identification and classification, Sharks -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged [...]
Published: 2014
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150. Gibbon genome and the fast karyotype evolution of small apes

Author: Carbone, Lucia, Alan Harris, R., Gnerre, Sante, Veeramah, Krishna R., Lorente-Galdos, Belen, Huddleston, John, Meyer, Thomas J., Herrero, Javier, Roos, Christian, Aken, Bronwen, Anaclerio, Fabio, Archidiacono, Nicoletta, Baker, Carl, Barrell, Daniel, Batzer, Mark A., Beal, Kathryn, Blancher, Antoine, Bohrson, Craig L., Brameier, Markus, Campbell, Michael S., Capozzi, Oronzo, Casola, Claudio, Chiatante, Giorgia, Cree, Andrew, Damert, Annette, de Jong, Pieter J., Dumas, Laura, Fernandez-Callejo, Marcos, Flicek, Paul, Fuchs, Nina V., Gut, Ivo, Gut, Marta, Hahn, Matthew W., Hernandez-Rodriguez, Jessica, Hillier, LaDeana W., Hubley, Robert, Ianc, Bianca, Izsvák, Zsuzsanna, Jablonski, Nina G., Johnstone, Laurel M., Karimpour-Fard, Anis, Konkel, Miriam K., Kostka, Dennis, Lazar, Nathan H., Lee, Sandra L., Lewis, Lora R., Liu, Yue, Locke, Devin P., Mallick, Swapan, Mendez, Fernando L., Muffato, Matthieu, Nazareth, Lynne V., Nevonen, Kimberly A., O’Bleness, Majesta, Ochis, Cornelia, Odom, Duncan T., Pollard, Katherine S., Quilez, Javier, Reich, David, Rocchi, Mariano, Schumann, Gerald G., Searle, Stephen, Sikela, James M., Skollar, Gabriella, Smit, Arian, Sonmez, Kemal, Hallers, Boudewijn ten, Terhune, Elizabeth, Thomas, Gregg W. C., Ullmer, Brygg, Ventura, Mario, Walker, Jerilyn A., Wall, Jeffrey D., Walter, Lutz, Ward, Michelle C., Wheelan, Sarah J., Whelan, Christopher W., White, Simon, Wilhelm, Larry J., Woerner, August E., Yandell, Mark, Zhu, Baoli, Hammer, Michael F., Marques-Bonet, Tomas, Eichler, Evan E., Fulton, Lucinda, Fronick, Catrina, Muzny, Donna M., Warren, Wesley C., Worley, Kim C., Rogers, Jeffrey, Wilson, Richard K., and Gibbs, Richard A.
Published: 2014
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