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2. Building pangenome graphs

Author

Garrison, Erik, Guarracino, Andrea, Heumos, Simon, Villani, Flavia, Bao, Zhigui, Tattini, Lorenzo, Hagmann, Jörg, Vorbrugg, Sebastian, Marco-Sola, Santiago, Kubica, Christian, Ashbrook, David G., Thorell, Kaisa, Rusholme-Pilcher, Rachel L., Liti, Gianni, Rudbeck, Emilio, Golicz, Agnieszka A., Nahnsen, Sven, Yang, Zuyu, Mwaniki, Moses Njagi, Nobrega, Franklin L., Wu, Yi, Chen, Hao, de Ligt, Joep, Sudmant, Peter H., Huang, Sanwen, Weigel, Detlef, Soranzo, Nicole, Colonna, Vincenza, Williams, Robert W., and Prins, Pjotr

Published
2024
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3. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.

Author

Carey, Megan, Dyson, Zoe, Ingle, Danielle, Amir, Afreenish, Aworh, Mabel, Chattaway, Marie, Chew, Ka, Crump, John, Feasey, Nicholas, Howden, Benjamin, Keddy, Karen, Maes, Mailis, Parry, Christopher, Van Puyvelde, Sandra, Webb, Hattie, Afolayan, Ayorinde, Alexander, Anna, Anandan, Shalini, Andrews, Jason, Ashton, Philip, Basnyat, Buddha, Bavdekar, Ashish, Bogoch, Isaac, Clemens, John, da Silva, Kesia, De, Anuradha, de Ligt, Joep, Diaz Guevara, Paula, Dolecek, Christiane, Dutta, Shanta, Ehlers, Marthie, Francois Watkins, Louise, Garrett, Denise, Godbole, Gauri, Gordon, Melita, Greenhill, Andrew, Griffin, Chelsey, Gupta, Madhu, Hendriksen, Rene, Heyderman, Robert, Hooda, Yogesh, Hormazabal, Juan, Ikhimiukor, Odion, Iqbal, Junaid, Jacob, Jobin, Jenkins, Claire, Jinka, Dasaratha, John, Jacob, Kang, Gagandeep, Kanteh, Abdoulie, Kapil, Arti, Karkey, Abhilasha, Kariuki, Samuel, Kingsley, Robert, Koshy, Roshine, Lauer, A, Levine, Myron, Lingegowda, Ravikumar, Luby, Stephen, Mackenzie, Grant, Mashe, Tapfumanei, Msefula, Chisomo, Mutreja, Ankur, Nagaraj, Geetha, Nagaraj, Savitha, Nair, Satheesh, Naseri, Take, Nimarota-Brown, Susana, Njamkepo, Elisabeth, Okeke, Iruka, Perumal, Sulochana, Pollard, Andrew, Pragasam, Agila, Qadri, Firdausi, Qamar, Farah, Rahman, Sadia, Rambocus, Savitra, Rasko, David, Ray, Pallab, Robins-Browne, Roy, Rongsen-Chandola, Temsunaro, Rutanga, Jean, Saha, Samir, Saha, Senjuti, Saigal, Karnika, Sajib, Mohammad, Seidman, Jessica, Shakya, Jivan, Shamanna, Varun, Shastri, Jayanthi, Shrestha, Rajeev, Sia, Sonia, Sikorski, Michael, Singh, Ashita, Smith, Anthony, Tagg, Kaitlin, Tamrakar, Dipesh, Tanmoy, Arif, Thomas, Maria, and Thomas, Mathew

Subjects
S. enterica serovar typhi, antimicrobial resistance, epidemiology, genomics, global health, infectious disease, microbiology, typhoid conjugate vaccine, typhoid fever, Humans, Salmonella typhi, Typhoid Fever, Anti-Bacterial Agents, Travel, Drug Resistance, Bacterial, Ciprofloxacin
Abstract

BACKGROUND: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). METHODS: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. RESULTS: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal sentinel surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. CONCLUSIONS: The consortiums aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. FUNDING: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).

Published
2023

4. Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic

Author

Jelley, Lauren, Douglas, Jordan, O’Neill, Meaghan, Berquist, Klarysse, Claasen, Ana, Wang, Jing, Utekar, Srushti, Johnston, Helen, Bocacao, Judy, Allais, Margot, de Ligt, Joep, Tan, Chor Ee, Seeds, Ruth, Wood, Tim, Aminisani, Nayyereh, Jennings, Tineke, Welch, David, Turner, Nikki, McIntyre, Peter, Dowell, Tony, Trenholme, Adrian, Byrnes, Cass, Thomas, Paul, Webby, Richard, French, Nigel, Huang, Q. Sue, Winter, David, and Geoghegan, Jemma L.

Published
2024
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6. Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa)

Author

Fox-Lewis, Andrew, Williamson, Felicity, Harrower, Jay, Ren, Xiaoyun, Sonder, Gerard J.B., McNeill, Andrea, de Ligt, Joep, and Geoghegan, Jemma L.

Subjects
Aerosols -- Health aspects, Disease transmission -- Methods, Company distribution practices, Health
Abstract

Coronavirus disease (COVID-19) is a viral respiratory infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (1). Person-to-person transmission primarily occurs when respiratory particles containing SARS-CoV-2 are exhaled by [...]

Published
2022
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9. Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand

Author

Douglas, Jordan, Geoghegan, Jemma L., Hadfield, James, Bouckaert, Remco, Storey, Matthew, Ren, Xiaoyun, de Ligt, Joep, French, Nigel, and Welch, David

Subjects
Epidemics -- Control -- New Zealand, Genomics -- Methods, Sentinel health events -- Methods, Health
Abstract

Early in the coronavirus disease (COVID-19) pandemic, New Zealand (Aotearoa in Maori language) adopted a disease elimination approach. Elimination was first achieved in May 2020 (1,2), and through April 30, [...]

Published
2021
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10. Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand

Author

Geoghegan, Jemma L., Douglas, Jordan, Ren, Xiaoyun, Storey, Matthew, Hadfield, James, Silander, Olin K., Freed, Nikki E., Jelley, Lauren, Jefferies, Sarah, Sherwood, Jillian, Paine, Shevaun, Huang, Sue, Sporle, Andrew, Baker, Michael G., Murdoch, David R., Drummond, Alexei J., Welch, David, Simpson, Colin R., French, Nigel, Holmes, Edward C., and de Ligt, Joep

Subjects
Epidemics -- Statistics -- Control -- New Zealand, Genomics -- Methods, Sentinel health events -- Methods, Health
Abstract

A genome of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was published only 12 days after the virus was identified (1). This information was pivotal to the subsequent [...]

Published
2021
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11. Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa)

Author

Eichler, Nick, Thornley, Craig, Swadi, Tara, Devine, Tom, McElnay, Caroline, Sherwood, Jillian, Brunton, Cheryl, Williamson, Felicity, Freeman, Josh, Berger, Sarah, Ren, Xiaoyun, Storey, Matt, de Ligt, Joep, and Geoghegan, Jemma L.

Subjects
Epidemics -- Case studies -- Control -- New Zealand, Quarantine -- Case studies, Disease transmission -- Case studies -- Control -- Risk factors, Air travel -- Case studies -- Health aspects -- New Zealand, Health
Abstract

New Zealand (Aotearoa in Maori) has a goal of eliminating coronavirus disease (COVID-19), which has resulted in a low incidence of this disease in this country (1-3). Managed isolation and [...]

Published
2021
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12. Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing

Author

Swadi, Tara, Geoghegan, Jemma L., Devine, Tom, McElnay, Caroline, Sherwood, Jillian, Shoemack, Phil, Ren, Xiaoyun, Storey, Matt, Jefferies, Sarah, Smit, Erasmus, Hadfield, James, Kenny, Aoife, Jelley, Lauren, Sporle, Andrew, McNeill, Andrea, Reynolds, G. Edwin, Mouldey, Kip, Lowe, Lindsay, Sonder, Gerard, Drummond, Alexei J., Huang, Sue, Welch, David, Holmes, Edward C., French, Nigel, Simpson, Colin R., and de Ligt, Joep

Subjects
Epidemics -- Distribution -- New Zealand, Airline passengers -- Health aspects, Disease transmission -- Demographic aspects -- Causes of, Company distribution practices, Health
Abstract

In response to the growing international risks associated with importation of coronavirus disease (COVID-19), on March 20, 2020, New Zealand closed its borders to all but New Zealand citizens, permanent [...]

Published
2021
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13. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

Author

Hehir-Kwa, Jayne Y, Marschall, Tobias, Kloosterman, Wigard P, Francioli, Laurent C, Baaijens, Jasmijn A, Dijkstra, Louis J, Abdellaoui, Abdel, Koval, Vyacheslav, Thung, Djie Tjwan, Wardenaar, René, Renkens, Ivo, Coe, Bradley P, Deelen, Patrick, de Ligt, Joep, Lameijer, Eric-Wubbo, van Dijk, Freerk, Hormozdiari, Fereydoun, Genome of the Netherlands Consortium, Uitterlinden, André G, van Duijn, Cornelia M, Eichler, Evan E, de Bakker, Paul IW, Swertz, Morris A, Wijmenga, Cisca, van Ommen, Gert-Jan B, Slagboom, P Eline, Boomsma, Dorret I, Schönhuth, Alexander, Ye, Kai, and Guryev, Victor

Subjects
Genome of the Netherlands Consortium, Chromosomes, Humans, RNA, Polymerase Chain Reaction, Sequence Analysis, DNA, Sequence Analysis, RNA, Computational Biology, Genomics, Gene Deletion, Genotype, Haplotypes, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genome, Human, Algorithms, Software, Netherlands, INDEL Mutation, Genomic Structural Variation, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genome, Human
Abstract

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

Published
2016

15. Building expertise on FAIR through evolving Bring Your Own Data (BYOD) workshops: describing the data, software, and management- focused approaches and their evolution

Author

Bernabé, César H., primary, Thielemans, Lieze, additional, Kaliyaperumal, Rajaram, additional, Carta, Claudio, additional, Zhang, Shuxin, additional, van Gelder, Celia W.G., additional, Benis, Nirupama, additional, da Silva Santos, Luiz Olavo Bonino, additional, Cornet, Ronald, additional, Vieira, Bruna dos Santos, additional, Lalout, Nawel, additional, Henriques, Ines, additional, Ballesteros, Alberto Cámara, additional, Burger, Kees, additional, Kersloot, Martijn G., additional, Ehrhart, Friederike, additional, van Enckevort, Esther, additional, Evelo, Chris T., additional, Gray, Alasdair J. G., additional, Hanauer, Marc, additional, Hettne, Kristina, additional, de Ligt, Joep, additional, Pereira, Arnaldo, additional, Queralt-Rosinach, Núria, additional, Schultes, Erik, additional, Taruscio, Domenica, additional, Waagmeester, Andra, additional, Wilkinson, Mark D., additional, Willighagen, Egon L., additional, Jansen, Mascha, additional, Mons, Barend, additional, Roos, Marco, additional, and Jacobsen, Annika, additional

Published
2023
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16. Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

Author

Geoghegan, Jemma L., Ren, Xiaoyun, Storey, Matthew, Hadfield, James, Jelley, Lauren, Jefferies, Sarah, Sherwood, Jill, Paine, Shevaun, Huang, Sue, Douglas, Jordan, Mendes, Fábio K., Sporle, Andrew, Baker, Michael G., Murdoch, David R., French, Nigel, Simpson, Colin R., Welch, David, Drummond, Alexei J., Holmes, Edward C., Duchêne, Sebastián, and de Ligt, Joep

Published
2020
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20. Impact of the COVID‐19 related border restrictions on influenza and other common respiratory viral infections in New Zealand.

Author

Huang, Q. Sue, Turner, Nikki, Wood, Tim, Anglemyer, Andrew, McIntyre, Peter, Aminisani, Nayyereh, Dowell, Tony, Trenholme, Adrian, Byrnes, Cass, Balm, Michelle, McIntosh, Christine, Jefferies, Sarah, Grant, Cameron C., Nesdale, Annette, Dobinson, Hazel C., Campbell‐Stokes, Priscilla, Daniells, Karen, Geoghegan, Jemma, de Ligt, Joep, and Jelley, Lauren

Subjects
RESPIRATORY infections, RESPIRATORY syncytial virus infections, INFLUENZA, PARAINFLUENZA viruses, VIRUS diseases, PANDEMIC preparedness, INFECTIOUS disease transmission
Abstract

Background: New Zealand's (NZ) complete absence of community transmission of influenza and respiratory syncytial virus (RSV) after May 2020, likely due to COVID‐19 elimination measures, provided a rare opportunity to assess the impact of border restrictions on common respiratory viral infections over the ensuing 2 years. Methods: We collected the data from multiple surveillance systems, including hospital‐based severe acute respiratory infection surveillance, SHIVERS‐II, ‐III and ‐IV community cohorts for acute respiratory infection (ARI) surveillance, HealthStat sentinel general practice (GP) based influenza‐like illness surveillance and SHIVERS‐V sentinel GP‐based ARI surveillance, SHIVERS‐V traveller ARI surveillance and laboratory‐based surveillance. We described the data on influenza, RSV and other respiratory viral infections in NZ before, during and after various stages of the COVID related border restrictions. Results: We observed that border closure to most people, and mandatory government‐managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Border restrictions did not affect community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type‐1. Partial border relaxations through quarantine‐free travel with Australia and other countries were quickly followed by importation of RSV in 2021 and influenza in 2022. Conclusion: Our findings inform future pandemic preparedness and strategies to model and manage the impact of influenza and other respiratory viral threats. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Scalable Workflows and Reproducible Data Analysis for Genomics

Author

Strozzi, Francesco, primary, Janssen, Roel, additional, Wurmus, Ricardo, additional, Crusoe, Michael R., additional, Githinji, George, additional, Di Tommaso, Paolo, additional, Belhachemi, Dominique, additional, Möller, Steffen, additional, Smant, Geert, additional, de Ligt, Joep, additional, and Prins, Pjotr, additional

Published
2019
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22. Building pangenome graphs

Author

Garrison, Erik, primary, Guarracino, Andrea, additional, Heumos, Simon, additional, Villani, Flavia, additional, Bao, Zhigui, additional, Tattini, Lorenzo, additional, Hagmann, Jörg, additional, Vorbrugg, Sebastian, additional, Marco-Sola, Santiago, additional, Kubica, Christian, additional, Ashbrook, David G., additional, Thorell, Kaisa, additional, Rusholme-Pilcher, Rachel L., additional, Liti, Gianni, additional, Rudbeck, Emilio, additional, Nahnsen, Sven, additional, Yang, Zuyu, additional, Moses, Mwaniki N., additional, Nobrega, Franklin L., additional, Wu, Yi, additional, Chen, Hao, additional, de Ligt, Joep, additional, Sudmant, Peter H., additional, Soranzo, Nicole, additional, Colonna, Vincenza, additional, Williams, Robert W., additional, and Prins, Pjotr, additional

Published
2023
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23. Global diversity and antimicrobial resistance of typhoid fever pathogens:Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

Author

Carey, Megan E, Dyson, Zoe A, Ingle, Danielle J, Amir, Afreenish, Aworh, Mabel K, Chattaway, Marie Anne, Chew, Ka Lip, Crump, John A, Feasey, Nicholas A, Howden, Benjamin P, Keddy, Karen H, Maes, Mailis, Parry, Christopher M, Van Puyvelde, Sandra, Webb, Hattie E, Afolayan, Ayorinde Oluwatobiloba, Alexander, Anna P, Anandan, Shalini, Andrews, Jason R, Ashton, Philip M, Basnyat, Buddha, Bavdekar, Ashish, Bogoch, Isaac I, Clemens, John D, da Silva, Kesia Esther, De, Anuradha, de Ligt, Joep, Diaz Guevara, Paula Lucia, Dolecek, Christiane, Dutta, Shanta, Ehlers, Marthie M, Francois Watkins, Louise, Garrett, Denise O, Godbole, Gauri, Gordon, Melita A, Greenhill, Andrew R, Griffin, Chelsey, Gupta, Madhu, Hendriksen, Rene S, Heyderman, Robert S, Hooda, Yogesh, Hormazabal, Juan Carlos, Ikhimiukor, Odion O, Iqbal, Junaid, Jacob, Jobin John, Jenkins, Claire, Jinka, Dasaratha Ramaiah, John, Jacob, Kang, Gagandeep, Kanteh, Abdoulie, Kapil, Arti, Karkey, Abhilasha, Kariuki, Samuel, Kingsley, Robert A, Koshy, Roshine Mary, Lauer, AC, Levine, Myron M, Lingegowda, Ravikumar Kadahalli, Luby, Stephen P, Mackenzie, Grant Austin, Mashe, Tapfumanei, Msefula, Chisomo, Mutreja, Ankur, Nagaraj, Geetha, Nagaraj, Savitha, Nair, Satheesh, Naseri, Take K, Nimarota-Brown, Susana, Njamkepo, Elisabeth, Okeke, Iruka N, Perumal, Sulochana Putli Bai, Pollard, Andrew J, Pragasam, Agila Kumari, Qadri, Firdausi, Qamar, Farah N, Rahman, Sadia Isfat Ara, Rambocus, Savitra Devi, Rasko, David A, Ray, Pallab, Robins-Browne, Roy, Rongsen-Chandola, Temsunaro, Rutanga, Jean Pierre, Saha, Samir K, Saha, Senjuti, Saigal, Karnika, Sajib, Mohammad Saiful Islam, Seidman, Jessica C, Shakya, Jivan, Shamanna, Varun, Shastri, Jayanthi, Shrestha, Rajeev, Sia, Sonia, Sikorski, Michael J, Singh, Ashita, Smith, Anthony M, Tagg, Kaitlin A, Tamrakar, Dipesh, Tanmoy, Arif Mohammed, Thomas, Maria, Thomas, Mathew S, Thomsen, Robert, Thomson, Nicholas R, Tupua, Siaosi, Vaidya, Krista, Valcanis, Mary, Veeraraghavan, Balaji, Weill, François-Xavier, Wright, Jackie, Dougan, Gordon, Argimón, Silvia, Keane, Jacqueline A, Aanensen, David M, Baker, Stephen, Holt, Kathryn E, Carey, Megan E, Dyson, Zoe A, Ingle, Danielle J, Amir, Afreenish, Aworh, Mabel K, Chattaway, Marie Anne, Chew, Ka Lip, Crump, John A, Feasey, Nicholas A, Howden, Benjamin P, Keddy, Karen H, Maes, Mailis, Parry, Christopher M, Van Puyvelde, Sandra, Webb, Hattie E, Afolayan, Ayorinde Oluwatobiloba, Alexander, Anna P, Anandan, Shalini, Andrews, Jason R, Ashton, Philip M, Basnyat, Buddha, Bavdekar, Ashish, Bogoch, Isaac I, Clemens, John D, da Silva, Kesia Esther, De, Anuradha, de Ligt, Joep, Diaz Guevara, Paula Lucia, Dolecek, Christiane, Dutta, Shanta, Ehlers, Marthie M, Francois Watkins, Louise, Garrett, Denise O, Godbole, Gauri, Gordon, Melita A, Greenhill, Andrew R, Griffin, Chelsey, Gupta, Madhu, Hendriksen, Rene S, Heyderman, Robert S, Hooda, Yogesh, Hormazabal, Juan Carlos, Ikhimiukor, Odion O, Iqbal, Junaid, Jacob, Jobin John, Jenkins, Claire, Jinka, Dasaratha Ramaiah, John, Jacob, Kang, Gagandeep, Kanteh, Abdoulie, Kapil, Arti, Karkey, Abhilasha, Kariuki, Samuel, Kingsley, Robert A, Koshy, Roshine Mary, Lauer, AC, Levine, Myron M, Lingegowda, Ravikumar Kadahalli, Luby, Stephen P, Mackenzie, Grant Austin, Mashe, Tapfumanei, Msefula, Chisomo, Mutreja, Ankur, Nagaraj, Geetha, Nagaraj, Savitha, Nair, Satheesh, Naseri, Take K, Nimarota-Brown, Susana, Njamkepo, Elisabeth, Okeke, Iruka N, Perumal, Sulochana Putli Bai, Pollard, Andrew J, Pragasam, Agila Kumari, Qadri, Firdausi, Qamar, Farah N, Rahman, Sadia Isfat Ara, Rambocus, Savitra Devi, Rasko, David A, Ray, Pallab, Robins-Browne, Roy, Rongsen-Chandola, Temsunaro, Rutanga, Jean Pierre, Saha, Samir K, Saha, Senjuti, Saigal, Karnika, Sajib, Mohammad Saiful Islam, Seidman, Jessica C, Shakya, Jivan, Shamanna, Varun, Shastri, Jayanthi, Shrestha, Rajeev, Sia, Sonia, Sikorski, Michael J, Singh, Ashita, Smith, Anthony M, Tagg, Kaitlin A, Tamrakar, Dipesh, Tanmoy, Arif Mohammed, Thomas, Maria, Thomas, Mathew S, Thomsen, Robert, Thomson, Nicholas R, Tupua, Siaosi, Vaidya, Krista, Valcanis, Mary, Veeraraghavan, Balaji, Weill, François-Xavier, Wright, Jackie, Dougan, Gordon, Argimón, Silvia, Keane, Jacqueline A, Aanensen, David M, Baker, Stephen, and Holt, Kathryn E

Abstract

Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions: The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control s

Published
2023

24. Long‐term expanding human airway organoids for disease modeling

Author

Sachs, Norman, Papaspyropoulos, Angelos, Zomer‐van Ommen, Domenique D, Heo, Inha, Böttinger, Lena, Klay, Dymph, Weeber, Fleur, Huelsz‐Prince, Guizela, Iakobachvili, Nino, Amatngalim, Gimano D, de Ligt, Joep, van Hoeck, Arne, Proost, Natalie, Viveen, Marco C, Lyubimova, Anna, Teeven, Luc, Derakhshan, Sepideh, Korving, Jeroen, Begthel, Harry, Dekkers, Johanna F, Kumawat, Kuldeep, Ramos, Emilio, van Oosterhout, Matthijs FM, Offerhaus, G Johan, Wiener, Dominique J, Olimpio, Eduardo P, Dijkstra, Krijn K, Smit, Egbert F, van der Linden, Maarten, Jaksani, Sridevi, van de Ven, Marieke, Jonkers, Jos, Rios, Anne C, Voest, Emile E, van Moorsel, Coline HM, van der Ent, Cornelis K, Cuppen, Edwin, van Oudenaarden, Alexander, Coenjaerts, Frank E, Meyaard, Linde, Bont, Louis J, Peters, Peter J, Tans, Sander J, van Zon, Jeroen S, Boj, Sylvia F, Vries, Robert G, Beekman, Jeffrey M, and Clevers, Hans

Published
2019
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25. Temporal associations of the COVID-19 related border restrictions and respiratory viral infections in New Zealand

Author

Huang, Q. Sue, primary, Turner, Nikki, additional, Wood, Timothy, additional, Geoghegan, Jemma, additional, Anglemyer, Andrew, additional, McIntyre, Peter, additional, de Ligt, Joep, additional, Aminisani, Nayyereh, additional, Jelley, Lauren, additional, Jefferies, Sarah, additional, Dowell, Tony, additional, Trenholme, Adrian, additional, Brynes, Cass, additional, Balm, Michelle, additional, McIntosh, Christine, additional, Grant, Cameron, additional, Nesdale, Annette, additional, Dobinson, Hazel, additional, Campbell-Stokes, Priscilla, additional, Daniells, Karen, additional, Seeds, Ruth, additional, Jennings, Tineke, additional, Rensburg, Megan, additional, Cueto, Jort, additional, Caballero, Ernest, additional, John, Joshma, additional, Penghulan, Emmanuel, additional, Tan, Chor, additional, Ren, Xiaoyun, additional, Berquist, Klarysse, additional, O'Neill, Meaghan, additional, Marull, Maritza, additional, Yu, Chang, additional, McNeill, Andrea, additional, Kiedrzynski, Tomasz, additional, Roberts, Sally, additional, McArthur, Colin, additional, Stanley, Alicia, additional, Taylor, Susan, additional, Wong, Conroy, additional, Lawrence, Shirley, additional, Baker, Michael, additional, Kvalsvig, Amanda, additional, Werff, Koen, additional, McAuliffe, Gary, additional, Antoszewska, Hannah, additional, Dilcher, Meik, additional, Fahey, Jennifer, additional, Werno, Anja, additional, Elvy, Juliet, additional, Grant, Jennifer, additional, Addidle, Michael, additional, Zacchi, Nicolas, additional, Mansell, Chris, additional, Widdowson, Marc-Alain, additional, Thomas, Paul, additional, Consortium, NPIsImpactOnFlu, additional, and Webby, Richard, additional

Published
2022
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27. Using whole-genome sequencing in the rapid response to SARS-CoV-2 in Aotearoa New Zealand

Author

White, Rhys T, Jelley, Lauren, Douglas, Jordan, Xiaoyun Ren, Winter, David, Genomics Team, Covid-19 Wgs, Bunce, Michael, Carr, Sam, Mcneill, Andrea, Q Sue Huang, Swadi, Tara, Devine, Tom, Mcelnay, Caroline, Sherwood, Jillian, Shoemack, Phil, Fox-Lewis, Andrew, Williamson, Felicity, Harrower, Jay, Storey, Matt, Jefferies, Sarah, Smit, Erasmus, Hadfield, James, Kenny, Aoife, Sporle, Andrew, G Edwin Reynolds, Mouldey, Kip, Lowe, Lindsay, Sonder, Gerard, Drummond, Alexei J, Welch, David, Holmes, Edward C, French, Nigel, Simpson, Colin R, De Ligt, Joep, and Geoghegan, Jemma

Published
2023
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29. Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads.

Author

Zuyu Yang, Guarracino, Andrea, Biggs, Patrick J., Black, Michael A., Ismail, Nuzla, Wold, Jana Renee, Merriman, Tony R., Prins, Pjotr, Garrison, Erik, and de Ligt, Joep

Subjects
PAN-genome, GENETIC variation, NEISSERIA meningitidis, NUCLEOTIDE sequencing, BACTERIAL genomes, COMMUNICABLE diseases
Abstract

Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen Neisseria meningitidis. Overall, pangenome graphs offer a promising approach for comparative genomics and comprehensive genetic variation analysis in infectious disease. Moreover, this innovative pipeline, leveraging pangenome graphs, can bridge variant analysis, genome assembly, population genetics, and evolutionary biology, expanding the reach of genomic understanding and applications. [ABSTRACT FROM AUTHOR]

Published
2023
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32. Global disparities in SARS-CoV-2 genomic surveillance

Author

Brito, Anderson F; https://orcid.org/0000-0001-5785-7222, Semenova, Elizaveta; https://orcid.org/0000-0002-8271-2575, Dudas, Gytis; https://orcid.org/0000-0002-0227-4158, Hassler, Gabriel W, Kalinich, Chaney C, Kraemer, Moritz U G; https://orcid.org/0000-0001-8838-7147, Ho, Joses; https://orcid.org/0000-0002-9186-6322, Tegally, Houriiyah, Githinji, George; https://orcid.org/0000-0001-9640-7371, Agoti, Charles N; https://orcid.org/0000-0002-2160-567X, Matkin, Lucy E; https://orcid.org/0000-0003-0952-5818, Whittaker, Charles; https://orcid.org/0000-0002-5003-2575, Kantardjiev, Todor, Korsun, Nelly, Stoitsova, Savina, Dimitrova, Reneta, Trifonova, Ivelina, Dobrinov, Veselin, Grigorova, Lubomira, Stoykov, Ivan, Grigorova, Iliana, Gancheva, Anna, Jennison, Amy, Leong, Lex, Speers, David, Baird, Rob, Cooley, Louise, Kennedy, Karina, de Ligt, Joep, Rawlinson, William, et al, Brito, Anderson F; https://orcid.org/0000-0001-5785-7222, Semenova, Elizaveta; https://orcid.org/0000-0002-8271-2575, Dudas, Gytis; https://orcid.org/0000-0002-0227-4158, Hassler, Gabriel W, Kalinich, Chaney C, Kraemer, Moritz U G; https://orcid.org/0000-0001-8838-7147, Ho, Joses; https://orcid.org/0000-0002-9186-6322, Tegally, Houriiyah, Githinji, George; https://orcid.org/0000-0001-9640-7371, Agoti, Charles N; https://orcid.org/0000-0002-2160-567X, Matkin, Lucy E; https://orcid.org/0000-0003-0952-5818, Whittaker, Charles; https://orcid.org/0000-0002-5003-2575, Kantardjiev, Todor, Korsun, Nelly, Stoitsova, Savina, Dimitrova, Reneta, Trifonova, Ivelina, Dobrinov, Veselin, Grigorova, Lubomira, Stoykov, Ivan, Grigorova, Iliana, Gancheva, Anna, Jennison, Amy, Leong, Lex, Speers, David, Baird, Rob, Cooley, Louise, Kennedy, Karina, de Ligt, Joep, Rawlinson, William, and et al

Abstract

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.

Published
2022

36. Global disparities in SARS-CoV-2 genomic surveillance

Author

Brito, Anderson F, Semenova, Elizaveta, Dudas, Gytis, Hassler, Gabriel W, Kalinich, Chaney C, Kraemer, Moritz U G, Ho, Joses, Tegally, Houriiyah, Githinji, George, Agoti, Charles N, Matkin, Lucy E, Whittaker, Charles, Kantardjiev, Todor, Korsun, Nelly, Stoitsova, Savina, Dimitrova, Reneta, Trifonova, Ivelina, Dobrinov, Veselin, Grigorova, Lubomira, Stoykov, Ivan, Grigorova, Iliana, Gancheva, Anna, Jennison, Amy, Leong, Lex, Speers, David, Baird, Rob, Cooley, Louise, Kennedy, Karina, de Ligt, Joep, Rawlinson, William, et al, and University of Zurich

Subjects
1000 Multidisciplinary, Multidisciplinary, 1300 General Biochemistry, Genetics and Molecular Biology, General Biochemistry, 570 Life sciences, biology, General Physics and Astronomy, 610 Medicine & health, 10071 Functional Genomics Center Zurich, 1600 General Chemistry, Genetics and Molecular Biology, General Chemistry, 3100 General Physics and Astronomy
Published
2022
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37. COVID-19 vaccine strategies for Aotearoa New Zealand: a mathematical modelling study

Author

Nguyen, Trung, primary, Adnan, Mehnaz, additional, Nguyen, Binh P, additional, de Ligt, Joep, additional, Geoghegan, Jemma L, additional, Dean, Richard, additional, Jefferies, Sarah, additional, Baker, Michael G, additional, Seah, Winston KG, additional, Sporle, Andrew A, additional, French, Nigel Peter, additional, Murdoch, David R, additional, Welch, David, additional, and Simpson, Colin R, additional

Published
2021
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38. Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations

Author

Douglas, Jordan, primary, Mendes, Fábio K, additional, Bouckaert, Remco, additional, Xie, Dong, additional, Jiménez-Silva, Cinthy L, additional, Swanepoel, Christiaan, additional, de Ligt, Joep, additional, Ren, Xiaoyun, additional, Storey, Matt, additional, Hadfield, James, additional, Simpson, Colin R, additional, Geoghegan, Jemma L, additional, Drummond, Alexei J, additional, and Welch, David, additional

Published
2021
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40. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

Author

Hill, Verity, O'Toole, Áine, Pybus, Oliver G, Watts, Alexander, Bogoch, Issac I, Khan, Kamran, Messina, Jane P, Tegally, Houriiyah, Lessells, Richard R, Giandhari, Jennifer, Pillay, Sureshnee, Tumedi, Kefentse Arnold, Nyepetsi, Gape, Kebabonye, Malebogo, Matsheka, Maitshwarelo, Mine, Madisa, Tokajian, Sima, Hassan, Hamad, Salloum, Tamara, Merhi, Georgi, Koweyes, Jad, Geoghegan, Jemma L, de Ligt, Joep, Ren, Xiaoyun, Storey, Matthew, Freed, Nikki E, Pattabiraman, Chitra, Prasad, Pramada, Desai, Anita S, Vasanthapuram, Ravi, Schulz, Thomas F, Steinbrück, Lars, Stadler, Tanja, Parisi, Antonio, Bianco, Angelica, García de Viedma, Darío, Buenestado-Serrano, Sergio, Borges, Vítor, Isidro, Joana, Duarte, Sílvia, Gomes, João Paulo, Zuckerman, Neta S, Mandelboim, Michal, Mor, Orna, Seemann, Torsten, Sikkema, Reina S, Oude Munnink, Bas, Koopmans, Marion, Eggink, Dirk, Reusken, Chantal, Hill, Verity, O'Toole, Áine, Pybus, Oliver G, Watts, Alexander, Bogoch, Issac I, Khan, Kamran, Messina, Jane P, Tegally, Houriiyah, Lessells, Richard R, Giandhari, Jennifer, Pillay, Sureshnee, Tumedi, Kefentse Arnold, Nyepetsi, Gape, Kebabonye, Malebogo, Matsheka, Maitshwarelo, Mine, Madisa, Tokajian, Sima, Hassan, Hamad, Salloum, Tamara, Merhi, Georgi, Koweyes, Jad, Geoghegan, Jemma L, de Ligt, Joep, Ren, Xiaoyun, Storey, Matthew, Freed, Nikki E, Pattabiraman, Chitra, Prasad, Pramada, Desai, Anita S, Vasanthapuram, Ravi, Schulz, Thomas F, Steinbrück, Lars, Stadler, Tanja, Parisi, Antonio, Bianco, Angelica, García de Viedma, Darío, Buenestado-Serrano, Sergio, Borges, Vítor, Isidro, Joana, Duarte, Sílvia, Gomes, João Paulo, Zuckerman, Neta S, Mandelboim, Michal, Mor, Orna, Seemann, Torsten, Sikkema, Reina S, Oude Munnink, Bas, Koopmans, Marion, Eggink, Dirk, and Reusken, Chantal

Abstract

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

Published
2021

41. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

Author

O'Toole, Áine, Kraemer, Moritz U.G., Hill, Verity, Pybus, Oliver G., Watts, Alexander, Bogoch, Issac I., Khan, Kamran, Messina, Jane P., Tegally, Houriiyah, Lessells, Richard R., Giandhari, Jennifer, Pillay, Sureshnee, Tumedi, Kefentse Arnold, Nyepetsi, Gape, Kebabonye, Malebogo, Matsheka, Maitshwarelo, Mine, Madisa, Tokajian, Sima, Hassan, Hamad, Salloum, Tamara, Merhi, Georgi, Koweyes, Jad, Geoghegan, Jemma L., de Ligt, Joep, Ren, Xiaoyun, Storey, Matthew, Freed, Nikki E., Pattabiraman, Chitra, Prasad, Pramada, Desai, Anita S., Vasanthapuram, Ravi, Schulz, Thomas F., Steinbrück, Lars, Stadler, Tanja, Parisi, Antonio, Bianco, Angelica, García de Viedma, Darío, Buenestado-Serrano, Sergio, Borges, Vítor, Isidro, Joana, Duarte, Sílvia, Gomes, João Paulo, Zuckerman, Neta S., Mandelboim, Michal, Mor, Orna, Sikkema, Reina S., Oude Munnink, Bas, Koopmans, Marion, Eggink, Dirk, Reusken, Chantal, O'Toole, Áine, Kraemer, Moritz U.G., Hill, Verity, Pybus, Oliver G., Watts, Alexander, Bogoch, Issac I., Khan, Kamran, Messina, Jane P., Tegally, Houriiyah, Lessells, Richard R., Giandhari, Jennifer, Pillay, Sureshnee, Tumedi, Kefentse Arnold, Nyepetsi, Gape, Kebabonye, Malebogo, Matsheka, Maitshwarelo, Mine, Madisa, Tokajian, Sima, Hassan, Hamad, Salloum, Tamara, Merhi, Georgi, Koweyes, Jad, Geoghegan, Jemma L., de Ligt, Joep, Ren, Xiaoyun, Storey, Matthew, Freed, Nikki E., Pattabiraman, Chitra, Prasad, Pramada, Desai, Anita S., Vasanthapuram, Ravi, Schulz, Thomas F., Steinbrück, Lars, Stadler, Tanja, Parisi, Antonio, Bianco, Angelica, García de Viedma, Darío, Buenestado-Serrano, Sergio, Borges, Vítor, Isidro, Joana, Duarte, Sílvia, Gomes, João Paulo, Zuckerman, Neta S., Mandelboim, Michal, Mor, Orna, Sikkema, Reina S., Oude Munnink, Bas, Koopmans, Marion, Eggink, Dirk, and Reusken, Chantal

Abstract

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

Published
2021

43. Supplement to: Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability

Author

de Ligt, Joep, Willemsen, Marjolein H, van Bon, Bregje WM, Kleefstra, Tjitske, Yntema, Helger G, Kroes, Thessa, Vulto-van Silfhout, Anneke T, Koolen, David A., de Vries, Petra, Gilissen, Christian, del Rosario, Marisol, Hoischen, Alexander, Scheffer, Hans, de Vries, Bert BA, Brunner, Han G, Veltman, Joris A, and Vissers, Lisenka ELM

Published
2012

46. Identification of pathogenic gene variants in small families with intellectually disabled siblings by exome sequencing

Author

Schuurs-Hoeijmakers, Janneke H M, Vulto-van Silfhout, Anneke T, Vissers, Lisenka E L M, van de Vondervoort, Ilse I G M, van Bon, Bregje W M, de Ligt, Joep, Gilissen, Christian, Hehir-Kwa, Jayne Y, Neveling, Kornelia, del Rosario, Marisol, Hira, Gausiya, Reitano, Santina, Vitello, Aurelio, Failla, Pinella, Greco, Donatella, Fichera, Marco, Galesi, Ornella, Kleefstra, Tjitske, Greally, Marie T, Ockeloen, Charlotte W, Willemsen, Marjolein H, Bongers, Ernie M H F, Janssen, Irene M, Pfundt, Rolph, Veltman, Joris A, Romano, Corrado, Willemsen, Michèl A, van Bokhoven, Hans, Brunner, Han G, de Vries, Bert B A, and de Brouwer, Arjan P M

Published
2013
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47. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

Author

Eden, John-Sebastian, Rockett, Rebecca, Carter, Ian, Rahman, Hossinur, de Ligt, Joep, Hadfield, James, Storey, Matthew, Ren, Xiaoyun, Tulloch, Rachel, Basile, Kerri, Wells, Jessica, Byun, Roy, Gilroy, Nicky, O’Sullivan, Matthew V, Sintchenko, Vitali, Chen, Sharon C, Maddocks, Susan, Sorrell, Tania C, Holmes, Edward C, Dwyer, Dominic E, Kok, Jen, Donovan, Linda, Kumar, Shanil, Tran, Tyna, Ko, Danny, Ngo, Christine, Sivaruban, Tharshini, Timms, Verlaine, Lam, Connie, Gall, Mailie, Gray, Karen-Ann, Sadsad, Rosemarie, and Arnott, Alicia

Subjects
2019-20 coronavirus outbreak, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Sequencing data, Biology, Microbiology, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, Virology, 030212 general & internal medicine, China, Socioeconomics, Clade, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Phylogenetic tree, SARS-CoV-2, Outbreak, COVID-19, 3. Good health, genome sequencing, phylogenetics, Coronavirus, Geography, Evolutionary biology, Rapid Communication
Abstract

The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.

Published
2020

50. GATAD2B loss-of-function mutations cause a recognisable syndrome with intellectual disability and are associated with learning deficits and synaptic undergrowth in Drosophila

Author

Willemsen, Marjolein H, Nijhof, Bonnie, Fenckova, Michaela, Nillesen, Willy M, Bongers, Ernie M H F, Castells-Nobau, Anna, Asztalos, Lenke, Viragh, Erika, van Bon, Bregje W M, Tezel, Emre, Veltman, Joris A, Brunner, Han G, de Vries, Bert B A, de Ligt, Joep, Yntema, Helger G, van Bokhoven, Hans, Isidor, Bertrand, Le Caignec, Cédric, Lorino, Elsa, Asztalos, Zoltan, Koolen, David A, Vissers, Lisenka E L M, Schenck, Annette, and Kleefstra, Tjitske

Published
2013
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