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2. Immunoglobulin, glucocorticoid, or combination therapy for multisystem inflammatory syndrome in children: a propensity-weighted cohort study

Author

Channon-Wells, Samuel, Vito, Ortensia, McArdle, Andrew J, Seaby, Eleanor G, Patel, Harsita, Shah, Priyen, Pazukhina, Ekaterina, Wilson, Clare, Broderick, Claire, D'Souza, Giselle, Keren, Ilana, Nijman, Ruud G, Tremoulet, Adriana, Munblit, Daniel, Ulloa-Gutierrez, Rolando, Carter, Michael J, Ramnarayan, Padmanabhan, De, Tisham, Hoggart, Clive, Whittaker, Elizabeth, Herberg, Jethro A, Kaforou, Myrsini, Cunnington, Aubrey J, Blyuss, Oleg, Levin, Michael, consortium, Best Available Treatment Study, Chouli, Mohamed, Hamadouche, Nacera, Ladj, Mohamed Samir, Vázquez, Jorge Agrimbau, Carmona, Rodrigo, Collia, Adrian Gustavo, Ellis, Alejandro, Natta, Diego, Pérez, Laura, Rubiños, Mayra, Veliz, Natalia, Yori, Silvana, Britton, Philip N, Burgner, David P, Carey, Emma, Crawford, Nigel W, Giuliano, Hayley, McMinn, Alissa, Wong, Shirley, Wood, Nicholas, Holter, Wolfgang, Krainz, Matthias, Ulreich, Raphael, Zurl, Christoph, Dehoorne, Joke, Haerynck, Filomeen, Hoste, Levi, Schelstraete, Petra, Vandekerckhove, Kristof, Willems, Jef, Farias, Camila Giuliana Almeida, Almeida, Flávia Jacqueline, Leal, Izabel Alves, da Silva, André Ricardo Araujo, Araujo e Silva, Anna Esther, Barreiro, Sabrina TA, da Silva, Daniella Gregória Bomfim Prado, Cervi, Maria Celia, dos Santos Naja Cardoso, Mirian Viviane, Teixeira, Cristiane Henriques, Jarovsky, Daniel, Araujo, Julienne Martins, Berezin, Eitan Naaman, Sáfadi, Marco Aurélio Palazzi, la Ossa, Rolando Andres Paternina-de, Vieira, Cristina Souza, Dimitrova, Anna, Ganeva, Margarita, Stefanov, Stefan, Telcharova-Mihaylovska, Albena, Biggs, Catherine M, Lopez, Alison, Scuccimarri, Rosie, Tan, Ryan, Wasserman, Sam, Withington, Davinia, Ampuero, Camila, Aravena, Javiera, B, Raul Bustos, Casanova, Daniel, Cruces, Pablo, Diaz, Franco, García-Salum, Tamara, Godoy, Loreto, Medina, Rafael A, Galaz, Gonzalo Valenzuela, Camacho-Moreno, Germán, Avila-Aguero, María L, Brenes-Chacón, Helena, Camacho-Badilla, Kattia, Ivankovich-Escoto, Gabriela, Naranjo-Zuniga, Gabriela, and Soriano-Fallas, Alejandra

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Comparative Effectiveness Research, Clinical Research, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Best Available Treatment Study (BATS) consortium, Clinical sciences
Abstract

BackgroundMultisystem inflammatory syndrome in children (MIS-C), a hyperinflammatory condition associated with SARS-CoV-2 infection, has emerged as a serious illness in children worldwide. Immunoglobulin or glucocorticoids, or both, are currently recommended treatments.MethodsThe Best Available Treatment Study evaluated immunomodulatory treatments for MIS-C in an international observational cohort. Analysis of the first 614 patients was previously reported. In this propensity-weighted cohort study, clinical and outcome data from children with suspected or proven MIS-C were collected onto a web-based Research Electronic Data Capture database. After excluding neonates and incomplete or duplicate records, inverse probability weighting was used to compare primary treatments with intravenous immunoglobulin, intravenous immunoglobulin plus glucocorticoids, or glucocorticoids alone, using intravenous immunoglobulin as the reference treatment. Primary outcomes were a composite of inotropic or ventilator support from the second day after treatment initiation, or death, and time to improvement on an ordinal clinical severity scale. Secondary outcomes included treatment escalation, clinical deterioration, fever, and coronary artery aneurysm occurrence and resolution. This study is registered with the ISRCTN registry, ISRCTN69546370.FindingsWe enrolled 2101 children (aged 0 months to 19 years) with clinically diagnosed MIS-C from 39 countries between June 14, 2020, and April 25, 2022, and, following exclusions, 2009 patients were included for analysis (median age 8·0 years [IQR 4·2-11·4], 1191 [59·3%] male and 818 [40·7%] female, and 825 [41·1%] White). 680 (33·8%) patients received primary treatment with intravenous immunoglobulin, 698 (34·7%) with intravenous immunoglobulin plus glucocorticoids, 487 (24·2%) with glucocorticoids alone; 59 (2·9%) patients received other combinations, including biologicals, and 85 (4·2%) patients received no immunomodulators. There were no significant differences between treatments for primary outcomes for the 1586 patients with complete baseline and outcome data that were considered for primary analysis. Adjusted odds ratios for ventilation, inotropic support, or death were 1·09 (95% CI 0·75-1·58; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids and 0·93 (0·58-1·47; corrected p value=1·00) for glucocorticoids alone, versus intravenous immunoglobulin alone. Adjusted average hazard ratios for time to improvement were 1·04 (95% CI 0·91-1·20; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids, and 0·84 (0·70-1·00; corrected p value=0·22) for glucocorticoids alone, versus intravenous immunoglobulin alone. Treatment escalation was less frequent for intravenous immunoglobulin plus glucocorticoids (OR 0·15 [95% CI 0·11-0·20]; p

Published
2023

3. Impaired expression of metallothioneins contributes to allergen-induced inflammation in patients with atopic dermatitis

Author

Sirvent, Sofia, Vallejo, Andres F., Corden, Emma, Teo, Ying, Davies, James, Clayton, Kalum, Seaby, Eleanor G., Lai, Chester, Ennis, Sarah, Alyami, Rfeef, Douilhet, Gemma, Dean, Lareb S. N., Loxham, Matthew, Horswill, Sarah, Healy, Eugene, Roberts, Graham, Hall, Nigel J., Friedmann, Peter S., Singh, Harinder, Bennett, Clare L., Ardern-Jones, Michael R, and Polak, Marta E.

Published
2023
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4. A gene pathogenicity tool “GenePy” identifies missed biallelic diagnoses in the 100,000 Genomes Project

Author

Ambrose, J.C., Arumugam, P., Bevers, R., Bleda, M., Boardman-Pretty, F., Boustred, C.R., Brittain, H., Brown, M.A., Caulfield, M.J., Chan, G.C., Giess, A., Griffin, J.N., Hamblin, A., Henderson, S., Hubbard, T.J.P., Jackson, R., Jones, L.J., Kasperaviciute, D., Kayikci, M., Kousathanas, A., Lahnstein, L., Lakey, A., Leigh, S.E.A., Leong, I.U.S., Lopez, F.J., Maleady-Crowe, F., McEntagart, M., Minneci, F., Mitchell, J., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A.C., O‘Donovan, P., Odhams, C.A., Patch, C., Perez-Gil, D., Pereira, M.B., Pullinger, J., Rahim, T., Rendon, A., Rogers, T., Savage, K., Sawant, K., Scott, R.H., Siddiq, A., Sieghart, A., Smith, S.C., Sosinsky, A., Stuckey, A., Tanguy, M., Taylor Tavares, A.L., Thomas, E.R.A., Thompson, S.R., Tucci, A., Welland, M.J., Williams, E., Witkowska, K., Wood, S.M., Zarowiecki, M., Seaby, Eleanor G., Leggatt, Gary, Cheng, Guo, Thomas, N. Simon, Ashton, James J., Stafford, Imogen, Baralle, Diana, Rehm, Heidi L., O’Donnell-Luria, Anne, and Ennis, Sarah

Published
2024
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5. Haploinsufficiency of ZFHX3, encoding a key player in neuronal development, causes syndromic intellectual disability

Author

Agrawal, Pankaj, Armstrong Scott, Daryl, Barkoudah, Elizabeth, Bellini, Melissa, Beneteau, Claire, Bjørgo, Kathrine, Brooks, Alice, Brown, Natasha, Castle, Alison, Castro, Diana, Chorin, Odelia, Cleghorn, Mark, Clement, Emma, Coman, David, Costin, Carrie, Devriendt, Koen, Dong, Dexin, Dries, Annika, Duelund Hjortshøj, Tina, Dyment, David, Eng, Christine, Genetti, Casie, Grano, Siera, Henneman, Peter, Heron, Delphine, Hoffmann, Katrin, Hom, Jason, Du, Haowei, Iascone, Maria, Isidor, Bertrand, Järvelä, Irma E., Jones, Julie, Keren, Boris, Koenig, Mary Kay, Kohlhase, Jürgen, Lalani, Seema, Le Caignec, Cedric, Lewis, Andi, Liu, Pengfei, Lovgren, Alysia, Lupski, James R., Lyons, Mike, Lysy, Philippe, Manning, Melanie, Marcelis, Carlo, McLean, Scott Douglas, Mercie, Sandra, Mertens, Mareike, Molin, Arnaud, Nizon, Mathilde, Nugent, Kimberly Margaret, Öhman, Susanna, O'Leary, Melanie, Okashah Littlejohn, Rebecca, Petit, Florence, Pfundt, Rolph, Pottocki, Lorraine, Raas-Rotschild, Annick, Ranguin, Kara, Revencu, Nicole, Rosenfeld, Jill, Rhodes, Lindsay, Santos Simmaro, Fernando, Sals, Karen, Schieving, Jolanda, Schrauwen, Isabelle, Schuurs-Hoeijmakers, Janneke H.M., Seaby, Eleanor G., Sheffer, Ruth, Snijders Blok, Lot, Sørensen, Kristina P., Srivastava, Siddharth, Stark, Zornitza, Stoeva, Radka, Stutterd, Chloe, Tan, Natalie B., Mathiesen Torring, Pernille, Vanakker, Olivier, van der Laan, Liselot, Ververi, Athina, Villavicencio-Lorini, Pablo, Vincent, Marie, Wand, Dorothea, Wessels, Marja, White, Sue, Wojcik, Monica H., Wu, Nan, Zhao, Sen, Pérez Baca, María del Rocío, Jacobs, Eva Z., Vantomme, Lies, Leblanc, Pontus, Bogaert, Elke, Dheedene, Annelies, De Cock, Laurenz, Haghshenas, Sadegheh, Foroutan, Aidin, Levy, Michael A., Kerkhof, Jennifer, McConkey, Haley, Chen, Chun-An, Batzir, Nurit Assia, Wang, Xia, Palomares, María, Carels, Marieke, Dermaut, Bart, Sadikovic, Bekim, Menten, Björn, Yuan, Bo, Vergult, Sarah, and Callewaert, Bert

Published
2024
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6. Identification of novel locus associated with coronary artery aneurysms and validation of loci for susceptibility to Kawasaki disease.

Author

Hoggart, Clive, Shimizu, Chisato, Galassini, Rachel, Wright, Victoria J, Shailes, Hannah, Bellos, Evan, Herberg, Jethro A, Pollard, Andrew J, O'Connor, Daniel, Choi, Shing Wan, Seaby, Eleanor G, Menikou, Stephanie, Hibberd, Martin, Sallah, Neneh, Burgner, David, Brogan, Paul, Patel, Harsita, Kim, Jihoon, Tremoulet, Adriana H, Salo, Eeva, van Stijn, Diana, Kuijpers, Taco, Burns, Jane C, Levin, Michael, International Kawasaki Disease Genetics Consortium, UK Kawasaki Disease Genetics Consortium, and EUCLIDS Consortium

Subjects
International Kawasaki Disease Genetics Consortium, UK Kawasaki Disease Genetics Consortium, EUCLIDS Consortium, Humans, Coronary Aneurysm, Mucocutaneous Lymph Node Syndrome, Phosphotransferases (Alcohol Group Acceptor), Proteins, Receptors, IgG, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Caspase 3, Rare Diseases, Human Genome, Prevention, Genetics, Autoimmune Disease, Aetiology, 2.1 Biological and endogenous factors, Clinical Sciences, Genetics & Heredity
Abstract

Kawasaki disease (KD) is a paediatric vasculitis associated with coronary artery aneurysms (CAA). Genetic variants influencing susceptibility to KD have been previously identified, but no risk alleles have been validated that influence CAA formation. We conducted a genome-wide association study (GWAS) for CAA in KD patients of European descent with 200 cases and 276 controls. A second GWAS for susceptibility pooled KD cases with healthy paediatric controls from vaccine trials in the UK (n = 1609). Logistic regression mixed models were used for both GWASs. The susceptibility GWAS was meta-analysed with 400 KD cases and 6101 controls from a previous European GWAS, these results were further meta-analysed with Japanese GWASs at two putative loci. The CAA GWAS identified an intergenic region of chromosome 20q13 with multiple SNVs showing genome-wide significance. The risk allele of the most associated SNV (rs6017006) was present in 13% of cases and 4% of controls; in East Asian 1000 Genomes data, the allele was absent or rare. Susceptibility GWAS with meta-analysis with previously published European data identified two previously associated loci (ITPKC and FCGR2A). Further meta-analysis with Japanese GWAS summary data from the CASP3 and FAM167A genomic regions validated these loci in Europeans showing consistent effects of the top SNVs in both populations. We identified a novel locus for CAA in KD patients of European descent. The results suggest that different genes determine susceptibility to KD and development of CAA and future work should focus on the function of the intergenic region on chromosome 20q13.

Published
2021

8. Treatment of Multisystem Inflammatory Syndrome in Children

Author

McArdle, Andrew J, Vito, Ortensia, Patel, Harsita, Seaby, Eleanor G, Shah, Priyen, Wilson, Clare, Broderick, Claire, Nijman, Ruud, Tremoulet, Adriana H, Munblit, Daniel, Ulloa-Gutierrez, Rolando, Carter, Michael J, De, Tisham, Hoggart, Clive, Whittaker, Elizabeth, Herberg, Jethro A, Kaforou, Myrsini, Cunnington, Aubrey J, and Levin, Michael

Subjects
Clinical Research, Inflammatory and immune system, Adolescent, Antibodies, Viral, COVID-19, Child, Child, Preschool, Cohort Studies, Confidence Intervals, Drug Therapy, Combination, Female, Glucocorticoids, Hospitalization, Humans, Immunoglobulins, Intravenous, Immunomodulation, Male, Propensity Score, Regression Analysis, Respiration, Artificial, SARS-CoV-2, Systemic Inflammatory Response Syndrome, Treatment Outcome, COVID-19 Drug Treatment, BATS Consortium, Medical and Health Sciences, General & Internal Medicine
Abstract

BackgroundEvidence is urgently needed to support treatment decisions for children with multisystem inflammatory syndrome (MIS-C) associated with severe acute respiratory syndrome coronavirus 2.MethodsWe performed an international observational cohort study of clinical and outcome data regarding suspected MIS-C that had been uploaded by physicians onto a Web-based database. We used inverse-probability weighting and generalized linear models to evaluate intravenous immune globulin (IVIG) as a reference, as compared with IVIG plus glucocorticoids and glucocorticoids alone. There were two primary outcomes: the first was a composite of inotropic support or mechanical ventilation by day 2 or later or death; the second was a reduction in disease severity on an ordinal scale by day 2. Secondary outcomes included treatment escalation and the time until a reduction in organ failure and inflammation.ResultsData were available regarding the course of treatment for 614 children from 32 countries from June 2020 through February 2021; 490 met the World Health Organization criteria for MIS-C. Of the 614 children with suspected MIS-C, 246 received primary treatment with IVIG alone, 208 with IVIG plus glucocorticoids, and 99 with glucocorticoids alone; 22 children received other treatment combinations, including biologic agents, and 39 received no immunomodulatory therapy. Receipt of inotropic or ventilatory support or death occurred in 56 patients who received IVIG plus glucocorticoids (adjusted odds ratio for the comparison with IVIG alone, 0.77; 95% confidence interval [CI], 0.33 to 1.82) and in 17 patients who received glucocorticoids alone (adjusted odds ratio, 0.54; 95% CI, 0.22 to 1.33). The adjusted odds ratios for a reduction in disease severity were similar in the two groups, as compared with IVIG alone (0.90 for IVIG plus glucocorticoids and 0.93 for glucocorticoids alone). The time until a reduction in disease severity was similar in the three groups.ConclusionsWe found no evidence that recovery from MIS-C differed after primary treatment with IVIG alone, IVIG plus glucocorticoids, or glucocorticoids alone, although significant differences may emerge as more data accrue. (Funded by the European Union's Horizon 2020 Program and others; BATS ISRCTN number, ISRCTN69546370.).

Published
2021

10. Immunoglobulin, glucocorticoid, or combination therapy for multisystem inflammatory syndrome in children: a propensity-weighted cohort study

Author

Chouli, Mohamed, Hamadouche, Nacera, Ladj, Mohamed Samir, Agrimbau Vázquez, Jorge, Carmona, Rodrigo, Collia, Adrian Gustavo, Ellis, Alejandro, Natta, Diego, Pérez, Laura, Rubiños, Mayra, Veliz, Natalia, Yori, Silvana, Britton, Philip N., Burgner, David P., Carey, Emma, Crawford, Nigel W., Giuliano, Hayley, McMinn, Alissa, Wong, Shirley, Wood, Nicholas, Holter, Wolfgang, Krainz, Matthias, Ulreich, Raphael, Zurl, Christoph, Dehoorne, Joke, Haerynck, Filomeen, Hoste, Levi, Schelstraete, Petra, Vandekerckhove, Kristof, Willems, Jef, Almeida Farias, Camila Giuliana, Almeida, Flávia Jacqueline, Alves Leal, Izabel, Araujo da Silva, André Ricardo, Araujo e Silva, Anna Esther, Barreiro, Sabrina T.A., Bomfim Prado da Silva, Daniella Gregória, Cervi, Maria Celia, dos Santos Naja Cardoso, Mirian Viviane, Henriques Teixeira, Cristiane, Jarovsky, Daniel, Martins Araujo, Julienne, Naaman Berezin, Eitan, Palazzi Sáfadi, Marco Aurélio, Paternina-de la Ossa, Rolando Andres, Souza Vieira, Cristina, Dimitrova, Anna, Ganeva, Margarita, Stefanov, Stefan, Telcharova-Mihaylovska, Albena, Biggs, Catherine M., Lopez, Alison, Scuccimarri, Rosie, Tan, Ryan, Wasserman, Sam, Withington, Davinia, Ampuero, Camila, Aravena, Javiera, Bustos B, Raul, Casanova, Daniel, Cruces, Pablo, Diaz, Franco, García-Salum, Tamara, Godoy, Loreto, Medina, Rafael A., Valenzuela Galaz, Gonzalo, Camacho-Moreno, Germán, Avila-Aguero, María L., Brenes-Chacón, Helena, Camacho-Badilla, Kattia, Ivankovich-Escoto, Gabriela, Naranjo-Zuniga, Gabriela, Soriano-Fallas, Alejandra, Ulloa-Gutierrez, Rolando, Yock-Corrales, Adriana, Amer, Maysa Abbas, Abdelmeguid, Yasmine, Ahmed, Yomna H.H.Z., Badib, Adham, Badreldin, Karim, Elkhashab, Yara, Heshmat, Hassan, Hussein, Amna, Mohamed Hussein, Amna Hussein, Ibrahim, Sandra, Shoman, Walaa, Yakout, Radwa M, Heinonen, Santtu, Angoulvant, François, Belot, Alexandre, Ouldali, Naïm, Beske, Florian, Heep, Axel, Masjosthusmann, Katja, Reiter, Karl, van den Heuvel, Ingeborg, von Both, Ulrich, Agrafiotou, Aikaterini, Antachopoulos, Charalampos, Charisi, Konstantina, Eleftheriou, Irini, Farmaki, Evangelia, Fotis, Lampros, Kafetzis, Dimitrios, Koletsi, Patra, Kourtesi, Katerina, Lampidi, Stavroula, Liakopoulou, Theodota, Maritsi, Despoina, Michailidou, Elisa, Milioudi, Maria, Mparmpounaki, Ioanna, Papadimitriou, Eleni, Papaevangelou, Vassiliki, Roilides, Emmanuel, Tsiatsiou, Olga, Tsolas, Georgios, Tsolia, Maria, Vantsi, Petrina, Banegas Pineda, Linda Yajeira, Borjas Aguilar, Karla Leversia, Cantillano Quintero, Edwin Mauricio, Ip, Patrick, Kwan, Mike Yat Wah, Kwok, Janette, Lau, Yu Lung, To, Kelvin, Wong, Joshua Sung Chih, David, Mate, Farkas, David, Kalcakosz, Szofia, Szekeres, Klaudia, Zsigmond, Borbala, Aslam, Nadeem, Luder, Anthony, Andreozzi, Laura, Bianco, Francesco, Bucciarelli, Valentina, Buonsenso, Danilo, Cimaz, Rolando, De Luca, Maia, Dellepiane, Rosa Maria, Fabi, Marianna, Filice, Emanuele, Lanari, Marcello, Lo Vecchio, Andrea, Mastrolia, Maria Vincenza, Mauro, Angela, Mazza, Angelo, Papa, Mario Virgilio, Romani, Lorenza, Scarano, Sara Maria, Simonini, Gabriele, Tipo, Vincenzo, Verdoni, Lucio, Macharia, Anne-Marie, Musiime, Grace, Reel, Bhupi, Wangai, Frederick, Pace, David, Torpiano, Paul, Anaya-Enriquez, Nancy, Carreon-Guerrero, Juan Manuel, Chacon-Cruz, Enrique, Cheung López, Mariana, Faugier Fuentes, Enrique, Fonseca Flores, Marisol, García-Domínguez, Miguel, Giron Vargas, Ana Luisa, Lopez-Delgado, Ivan, Lopez Hernández, Liliana, Menchaca Aguayo, Hector F., Montaño-Duron, Jesus Gilberto, Pérez-Gaxiola, Giordano, Ramos Tiñini, Pamela, Tostado-Morales, Edgardo, Valadez, Julio, Inchley, Christopher, Klevberg, Sjur, Knudsen, Per Kristian, Måseide, Per Helge, Carrera, Jose Manuel, Castaño, Elizabeth, Daza Timana, Carlos Alberto, De Leon, Tirza, Estripeaut, Dora, Levy, Jacqueline, Norero, Ximena, Record, Javier, Rojas-Bonilla, Magda, Wong, Mayra, Iramain, Ricardo, Hernandez, Roger, Huamán, Gian, Munaico, Manuel, Peralta, Carlos, Seminario, Diego, Zapata Yarlequé, Elmer Hans, Gadzinska, Justyna, Ludwikowska, Kamila, Mandziuk, Joanna, Okarska-Napierała, Magdalena, Alacheva, Zalina A., Alexeeva, Ekaterina, Ananin, Petr V., Antsupova, Margarita, Bakradze, Maya D., Berbenyuk, Anna, Bobkova, Polina, Borzakova, Svetlana, Chashchina, Irina L., El-Taravi, Yasmin, Fisenko, Andrey P., Gautier, Marina S., Glazyrina, Anastasia, Gorlenko, Cyrill, Grosheva, Mariia, Kiselev, Herman, Kondrikova, Elena, Korobyants, Evgeniya, Korsunskiy, Anatoliy A., Kovygina, Karina, Krasnaya, Ekaterina, Kurbanova, Seda, Kurdup, Maria K., Mamutova, Anna V., Mazankova, Lyudmila, Mitushin, Ilya L., Munblit, Daniel, Nargizyan, Anzhelika, Orlova, Yanina O., Osmanov, Ismail M., Polyakova, Anastasia S., Pushkareva, Anna, Romanova, Olga, Samitova, Elmira, Shvedova, Anastasia, Sologub, Anna, Iakovleva, Ekaterina, Tepaev, Rustem F., Tkacheva, Anna A., Yegiyan, Margarita, Yusupova, Valeriya, Zholobova, Elena, Grasa, Carlos Daniel, Epalza, Cristina, Lopez Segura, Nuria, Martinon-Torres, Federico, Melendo, Susana, Mendez-Echevarria, Ana, Mesa Guzmán, Juan Miguel, Palacios Argueta, Jorge Roberto, Rivero-Calle, Irene, Rivière, Jacques, Rodríguez-González, Moisés, Rojo, Pablo, Sanchez Manubens, Judith, Soler-Palacin, Pere, Soriano-Arandes, Antoni, Tagarro, Alfredo, Villaverde, Serena, Altman, Maria, Brodin, Petter, Horne, AnnaCarin, Palmblad, Karin, Brotschi, Barbara, Meyer Sauteur, Patrick, Pachlopnik Schmid, Jana, Prader, Seraina, Relly, Christa, Schlapbach, Luregn J., Seiler, Michelle, Strasser, Sophie, Trück, Johannes, Weber, Kathrin, Wütz, Daniela, Hamdan, Alaa, Melhem, Ibrahim, Moussa, Ahmed, Dunk, Joke, Ketharanathan, Naomi, Vermont, Clementien, Akyüz Özkan, Esra, Cetin, Benhur Sirvan, Erdeniz, Emine Hafize, Şahin, Irfan Oğuz, Borisova, Galina, Boyarchuk, Oksana, Boychenko, Lidiya, Boyko, Yaryna, Diudenko, Nadiia, Dyvonyak, Olha, Kasiyan, Olexandr, Katerynych, Kostiantyn, Kostyuchenko, Larysa, Mamenko, Marina, Melnyk, Kateryna, Miagka, Nelia, Nazarenko, Liliya, Nezgoda, Iryna, Rykova, Stanislava, Svyst, Olga, Teslenko, Maria, Trykosh, Mykola, Vasilenko, Nataliya, Volokha, Alla, Adams, Charlotte, Akomolafe, Toju, Al-Abadi, Eslam, Alders, Nele, Alifieraki, Styliani, Ansumanu, Hareef, Aston, Emily, Avram, Paula, Bamford, Alasdair, Banks, Millie, Basu Roy, Robin, Beattie, Thomas, Boleti, Olga, Bracken, Abbey, Broad, Jonathan, Cai, James, Carrol, Enitan D., Carter, Michael, Chandran, Anchit, Charlesworth, James, Chawla, Jaya, Cooper, Hannah, Cooray, Samantha, Davies, Patrick, Davis, Francesca, Drysdale, Simon B., Dzora, Ella, Emonts, Marieke, Evans, Ceri, Fidler, Katy, Foster, Caroline, Gong, Chen, Gongrun, Berin, Gonzalez, Carmen, Gorgun, Berin, Grandjean, Louis, Grant, Karlie, Guo, Jonathan, Hacohen, Yael, Hall, Jack, Hamid, Hytham K.S., Hassell, Jane, Hesketh, Christine, Hewlett, Jessica, Hnieno, Ahmad, Holt-Davis, Hannah, Hossain, Aleena, Hu, Shiying, Hudson, Lee D., Jheeta, Sharon, Johnson, Mae, Johnson, Sarah, Jyothish, Deepthi, Kampmann, Beate, Kavirayani, Akhila, Kelly, Deborah, Kirubakaran, Arangan, Kucera, Filip, Langer, Daniel, Lawson, George, Lees, Emily A, Lenihan, Rebecca, Lillie, Jon, Longbottom, Katherine, Lyall, Hermione, Mackdermott, Niamh, Maltby, Sarah, Mclelland, Thomas, McMahon, Anne-Marie, Miller, Danielle, Miranda, Mariana, Mirza, Luwaiza, Morrison, Zoe, Moshal, Karyn, Muller, Jennifer, Musuka, Phoebe, Myttaraki, Evangelia, Nadel, Simon, Nair, Sreedevi, Nuttall, Luke, Oremakinde, Oyinkansola, Osaghae, Daniella, Osman, Fatima, Ostrzewska, Anna, Paccagnella, Davide, Panthula, Mrinalini, Papachatzi, Eleni, Papadopoulou, Charalampia, Patel, Fahim, Patel, Harsita, Payne, Helen, Penner, Justin, Polandi, Shervin, Prendergast, Andrew J., Ramnarayan, Padmanabhan, Ranasinghe, Lasith, Ravichandran, Muthukumaran, Rhys-Evans, Sophie, Riordan, Andrew, Rodrigues, Charlene M.C., Roe, Lauren, Romaine, Sam, Schobi, Nina, Seddon, James, Shingadia, Delane, Sikdar, Oishi, Srivastava, Anand, Struik, Siske, Sun, Thomas, Tan, Rachel Wei, Taylor, Alice, Taylor, Amanda, Taylor, Andrew, Tran, Steven, Tsagkaris, Stavros, Tudor-Williams, Gareth, van den Berg, Sarah, van der Velden, Fabian, Ventilacion, Lyn, Wellman, Paul A., Withers Green, Joseph, Yanney, Michael P., Yeung, Shunmay, Badheka, Aditya, Badran, Sarah, Bailey, Dwight M., Burch, Anna Kathryn, Burns, Jane C., Cichon, Catherine, Cirks, Blake, Dallman, Michael D., Delany, Dennis R., Fairchok, Mary, Friedman, Samantha, Geracht, Jennifer, Langs-Barlow, Allison, Mann, Kelly, Padhye, Amruta, Quade, Alexis, Ramirez, Kacy Alyne, Rockett, John, Sayed, Imran Ali, Santos, Roberto P., Shahin, Amr A., Tremoulet, Adriana, Umaru, Samuel, Widener, Rebecca, Mujuru, Hilda Angela, Kandawasvika, Gwendoline, Channon-Wells, Samuel, Vito, Ortensia, McArdle, Andrew J, Seaby, Eleanor G, Shah, Priyen, Pazukhina, Ekaterina, Wilson, Clare, Broderick, Claire, D'Souza, Giselle, Keren, Ilana, Nijman, Ruud G, Carter, Michael J, De, Tisham, Hoggart, Clive, Whittaker, Elizabeth, Herberg, Jethro A, Kaforou, Myrsini, Cunnington, Aubrey J, Blyuss, Oleg, and Levin, Michael

Published
2023
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11. Genome Sequencing for Diagnosing Rare Diseases

Author

Wojcik, Monica H., primary, Lemire, Gabrielle, additional, Berger, Eva, additional, Zaki, Maha S., additional, Wissmann, Mariel, additional, Win, Wathone, additional, White, Susan M., additional, Weisburd, Ben, additional, Wieczorek, Dagmar, additional, Waddell, Leigh B., additional, Verboon, Jeffrey M., additional, VanNoy, Grace E., additional, Töpf, Ana, additional, Tan, Tiong Yang, additional, Syrbe, Steffen, additional, Strehlow, Vincent, additional, Straub, Volker, additional, Stenton, Sarah L., additional, Snow, Hana, additional, Singer-Berk, Moriel, additional, Silver, Josh, additional, Shril, Shirlee, additional, Seaby, Eleanor G., additional, Schneider, Ronen, additional, Sankaran, Vijay G., additional, Sanchis-Juan, Alba, additional, Russell, Kathryn A., additional, Reinson, Karit, additional, Ravenscroft, Gianina, additional, Radtke, Maximilian, additional, Popp, Denny, additional, Polster, Tilman, additional, Platzer, Konrad, additional, Pierce, Eric A., additional, Place, Emily M., additional, Pajusalu, Sander, additional, Pais, Lynn, additional, Õunap, Katrin, additional, Osei-Owusu, Ikeoluwa, additional, Opperman, Henry, additional, Okur, Volkan, additional, Oja, Kaisa Teele, additional, O’Leary, Melanie, additional, O’Heir, Emily, additional, Morel, Chantal F., additional, Merkenschlager, Andreas, additional, Marchant, Rhett G., additional, Mangilog, Brian E., additional, Madden, Jill A., additional, MacArthur, Daniel, additional, Lovgren, Alysia, additional, Lerner-Ellis, Jordan P., additional, Lin, Jasmine, additional, Laing, Nigel, additional, Hildebrandt, Friedhelm, additional, Hentschel, Julia, additional, Groopman, Emily, additional, Goodrich, Julia, additional, Gleeson, Joseph G., additional, Ghaoui, Roula, additional, Genetti, Casie A., additional, Gburek-Augustat, Janina, additional, Gazda, Hanna T., additional, Ganesh, Vijay S., additional, Ganapathi, Mythily, additional, Gallacher, Lyndon, additional, Fu, Jack M., additional, Evangelista, Emily, additional, England, Eleina, additional, Donkervoort, Sandra, additional, DiTroia, Stephanie, additional, Cooper, Sandra T., additional, Chung, Wendy K., additional, Christodoulou, John, additional, Chao, Katherine R., additional, Cato, Liam D., additional, Bujakowska, Kinga M., additional, Bryen, Samantha J., additional, Brand, Harrison, additional, Bönnemann, Carsten G., additional, Beggs, Alan H., additional, Baxter, Samantha M., additional, Bartolomaeus, Tobias, additional, Agrawal, Pankaj B., additional, Talkowski, Michael, additional, Austin-Tse, Christina, additional, Abou Jamra, Rami, additional, Rehm, Heidi L., additional, and O’Donnell-Luria, Anne, additional

Published
2024
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13. A gene pathogenicity tool “GenePy” identifies missed biallelic diagnoses in the 100,000 Genomes Project

Author

Seaby, Eleanor G., primary, Leggatt, Gary, additional, Cheng, Guo, additional, Thomas, N. Simon, additional, Ashton, James J., additional, Stafford, Imogen, additional, Baralle, Diana, additional, Rehm, Heidi L., additional, O’Donnell-Luria, Anne, additional, Ennis, Sarah, additional, Ambrose, J.C., additional, Arumugam, P., additional, Bevers, R., additional, Bleda, M., additional, Boardman-Pretty, F., additional, Boustred, C.R., additional, Brittain, H., additional, Brown, M.A., additional, Caulfield, M.J., additional, Chan, G.C., additional, Giess, A., additional, Griffin, J.N., additional, Hamblin, A., additional, Henderson, S., additional, Hubbard, T.J.P., additional, Jackson, R., additional, Jones, L.J., additional, Kasperaviciute, D., additional, Kayikci, M., additional, Kousathanas, A., additional, Lahnstein, L., additional, Lakey, A., additional, Leigh, S.E.A., additional, Leong, I.U.S., additional, Lopez, F.J., additional, Maleady-Crowe, F., additional, McEntagart, M., additional, Minneci, F., additional, Mitchell, J., additional, Moutsianas, L., additional, Mueller, M., additional, Murugaesu, N., additional, Need, A.C., additional, O‘Donovan, P., additional, Odhams, C.A., additional, Patch, C., additional, Perez-Gil, D., additional, Pereira, M.B., additional, Pullinger, J., additional, Rahim, T., additional, Rendon, A., additional, Rogers, T., additional, Savage, K., additional, Sawant, K., additional, Scott, R.H., additional, Siddiq, A., additional, Sieghart, A., additional, Smith, S.C., additional, Sosinsky, A., additional, Stuckey, A., additional, Tanguy, M., additional, Taylor Tavares, A.L., additional, Thomas, E.R.A., additional, Thompson, S.R., additional, Tucci, A., additional, Welland, M.J., additional, Williams, E., additional, Witkowska, K., additional, Wood, S.M., additional, and Zarowiecki, M., additional

Published
2024
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14. The Efficacy of Frontline Near-Peer Teaching in a Modern Medical Curriculum

Author

Harrison, Charlotte H., Elmansouri, Ahmad, Parton, William, Myers, Matthew A., Hall, Samuel, Stephens, Jonny R., Seaby, Eleanor G., and Border, Scott

Abstract

Within medical education a reduction in curriculum time for subjects, such as anatomy puts pressure on educators to ensure the same learning outcomes are conveyed in less time. This has the potential to impact negatively on student experience. Near-peer teaching (NPT) is often praised as an effective revision tool, but its use as a frontline teaching resource remains unreported. The study explores the potential for NPT to promote delivery of learning outcomes and maximize student experience within a neuroanatomy module for second year medical students. The study occurred in three educational settings, (1) frontline NPT of cranial nerves, (2) revision session NPT of cranial nerves, and (3) NPT alongside faculty staff in laboratory-based neuroanatomy practical exercises. For the first and second components, knowledge was measured using a pre- and post-session test and student perception was ascertained with a questionnaire. For the third component, student perception was assessed with an end-of-module survey. The results show that overall, NPT was well received by learners. A significant knowledge gain was seen between the pre- and post-session test of the frontline NPT session. The study presents evidence in favor of using NPTs to supplement the delivery of learning outcomes in a time and resource constrained curriculum. In particular, for the effective delivery of frontline material.

Published
2019
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16. Transcript expression-aware annotation improves rare variant interpretation

Author

Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, and Mudge, Jonathan M.

Subjects
Genetic variation -- Analysis -- Usage, Human genome -- Identification and classification -- Analysis -- Usage, Genetic transcription -- Usage -- Analysis, Citation indexes -- Management -- Analysis -- Usage, Company business management, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD).sup.1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the 'proportion expressed across transcripts', which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project.sup.2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies. A novel variant annotation metric that quantifies the level of expression of genetic variants across tissues is validated in the Genome Aggregation Database (gnomAD) and is shown to improve rare variant interpretation., Author(s): Beryl B. Cummings [sup.1] [sup.2] [sup.3] , Konrad J. Karczewski [sup.1] [sup.2] , Jack A. Kosmicki [sup.1] [sup.2] [sup.4] , Eleanor G. Seaby [sup.1] [sup.2] [sup.5] , Nicholas A. [...]

Published
2020
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17. Monoallelic de novo variants in DDX17 cause a novel neurodevelopmental disorder

Author

Seaby, Eleanor G, primary, Godwin, Annie, additional, Clerc, Valentine, additional, Meyer-Dilhet, Geraldine, additional, Grand, Xavier, additional, Fletcher, Tia, additional, Monteiro, Laloe, additional, Carelli, Valerio, additional, Palombo, Flavia, additional, Seri, Marco, additional, Olivucci, Giulia, additional, Grippa, Mina, additional, Ciaccio, Claudia, additional, D'Arrigo, Stefano, additional, Iascone, Maria, additional, Bermudez, Marion, additional, Fischer, Jan, additional, Di Donato, Nataliya, additional, Leung, Marco L, additional, Koboldt, Daniel, additional, Myers, Cortlandt, additional, Bartholomew, Dennis, additional, Arnadottir, Gudny Anna, additional, Stefansson, Kari, additional, Sulem, Patrick, additional, Goldberg, Ethan M, additional, BRUEL, Ange-Line, additional, TRAN-MAU THEM, Frederic, additional, Willems, Marjolaine, additional, Bjornsson, Hans Tomas, additional, Hognason, Hakon Bjorn, additional, Thorolfsdottir, Eirny Tholl, additional, Agolini, Emanuele, additional, Novelli, Antonio, additional, Zampino, Giuseppe, additional, Onesimo, Roberta, additional, Lachlan, Katherine, additional, Goesswein, Sophie, additional, Baralle, Diana, additional, Rehm, Heidi L, additional, O'Donnell-Luria, Anne L, additional, Courchet, Julien, additional, Guille, Matt, additional, Bourgeois, Cyril, additional, and Ennis, Sarah, additional

Published
2023
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18. Unique Capabilities of Genome Sequencing for Rare Disease Diagnosis

Author

Wojcik, Monica H, primary, Lemire, Gabrielle, additional, Zaki, Maha S, additional, Wissmann, Mariel, additional, Win, Wathone, additional, White, Sue, additional, Weisburd, Ben, additional, Waddell, Leigh B, additional, Verboon, Jeffrey M, additional, VanNoy, Grace E, additional, Topf, Ana, additional, Tan, Tiong Yang, additional, Straub, Volker, additional, Stenton, Sarah L, additional, Snow, Hana, additional, Singer-Berk, Moriel, additional, Silver, Josh, additional, Shril, Shirlee, additional, Seaby, Eleanor G, additional, Schneider, Ronen, additional, Sankaran, Vijay G, additional, Sanchis-Juan, Alba, additional, Russell, Kathryn A, additional, Reinson, Karit, additional, Ravenscroft, Gina, additional, Pierce, Eric A, additional, Place, Emily M, additional, Pajusalu, Sander, additional, Pais, Lynn, additional, Ounap, Katrin, additional, Osei-Owusu, Ikeoluwa, additional, Okur, Volkan, additional, Oja, Kaisa Teele, additional, OLeary, Melanie, additional, OHeir, Emily, additional, Morel, Chantal, additional, Marchant, Rhett G, additional, Mangilog, Brian E, additional, Madden, Jill A, additional, MacArthur, Daniel, additional, Lovgren, Alysia, additional, Lerner-Ellis, Jordan P, additional, Lin, Jasmine, additional, Laing, Nigel, additional, Hildebrandt, Friedhelm, additional, Groopman, Emily, additional, Goodrich, Julia, additional, Gleeson, Joseph G, additional, Ghaoui, Roula, additional, Genetti, Casie A, additional, Gazda, Hanna, additional, Ganesh, Vijay S, additional, Ganapathi, Mythily, additional, Gallacher, Lyndon, additional, Fu, Jack, additional, Evangelista, Emily, additional, England, Eleina, additional, Donkervoort, Sandra, additional, DiTroia, Stephanie, additional, Cooper, Sandra T, additional, Chung, Wendy K, additional, Christodoulou, John, additional, Chao, Katherine R, additional, Cato, Liam D, additional, Bujakowska, Kinga M, additional, Bryen, Samantha J, additional, Brand, Harrison, additional, Bonnemann, Carsten, additional, Beggs, Alan H, additional, Baxter, Samantha M, additional, Agrawal, Pankaj B, additional, Talkowski, Michael, additional, Austin-Tse, Christina, additional, Rehm, Heidi L, additional, and ODonnell-Luria, Anne, additional

Published
2023
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20. Can Medical Students Accurately Predict Their Learning? A Study Comparing Perceived and Actual Performance in Neuroanatomy

Author

Hall, Samuel R., Stephens, Jonny R., Seaby, Eleanor G., Andrade, Matheus Gesteira, Lowry, Andrew F., Parton, Will J. C., Smith, Claire F., and Border, Scott

Abstract

It is important that clinicians are able to adequately assess their level of knowledge and competence in order to be safe practitioners of medicine. The medical literature contains numerous examples of poor self-assessment accuracy amongst medical students over a range of subjects however this ability in neuroanatomy has yet to be observed. Second year medical students attending neuroanatomy revision sessions at the University of Southampton and the competitors of the National Undergraduate Neuroanatomy Competition were asked to rate their level of knowledge in neuroanatomy. The responses from the former group were compared to performance on a ten item multiple choice question examination and the latter group were compared to their performance within the competition. In both cohorts, self-assessments of perceived level of knowledge correlated weakly to their performance in their respective objective knowledge assessments (r = 0.30 and r = 0.44). Within the NUNC, this correlation improved when students were instead asked to rate their performance on a specific examination within the competition (spotter, rS = 0.68; MCQ, rS = 0.58). Despite its inherent difficulty, medical student self-assessment accuracy in neuroanatomy is comparable to other subjects within the medical curriculum.

Published
2016
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21. Thrombotic microangiopathy following haematopoietic stem cell transplant

Author

Seaby, Eleanor G. and Gilbert, Rodney D.

Subjects
Rituximab -- Usage -- Dosage and administration, Thrombosis -- Drug therapy -- Diagnosis -- Research, Pathological physiology -- Analysis, Stem cell transplantation -- Usage -- Complications and side effects, Health
Abstract

Thrombotic microangiopathy is a potentially lethal complication of haematopoietic stem cell (bone marrow) transplantation. The pathophysiology is incompletely understood, although endothelial damage appears to be central. Platelet activation, neutrophil extracellular traps and complement activation appear to play key roles. Diagnosis may be difficult and universally accepted diagnostic criteria are not available. Treatment remains controversial. In some cases, withdrawal of calcineurin inhibitors is adequate. Rituximab and defibrotide also appear to have been used successfully. In severe cases, complement inhibitors such as eculizumab may play a valuable role. Further research is required to define the pathophysiology and determine both robust diagnostic criteria and the optimal treatment., Author(s): Eleanor G. Seaby [sup.1] , Rodney D. Gilbert [sup.2] Author Affiliations: (Aff1) 0000 0004 1936 9297, grid.5491.9, Human Genetics and Genomics Department, University of Southampton, , Southampton, UK (Aff2) [...]

Published
2018
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23. A Palindrome-Like Structure on 16p13.3 Is Associated with the Formation of Complex Structural Variations and SRRM2 Haploinsufficiency

Author

Pagnamenta, Alistair T., primary, Yu, Jing, additional, Willis, Tracey A., additional, Hashim, Mona, additional, Seaby, Eleanor G., additional, Walker, Susan, additional, Xian, Jiaqi, additional, Cheng, Emily W. Y., additional, Tavares, Ana Lisa Taylor, additional, Forzano, Francesca, additional, Cox, Helen, additional, Dabir, Tabib, additional, Brady, Angela F., additional, Ghali, Neeti, additional, Atanur, Santosh S., additional, Ennis, Sarah, additional, Baralle, Diana, additional, and Taylor, Jenny C., additional

Published
2023
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24. Advanced variant classification framework reduces the false positive rate of predicted loss of function (pLoF) variants in population sequencing data

Author

Singer-Berk, Moriel, primary, Gudmundsson, Sanna, additional, Baxter, Samantha, additional, Seaby, Eleanor G, additional, Wood, Jordan C, additional, Son, Rachel G, additional, Watts, Nicholas A, additional, Karczewski, Konrad, additional, Harrison, Steven, additional, MacArthur, Daniel G, additional, Rehm, Heidi L, additional, and O'Donnell-Luria, Anne, additional

Published
2023
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25. Identification of novel locus associated with coronary artery aneurysms and validation of loci for susceptibility to Kawasaki disease

Author

Hoggart, Clive, Shimizu, Chisato, Galassini, Rachel, Wright, Victoria J., Shailes, Hannah, Bellos, Evan, Herberg, Jethro A., Pollard, Andrew J., O’Connor, Daniel, Choi, Shing Wan, Seaby, Eleanor G., Menikou, Stephanie, Hibberd, Martin, Sallah, Neneh, Burgner, David, Brogan, Paul, Patel, Harsita, Kim, Jihoon, Tremoulet, Adriana H., Salo, Eeva, van Stijn, Diana, Kuijpers, Taco, Burns, Jane C., and Levin, Michael

Abstract

Kawasaki disease (KD) is a paediatric vasculitis associated with coronary artery aneurysms (CAA). Genetic variants influencing susceptibility to KD have been previously identified, but no risk alleles have been validated that influence CAA formation. We conducted a genome-wide association study (GWAS) for CAA in KD patients of European descent with 200 cases and 276 controls. A second GWAS for susceptibility pooled KD cases with healthy paediatric controls from vaccine trials in the UK (n= 1609). Logistic regression mixed models were used for both GWASs. The susceptibility GWAS was meta-analysed with 400 KD cases and 6101 controls from a previous European GWAS, these results were further meta-analysed with Japanese GWASs at two putative loci. The CAA GWAS identified an intergenic region of chromosome 20q13 with multiple SNVs showing genome-wide significance. The risk allele of the most associated SNV (rs6017006) was present in 13% of cases and 4% of controls; in East Asian 1000 Genomes data, the allele was absent or rare. Susceptibility GWAS with meta-analysis with previously published European data identified two previously associated loci (ITPKCand FCGR2A). Further meta-analysis with Japanese GWAS summary data from the CASP3and FAM167Agenomic regions validated these loci in Europeans showing consistent effects of the top SNVs in both populations. We identified a novel locus for CAA in KD patients of European descent. The results suggest that different genes determine susceptibility to KD and development of CAA and future work should focus on the function of the intergenic region on chromosome 20q13.

Published
2024
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26. A clustering of heterozygous missense variants in the crucial chromatin modifier WDR5 defines a new neurodevelopmental disorder

Author

Snijders Blok, Lot, primary, Verseput, Jolijn, additional, Rots, Dmitrijs, additional, Venselaar, Hanka, additional, Innes, A. Micheil, additional, Stumpel, Connie, additional, Õunap, Katrin, additional, Reinson, Karit, additional, Seaby, Eleanor G., additional, McKee, Shane, additional, Burton, Barbara, additional, Kim, Katherine, additional, van Hagen, Johanna M., additional, Waisfisz, Quinten, additional, Joset, Pascal, additional, Steindl, Katharina, additional, Rauch, Anita, additional, Li, Dong, additional, Zackai, Elaine H., additional, Sheppard, Sarah E., additional, Keena, Beth, additional, Hakonarson, Hakon, additional, Roos, Andreas, additional, Kohlschmidt, Nicolai, additional, Cereda, Anna, additional, Iascone, Maria, additional, Rebessi, Erika, additional, Kernohan, Kristin D., additional, Campeau, Philippe M., additional, Millan, Francisca, additional, Taylor, Jesse A., additional, Lochmüller, Hanns, additional, Higgs, Martin R., additional, Goula, Amalia, additional, Bernhard, Birgitta, additional, Velasco, Danita J., additional, Schmanski, Andrew A., additional, Stark, Zornitza, additional, Gallacher, Lyndon, additional, Pais, Lynn, additional, Marcogliese, Paul C., additional, Yamamoto, Shinya, additional, Raun, Nicholas, additional, Jakub, Taryn E., additional, Kramer, Jamie M., additional, den Hoed, Joery, additional, Fisher, Simon E., additional, Brunner, Han G., additional, and Kleefstra, Tjitske, additional

Published
2023
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27. Response to Ramos et al

Author

Seaby, Eleanor G., primary, Baralle, Diana, additional, Rehm, Heidi L., additional, O’Donnell-Luria, Anne, additional, and Ennis, Sarah, additional

Published
2022
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28. Targeting de novo loss-of-function variants in constrained disease genes improves diagnostic rates in the 100,000 Genomes Project

Author

Seaby, Eleanor G, Thomas, N Simon, Webb, Amy, Brittain, Helen, Taylor Tavares, Ana Lisa, Genomics England Consortium, Baralle, Diana, Rehm, Heidi L, O'Donnell-Luria, Anne, Ennis, Sarah, and Apollo - University of Cambridge Repository

Subjects
Genome, Phenotype, Whole Genome Sequencing
Abstract

Funder: Gerald Kerkut Charitable Trust; doi: http://dx.doi.org/10.13039/100012166, BACKGROUND: Genome sequencing was first offered clinically in the UK through the 100,000 Genomes Project (100KGP). Analysis was restricted to predefined gene panels associated with the patient's phenotype. However, panels rely on clearly characterised phenotypes and risk missing diagnoses outside of the panel(s) applied. We propose a complementary method to rapidly identify pathogenic variants, including those missed by 100KGP methods. METHODS: The Loss-of-function Observed/Expected Upper-bound Fraction (LOEUF) score quantifies gene constraint, with low scores correlated with haploinsufficiency. We applied DeNovoLOEUF, a filtering strategy to sequencing data from 13,949 rare disease trios in the 100KGP, by filtering for rare, de novo, loss-of-function variants in disease genes with a LOEUF score < 0.2. We compared our findings with the corresponding patient's diagnostic reports. RESULTS: 324/332 (98%) of the variants identified using DeNovoLOEUF were diagnostic or partially diagnostic (whereby the variant was responsible for some of the phenotype). We identified 39 diagnoses that were "missed" by 100KGP standard analyses, which are now being returned to patients. CONCLUSION: We have demonstrated a highly specific and rapid method with a 98% positive predictive value that has good concordance with standard analysis, low false-positive rate, and can identify additional diagnoses. Globally, as more patients are being offered genome sequencing, we anticipate that DeNovoLOEUF will rapidly identify new diagnoses and facilitate iterative analyses when new disease genes are discovered.

Published
2023
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29. Treatment of Multisystem Inflammatory Syndrome in Children: Understanding Differences in Results of Comparative Effectiveness Studies

Author

Melgar, Michael, Seaby, Eleanor G, McArdle, Andrew J, Young, Cameron C, Campbell, Angela P, Murray, Nancy L, Patel, Manish M, Levin, Michael, Randolph, Adrienne G, Son, Mary Beth F, BATS Consortium And The Overcoming COVID-19 Investigators, Melgar, Michael [0000-0003-3243-9854], Campbell, Angela P [0000-0002-2576-482X], and Apollo - University of Cambridge Repository

Subjects
BATS Consortium and the Overcoming COVID-19 Investigators
Abstract

OBJECTIVE: Two cohort studies in patients with multisystem inflammatory syndrome in children (MIS-C) demonstrated contrasting results regarding the benefit of initial immunomodulatory treatment with intravenous immunoglobulin (IVIG) alone versus IVIG and glucocorticoids. We sought to determine whether application of different MIS-C definitions and differing disease severity between cohorts underlay discrepant results. METHODS: The Overcoming COVID-19 Public Health Surveillance Registry (OC-19) included patients meeting the US Centers for Disease Control and Prevention (CDC) MIS-C definition, whereas the Best Available Treatment Study (BATS) applied the World Health Organization (WHO) definition. We applied the WHO definition to the OC-19 cohort and the CDC definition to the BATS cohort and determined the proportion that did not meet the alternate definition. We compared illness severity indicators between cohorts. RESULTS: Of 349 OC-19 patients, 9.5% did not meet the WHO definition. Of 350 BATS patients, 10.3% did not meet the CDC definition. Most organ system involvement was similar between the cohorts, but more OC-19 patients had WHO-defined cardiac involvement (87.1% vs 79.4%, P = 0.008). OC-19 patients were more often admitted to intensive care (61.0% vs 44.8%, P < 0.001) and more often received vasopressors or inotropes (39.5% vs 22.9%, P < 0.001) before immunomodulatory treatment. CONCLUSION: Greater illness severity and cardiovascular involvement in the OC-19 cohort compared with the BATS cohort, and not use of different MIS-C case definitions, may have contributed to differing study conclusions about optimal initial treatment for MIS-C. Disease severity should be considered in future MIS-C study designs and treatment recommendations to identify patients who would benefit from aggressive immunomodulatory treatment.

Published
2022
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32. Rare pathogenic variants in WNK3 cause X-linked intellectual disability

Author

Küry, Sébastien, primary, Zhang, Jinwei, additional, Besnard, Thomas, additional, Caro-Llopis, Alfonso, additional, Zeng, Xue, additional, Robert, Stephanie M., additional, Josiah, Sunday S., additional, Kiziltug, Emre, additional, Denommé-Pichon, Anne-Sophie, additional, Cogné, Benjamin, additional, Kundishora, Adam J., additional, Hao, Le T., additional, Li, Hong, additional, Stevenson, Roger E., additional, Louie, Raymond J., additional, Deb, Wallid, additional, Torti, Erin, additional, Vignard, Virginie, additional, McWalter, Kirsty, additional, Raymond, F. Lucy, additional, Rajabi, Farrah, additional, Ranza, Emmanuelle, additional, Grozeva, Detelina, additional, Coury, Stephanie A., additional, Blanc, Xavier, additional, Brischoux-Boucher, Elise, additional, Keren, Boris, additional, Õunap, Katrin, additional, Reinson, Karit, additional, Ilves, Pilvi, additional, Wentzensen, Ingrid M., additional, Barr, Eileen E., additional, Guihard, Solveig Heide, additional, Charles, Perrine, additional, Seaby, Eleanor G., additional, Monaghan, Kristin G., additional, Rio, Marlène, additional, van Bever, Yolande, additional, van Slegtenhorst, Marjon, additional, Chung, Wendy K., additional, Wilson, Ashley, additional, Quinquis, Delphine, additional, Bréhéret, Flora, additional, Retterer, Kyle, additional, Lindenbaum, Pierre, additional, Scalais, Emmanuel, additional, Rhodes, Lindsay, additional, Stouffs, Katrien, additional, Pereira, Elaine M., additional, Berger, Sara M., additional, Milla, Sarah S., additional, Jaykumar, Ankita B., additional, Cobb, Melanie H., additional, Panchagnula, Shreyas, additional, Duy, Phan Q., additional, Vincent, Marie, additional, Mercier, Sandra, additional, Gilbert-Dussardier, Brigitte, additional, Le Guillou, Xavier, additional, Audebert-Bellanger, Séverine, additional, Odent, Sylvie, additional, Schmitt, Sébastien, additional, Boisseau, Pierre, additional, Bonneau, Dominique, additional, Toutain, Annick, additional, Colin, Estelle, additional, Pasquier, Laurent, additional, Redon, Richard, additional, Bouman, Arjan, additional, Rosenfeld, Jill. A., additional, Friez, Michael J., additional, Pérez-Peña, Helena, additional, Akhtar Rizvi, Syed Raza, additional, Haider, Shozeb, additional, Antonarakis, Stylianos E., additional, Schwartz, Charles E., additional, Martínez, Francisco, additional, Bézieau, Stéphane, additional, Kahle, Kristopher T., additional, and Isidor, Bertrand, additional

Published
2022
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33. Inactivation of AMMECR1 is associated with growth, bone, and heart alterations

Author

Moysés‐Oliveira, Mariana, Giannuzzi, Giuliana, Fish, Richard J., Rosenfeld, Jill A., Petit, Florence, Soares, Maria de Fatima, Kulikowski, Leslie Domenici, Di‐Battista, Adriana, Zamariolli, Malú, Xia, Fan, Liehr, Thomas, Kosyakova, Nadezda, Carvalheira, Gianna, Parker, Michael, Seaby, Eleanor G., Ennis, Sarah, Gilbert, Rodney D., Hagelstrom, R. Tanner, Cremona, Maria L., Li, Wenhui L., Malhotra, Alka, Chandrasekhar, Anjana, Perry, Denise L., Taft, Ryan J., McCarrier, Julie, Basel, Donald G., Andrieux, Joris, Stumpp, Taiza, Antunes, Fernanda, Pereira, Gustavo José, Neerman‐Arbez, Marguerite, Meloni, Vera Ayres, Drummond‐Borg, Margaret, Melaragno, Maria Isabel, and Reymond, Alexandre

Published
2018
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36. De novo putative loss‐of‐function variants in TAF4 are associated with a neuro‐developmental disorder

Author

Janssen, Beau D. E., primary, van den Boogaard, Marie‐Jose H., additional, Lichtenbelt, Klaske, additional, Seaby, Eleanor G., additional, Stals, Karen, additional, Ellard, Sian, additional, Newbury‐Ecob, Ruth, additional, Dixit, Abhijit, additional, Roht, Laura, additional, Pajusalu, Sander, additional, Õunap, Katrin, additional, Firth, Helen V., additional, Buckley, Michael, additional, Wilson, Meredith, additional, Roscioli, Tony, additional, Tidwell, Timothy, additional, Mao, Rong, additional, Ennis, Sarah, additional, Holwerda, Sjoerd J., additional, van Gassen, Koen, additional, and van Jaarsveld, Richard H., additional

Published
2022
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38. De novo putative loss-of-function variants in TAF4 are associated with a neuro-developmental disorder

Author

Genetica Klinische Genetica, Child Health, Genetica Sectie Genoomdiagnostiek, Janssen, Beau D E, van den Boogaard, Marie-Jose H, Lichtenbelt, Klaske, Seaby, Eleanor G, Stals, Karen, Ellard, Sian, Newbury-Ecob, Ruth, Dixit, Abhijit, Roht, Laura, Pajusalu, Sander, Õunap, Katrin, Firth, Helen V, Buckley, Michael, Wilson, Meredith, Roscioli, Tony, Tidwell, Timothy, Mao, Rong, Ennis, Sarah, Holwerda, Sjoerd J, van Gassen, Koen, van Jaarsveld, Richard H, Genetica Klinische Genetica, Child Health, Genetica Sectie Genoomdiagnostiek, Janssen, Beau D E, van den Boogaard, Marie-Jose H, Lichtenbelt, Klaske, Seaby, Eleanor G, Stals, Karen, Ellard, Sian, Newbury-Ecob, Ruth, Dixit, Abhijit, Roht, Laura, Pajusalu, Sander, Õunap, Katrin, Firth, Helen V, Buckley, Michael, Wilson, Meredith, Roscioli, Tony, Tidwell, Timothy, Mao, Rong, Ennis, Sarah, Holwerda, Sjoerd J, van Gassen, Koen, and van Jaarsveld, Richard H

Published
2022

40. NOD2 in Crohn's Disease—Unfinished Business.

Author

Ashton, James J, Seaby, Eleanor G, Beattie, R Mark, and Ennis, Sarah

Abstract

Studies of Crohn's disease have consistently implicated NOD2 as the most important gene in disease pathogenesis since first being identified in 2001. Thereafter, genome-wide association, next-generation sequencing and functional analyses have all confirmed a key role for NOD2 , but despite this, NOD2 also has significant unresolved complexity. More recent studies have reinvigorated an early hypothesis that NOD2 may be a single-gene cause of disease, and the distinct ileal stricturing phenotype seen with NOD2 -related disease presents an opportunity for personalized diagnosis, disease prediction and targeted therapy. The genomics of NOD2 has much that remains unknown, including the role of rare variation, phasing of variants across the haplotype block and the role of variation in the NOD2 -regulatory regions. Here, we discuss the evidence and the unmet needs of NOD2 research, based on recently published evidence, and suggest methods that may meet these requirements. [ABSTRACT FROM AUTHOR]

Published
2023
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41. Blood RNA analysis can increase clinical diagnostic rate and resolve variants of uncertain significance

Author

Wai, Htoo A, Lord, Jenny, Lyon, Matthew, Gunning, Adam, Kelly, Hugh, Cibin, Penelope, Seaby, Eleanor G, Spiers-Fitzgerald, Kerry, Lye, Jed, Ellard, Sian, Thomas, N Simon, Bunyan, David J, Douglas, Andrew G L, Baralle, Diana, Naik, Swati, Ragge, Nicola, Cox, Helen, Morton, Jenny E., O'Driscoll, Mary, Lim, Derek, Osio, Deborah, Elmslie, Frances, Huber, Camilla, Hewitt, Julie, Brandon, Heidy, McEntagart, Meriel, Mansour, Sahar, Lahiri, Nayana, Dempsey, Esther, Manalo, Merrie, Homfray, Tessa, Saggar, Anand, Li, Jin, Barwell, Julian, Chandler, Kate E., Briggs, Tracy, Douzgou, Sofia, Adlard, Julian, Kraus, Alison, Mehta, Sarju, Watford, Amy, Donaldson, Alan, Low, Karen, Jones, Gabriela, Dixit, Abhijit, King, Elizabeth, Shannon, Nora, Kaliakatsos, Marios, Joss, Shelagh, Balasubramanian, Meena, Johnson, Diana, Everest, Sarah, Salter, Claire, Harrison, Victoria, Wise, Gillian, Torokwa, Audrey, Sands, Victoria, Pyle, Esther, Thomas, Tessy, Lachlan, Katherine, Foulds, Nicola, Lotery, Andrew, Hammans, Simon R., Pond, Emily, Horton, Rachel, Kharbanda, Mira, Hunt, David, Thomas, Charlene, Side, Lucy, Willis, Catherine, Greville-Heygate, Stephanie, Mawby, Rebecca, Mercer, Catherine, Temple, Karen, Kinning, Esther, Bojovic, Ognjen, and Archer, L.

Subjects
RNA splicing, RNA Splicing, RNA-Seq, RNA/genetics, Computational biology, Biology, exons, Article, genetic diagnosis, 03 medical and health sciences, symbols.namesake, computational biology, splice, humans, Genetics (clinical), 030304 developmental biology, Sanger sequencing, 0303 health sciences, variant interpretation, 030305 genetics & heredity, RNA, Exon skipping, Reverse transcription polymerase chain reaction, genomic medicine, Agarose gel electrophoresis, symbols, mutation, RNA-seq
Abstract

Diagnosis of genetic disorders is hampered by large numbers of variants of uncertain significance (VUSs) identified through next-generation sequencing. Many such variants may disrupt normal RNA splicing. We examined effects on splicing of a large cohort of clinically identified variants and compared performance of bioinformatic splicing prediction tools commonly used in diagnostic laboratories. Two hundred fifty-seven variants (coding and noncoding) were referred for analysis across three laboratories. Blood RNA samples underwent targeted reverse transcription polymerase chain reaction (RT-PCR) analysis with Sanger sequencing of PCR products and agarose gel electrophoresis. Seventeen samples also underwent transcriptome-wide RNA sequencing with targeted splicing analysis based on Sashimi plot visualization. Bioinformatic splicing predictions were obtained using Alamut, HSF 3.1, and SpliceAI software. Eighty-five variants (33%) were associated with abnormal splicing. The most frequent abnormality was upstream exon skipping (39/85 variants), which was most often associated with splice donor region variants. SpliceAI had greatest accuracy in predicting splicing abnormalities (0.91) and outperformed other tools in sensitivity and specificity. Splicing analysis of blood RNA identifies diagnostically important splicing abnormalities and clarifies functional effects of a significant proportion of VUSs. Bioinformatic predictions are improving but still make significant errors. RNA analysis should therefore be routinely considered in genetic disease diagnostics.

Published
2020

43. A novel variant in GATM causes idiopathic renal Fanconi syndrome and predicts progression to end‐stage kidney disease.

Author

Seaby, Eleanor G., Turner, Steven, Bunyan, David J., Seyed‐Rezai, Fariba, Essex, Jonathan, Gilbert, Rodney D., and Ennis, Sarah

Subjects
*FANCONI syndrome, *CHRONIC kidney failure, *KIDNEY failure, *MOLECULAR dynamics, *GENETIC testing, *DAUGHTERS
Abstract

Renal Fanconi syndrome (RFS) is a generalised disorder of the proximal convoluted tubule. Many genes have been associated with RFS including those that cause systemic disorders such as cystinosis, as well as isolated RFS. We discuss the case of a 10‐year‐old female who presented with leg pain and raised creatinine on a screening blood test. Her mother has RFS and required a kidney transplant in her thirties. Further investigations confirmed RFS in the daughter. Exome sequencing was performed on the affected mother, child, and unaffected father. We identified a novel variant in GATM; c.965G>C p.(Arg322Pro) segregating dominantly in the mother and daughter. We validated our finding with molecular dynamics simulations and demonstrated a dynamic signature that differentiates our variant and two previously identified pathogenic variants in GATM from wildtype. Genetic testing has uncovered a novel pathogenic variant that predicts progression to end stage kidney failure and has important implications for family planning and cascade testing. We recommend that GATM is screened for in children presenting with RFS, in addition to adults, particularly with kidney failure, who may have had previous negative gene testing. [ABSTRACT FROM AUTHOR]

Published
2023
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44. Strategies to uplift novel Mendelian gene discovery for improved clinical outcomes

Author

Seaby, Eleanor G., Rehm, Heidi L., and O'Donnell-Luria, Anne

Abstract

Rare genetic disorders, while individually rare, are collectively common. They represent some of the most severe disorders affecting patients worldwide with significant morbidity and mortality. Over the last decade, advances in genomic methods have significantly uplifted diagnostic rates for patients and facilitated novel and targeted therapies. However, many patients with rare genetic disorders still remain undiagnosed as the genetic etiology of only a proportion of Mendelian conditions has been discovered to date. This article explores existing strategies to identify novel Mendelian genes and how these discoveries impact clinical care and therapeutics. We discuss the importance of data sharing, phenotype-driven approaches, patient-led approaches, utilization of large-scale genomic sequencing projects, constraint-based methods, integration of multi-omics data, and gene-to-patient methods. We further consider the health economic advantages of novel gene discovery and speculate on potential future methods for improved clinical outcomes.

Published
2021

45. A clustering of missense variants in the crucial chromatin modifier WDR5 defines a new neurodevelopmental disorder

Author

Snijders Blok, Lot, primary, Verseput, Jolijn, additional, Rots, Dmitrijs, additional, Venselaar, Hanka, additional, Innes, A. Micheil, additional, Stumpel, Connie, additional, Ounap, Katrin, additional, Reinson, Karit, additional, Seaby, Eleanor G., additional, McKee, Shane, additional, Burton, Barbara, additional, Kim, Katherine, additional, van Hagen, Johanna M., additional, Waisfisz, Quinten, additional, Joset, Pascal, additional, Steindl, Katharina, additional, Rauch, Anita, additional, Li, Dong, additional, Zackai, Elaine, additional, Sheppard, Sarah, additional, Keena, Beth, additional, Hakonarson, Hakon, additional, Roos, Andreas, additional, Kohlschmidt, Nicolai, additional, Cereda, Anna, additional, Iascone, Maria, additional, Rebessi, Erika, additional, Kernohan, Kristin D., additional, Campeau, Philippe M., additional, Millan, Francisca, additional, Taylor, Jesse A., additional, Lochmuller, Hanns, additional, Higgs, Martin R., additional, Goula, Amalia, additional, Bernhard, Birgitta, additional, Fisher, Simon E., additional, Brunner, Han G., additional, and Kleefstra, Tjitske, additional

Published
2021
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47. Author Correction: The mutational constraint spectrum quantified from variation in 141,456 humanS

Author

Karczewski, Konrad J., Francioli, Laurent C., Tiao, Grace, Cummings, Beryl B., Alföldi, Jessica, Wang, Qingbo, Collins, Ryan L., Laricchia, Kristen M., Ganna, Andrea, Birnbaum, Daniel P., Gauthier, Laura D., Brand, Harrison, Solomonson, Matthew, Rhodes, Daniel, Singer-Berk, Moriel, England, Eleina M., Seaby, Eleanor G., Kosmicki, Jack A., Walters, Raymond K., Tashman, Katherine, Farjoun, Yossi, Banks, Eric, Poterba, Timothy, Wang, Arcturus, Seed, Cotton, Whiffin, Nicola, Chong, Jessica X., Samocha, Kaitlin E., Pierce-Hoffman, Emma, Zappala, Zachary, O’Donnell-Luria, Anne H., Minikel, Eric Vallabh, Weisburd, Ben, Lek, Monkol, Ware, James S., Vittal, Christopher, Armean, Irina M., Bergelson, Louis, Cibulskis, Kristian, Connolly, Kristen M., Covarrubias, Miguel, Donnelly, Stacey, Ferriera, Steven, Gabriel, Stacey, Gentry, Jeff, Gupta, Namrata, Jeandet, Thibault, Kaplan, Diane, Llanwarne, Christopher, Munshi, Ruchi, Novod, Sam, Petrillo, Nikelle, Roazen, David, Ruano-Rubio, Valentin, Saltzman, Andrea, Schleicher, Molly, Soto, Jose, Tibbetts, Kathleen, Tolonen, Charlotte, Wade, Gordon, Talkowski, Michael E., Aguilar Salinas, Carlos A., Ahmad, Tariq, Albert, Christine M., Ardissino, Diego, Atzmon, Gil, Barnard, John, Beaugerie, Laurent, Benjamin, Emelia J., Boehnke, Michael, Bonnycastle, Lori L., Bottinger, Erwin P., Bowden, Donald W., Bown, Matthew J., Chambers, John C., Chan, Juliana C., Chasman, Daniel, Cho, Judy, Chung, Mina K., Cohen, Bruce, Correa, Adolfo, Dabelea, Dana, Daly, Mark J., Darbar, Dawood, Duggirala, Ravindranath, Dupuis, Josée, Ellinor, Patrick T., Elosua, Roberto, Erdmann, Jeanette, Esko, Tõnu, Färkkilä, Martti, Florez, Jose, Franke, Andre, Getz, Gad, Glaser, Benjamin, Glatt, Stephen J., Goldstein, David, Gonzalez, Clicerio, Groop, Leif, Haiman, Christopher, Hanis, Craig, Harms, Matthew, Hiltunen, Mikko, Holi, Matti M., Hultman, Christina M., Kallela, Mikko, Kaprio, Jaakko, Kathiresan, Sekar, Kim, Bong Jo, Kim, Young Jin, Kirov, George, Kooner, Jaspal, Koskinen, Seppo, Krumholz, Harlan M., Kugathasan, Subra, Kwak, Soo Heon, Laakso, Markku, Lehtimäki, Terho, Loos, Ruth J.F., Lubitz, Steven A., Ma, Ronald C.W., MacArthur, Daniel G., Marrugat, Jaume, Mattila, Kari M., McCarthy, Mark I., McGovern, Dermot, McPherson, Ruth, Meigs, James B., Melander, Olle, Metspalu, Andres, Neale, Benjamin M., Nilsson, Peter M., O’Donovan, Michael C., Ongur, Dost, Orozco, Lorena, Palotie, Aarno, Park, Kyong Soo, Pato, Carlos, Pulver, Ann E., Rahman, Nazneen, Remes, Anne M., Rioux, John D., Ripatti, Samuli, Roden, Dan M., Saleheen, Danish, Salomaa, Veikko, Samani, Nilesh J., Scharf, Jeremiah, Schunkert, Heribert, Shoemaker, Moore B., Sklar, Pamela, Soininen, Hilkka, Sokol, Harry, Spector, Tim, Sullivan, Patrick F., Suvisaari, Jaana, Tai, E. Shyong, Teo, Yik Ying, Tiinamaija, Tuomi, Tsuang, Ming, Turner, Dan, Tusie-Luna, Teresa, Vartiainen, Erkki, Vawter, Marquis P., Watkins, Hugh, Weersma, Rinse K., Wessman, Maija, and Xavier, Ramnik J.

Subjects
Multidisciplinary, Science & Technology, General Science & Technology, Spectrum (functional analysis), Rare variants, Biology, Constraint (information theory), Multidisciplinary Sciences, Variation (linguistics), Genome Aggregation Database Consortium, Science & Technology - Other Topics, Author Correction, Medical genomics, Algorithm
Abstract

In this Article, author Marquis P. Vawter was missing from the Genome Aggregation Database Consortium list. They are associated with the affiliation: ‘Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, CA, USA’, and contributed to the generation of the primary data incorporated into the gnomAD resource. In addition, in the legend to Fig. 1, ‘ten’ should have been ‘seven’ in the sentence: “a, Uniform manifold approximation and projection (UMAP)46,47 plot depicting the ancestral diversity of all individuals in gnomAD, using seven principal components.” The original Article has been corrected online.

Published
2021

48. De novo TRIM8 variants impair its protein localization to nuclear bodies and cause developmental delay, epilepsy, and focal segmental glomerulosclerosis

Author

Weng, Patricia L., Majmundar, Amar J., Khan, Kamal, Lim, Tze Y., Shril, Shirlee, Jin, Gina, Musgrove, John, Wang, Minxian, Ahram, Dina F., Aggarwal, Vimla S., Bier, Louise E., Heinzen, Erin L., Onuchic-Whitford, Ana C., Mann, Nina, Buerger, Florian, Schneider, Ronen, Deutsch, Konstantin, Kitzler, Thomas M., Klambt, Verena, Kolb, Amy, Mao, Youying, El Achkar, Christelle Moufawad, Mitrotti, Adele, Martino, Jeremiah, Beck, Bodo B., Altmuller, Janine, Benz, Marcus R., Yano, Shoji, Mikati, Mohamad A., Gunduz, Talha, Cope, Heidi, Shashi, Vandana, Trachtman, Howard, Bodria, Monica, Caridi, Gianluca, Pisani, Isabella, Fiaccadori, Enrico, AbuMaziad, Asmaa S., Martinez-Agosto, Julian A., Yadin, Ora, Zuckerman, Jonathan, Kim, Arang, John-Kroegel, Ulrike, Tyndall, Amanda, V, Parboosingh, Jillian S., Innes, A. Micheil, Bierzynska, Agnieszka, Koziell, Ania B., Muorah, Mordi, Saleem, Moin A., Hoefele, Julia, Riedhammer, Korbinian M., Gharavi, Ali G., Jobanputra, Vaidehi, Pierce-Hoffman, Emma, Seaby, Eleanor G., O'Donnell-Luria, Anne, Rehm, Heidi L., Mane, Shrikant, D'Agati, Vivette D., Pollak, Martin R., Ghiggeri, Gian Marco, Lifton, Richard P., Goldstein, David B., Davis, Erica E., Hildebrandt, Friedhelm, Sanna-Cherchi, Simone, Weng, Patricia L., Majmundar, Amar J., Khan, Kamal, Lim, Tze Y., Shril, Shirlee, Jin, Gina, Musgrove, John, Wang, Minxian, Ahram, Dina F., Aggarwal, Vimla S., Bier, Louise E., Heinzen, Erin L., Onuchic-Whitford, Ana C., Mann, Nina, Buerger, Florian, Schneider, Ronen, Deutsch, Konstantin, Kitzler, Thomas M., Klambt, Verena, Kolb, Amy, Mao, Youying, El Achkar, Christelle Moufawad, Mitrotti, Adele, Martino, Jeremiah, Beck, Bodo B., Altmuller, Janine, Benz, Marcus R., Yano, Shoji, Mikati, Mohamad A., Gunduz, Talha, Cope, Heidi, Shashi, Vandana, Trachtman, Howard, Bodria, Monica, Caridi, Gianluca, Pisani, Isabella, Fiaccadori, Enrico, AbuMaziad, Asmaa S., Martinez-Agosto, Julian A., Yadin, Ora, Zuckerman, Jonathan, Kim, Arang, John-Kroegel, Ulrike, Tyndall, Amanda, V, Parboosingh, Jillian S., Innes, A. Micheil, Bierzynska, Agnieszka, Koziell, Ania B., Muorah, Mordi, Saleem, Moin A., Hoefele, Julia, Riedhammer, Korbinian M., Gharavi, Ali G., Jobanputra, Vaidehi, Pierce-Hoffman, Emma, Seaby, Eleanor G., O'Donnell-Luria, Anne, Rehm, Heidi L., Mane, Shrikant, D'Agati, Vivette D., Pollak, Martin R., Ghiggeri, Gian Marco, Lifton, Richard P., Goldstein, David B., Davis, Erica E., Hildebrandt, Friedhelm, and Sanna-Cherchi, Simone

Abstract

Focal segmental glomerulosclerosis (FSGS) is the main pathology underlying steroid-resistant nephrotic syndrome (SRNS) and a leading cause of chronic kidney disease. Monogenic forms of pediatric SRNS are predominantly caused by recessive mutations, while the contribution of de novo variants (DNVs) to this trait is poorly understood. Using exome sequencing (ES) in a proband with FSGS/SRNS, developmental delay, and epilepsy, we discovered a nonsense DNV in TRIM8, which encodes the E3 ubiquitin ligase tripartite motif containing 8. To establish whether TRIM8 variants represent a cause of FSGS, we aggregated exome/genome-sequencing data for 2,501 pediatric FSGS/SRNS-affected individuals and 48,556 control subjects, detecting eight heterozygous TRIM8 truncating variants in affected subjects but none in control subjects (p = 3.28 3 10(-11)). In all six cases with available parental DNA, we demonstrated de novo inheritance (p = 2.21 3 10(-15)). Reverse phenotyping revealed neurodevelopmental disease in all eight families. We next analyzed ES from 9,067 individuals with epilepsy, yielding three additional families with truncating TRIM8 variants. Clinical review revealed FSGS in all. All TRIM8 variants cause protein truncation clustering within the last exon between residues 390 and 487 of the 551 amino acid protein, indicating a correlation between this syndrome and loss of the TRIM8 C-terminal region. Wild-type TRIM8 overexpressed in immortalized human podocytes and neuronal cells localized to nuclear bodies, while constructs harboring patient-specific variants mislocalized diffusely to the nucleoplasm. Co-localization studies demonstrated that Gemini and Cajal bodies frequently abut a TRIM8 nuclear body. Truncating TRIM8 DNVs cause a neuro-renal syndrome via aberrant TRIM8 localization, implicating nuclear bodies in FSGS and developmental brain disease.

Published
2021

49. Author Correction: Transcript expression-aware annotation improves rare variant interpretation

Author

Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, and Mudge, Jonathan M.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41586-020-03175-7, Author(s): Beryl B. Cummings [sup.1] [sup.2] [sup.3], Konrad J. Karczewski [sup.1] [sup.2], Jack A. Kosmicki [sup.1] [sup.2] [sup.4], Eleanor G. Seaby [sup.1] [sup.2] [sup.5], Nicholas A. Watts [sup.1] [sup.2], Moriel [...]

Published
2021
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50. Transcript expression-aware annotation improves rare variant interpretation

Author

Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, Mudge, Jonathan M., Karjalainen, Juha, Satterstrom, F. Kyle, O’Donnell-Luria, Anne H., Poterba, Timothy, Seed, Cotton, Solomonson, Matthew, Alföldi, Jessica, Armean, Irina M., Banks, Eric, Bergelson, Louis, Cibulskis, Kristian, Collins, Ryan L., Connolly, Kristen M., Covarrubias, Miguel, Daly, Mark J., Donnelly, Stacey, Farjoun, Yossi, Ferriera, Steven, Francioli, Laurent, Gabriel, Stacey, Gauthier, Laura D., Gentry, Jeff, Gupta, Namrata, Jeandet, Thibault, Kaplan, Diane, Laricchia, Kristen M., Llanwarne, Christopher, Minikel, Eric V., Munshi, Ruchi, Neale, Benjamin M., Novod, Sam, Petrillo, Nikelle, Roazen, David, Ruano-Rubio, Valentin, Saltzman, Andrea, Lehtimäki, Terho, Mattila, Kari M., Suvisaari, Jaana, Tampere University, Clinical Medicine, Department of Clinical Chemistry, Centre of Excellence in Complex Disease Genetics, HUS Abdominal Center, Department of Medicine, Clinicum, Gastroenterologian yksikkö, HUS Psychiatry, Department of Psychiatry, HUS Neurocenter, Department of Neurosciences, Neurologian yksikkö, Institute for Molecular Medicine Finland, Department of Public Health, Aarno Palotie / Principal Investigator, Genomics of Neurological and Neuropsychiatric Disorders, Biosciences, Samuli Olli Ripatti / Principal Investigator, Complex Disease Genetics, and Biostatistics Helsinki

Subjects
Male, Transcription, Genetic, Autism Spectrum Disorder, Developmental Disabilities, Datasets as Topic, Haploinsufficiency, Human genetic variation, Genome, Exon, 0302 clinical medicine, Loss of Function Mutation, Disease, Poisson Distribution, Exome sequencing, 0303 health sciences, education.field_of_study, Multidisciplinary, Disease genetics, ARRHYTHMIA, 1184 Genetics, developmental biology, physiology, Genome Aggregation Database Production Team, Exons, Female, Medical genomics, GENES, Genotype, General Science & Technology, Population, Computational biology, Biology, 3121 Internal medicine, Article, DNA sequencing, 03 medical and health sciences, Rare Diseases, Intellectual Disability, Exome Sequencing, Humans, RNA, Messenger, Author Correction, Transcriptomics, education, Gene, 030304 developmental biology, MUTATIONS, Alternative splicing, Reproducibility of Results, Molecular Sequence Annotation, Genome Aggregation Database Consortium, 3111 Biomedicine, Transcriptome, 030217 neurology & neurosurgery
Abstract

The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD)1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the ‘proportion expressed across transcripts’, which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies., A novel variant annotation metric that quantifies the level of expression of genetic variants across tissues is validated in the Genome Aggregation Database (gnomAD) and is shown to improve rare variant interpretation.

Published
2020

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