22 results on '"Ibañez, Kristina"'
Search Results
2. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study
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McDonagh, Ellen M, Rueda, Antonio, Polychronopoulos, Dimitris, Chan, Georgia, Angus-Leppan, Heather, Bhatia, Kailash P, Davison, James E, Festenstein, Richard, Fratta, Pietro, Giunti, Paola, Howard, Robin, Venkata, Laxmi, Laurá, Matilde, McEntagart, Meriel, Menzies, Lara, Morris, Huw, Reilly, Mary M, Robinson, Robert, Rosser, Elisabeth, Faravelli, Francesca, Schrag, Anette, Schott, Jonathan M, Warner, Thomas T, Wood, Nicholas W, Bourn, David, Eggleton, Kelly, Labrum, Robyn, Twiss, Philip, Abbs, Stephen, Santos, Liana, Almheiri, Ghareesa, Sheikh, Isabella, Vandrovcova, Jana, Patch, Christine, Taylor Tavares, Ana Lisa, Hyder, Zerin, Need, Anna, Brittain, Helen, Baple, Emma, Moutsianas, Loukas, Deshpande, Viraj, Perry, Denise L, Ajay, Subramanian S., Chawla, Aditi, Rajan, Vani, Oprych, Kathryn, Chinnery, Patrick F, Douglas, Angela, Wilson, Gill, Ellard, Sian, Temple, I Karen, Mumford, Andrew, McMullan, Dom, Naresh, Kikkeri, Flinter, Frances A, Taylor, Jenny C, Greenhalgh, Lynn, Newman, William, Brennan, Paul, Sayer, John A, Raymond, F Lucy, Chitty, Lyn S, Ambrose, John C., Arumugam, Prabhu, Bleda, Marta, Boardman-Pretty, Freya, Boissiere, Jeanne M., Boustred, Christopher R., Craig, Clare E.H., de Burca, Anna, Devereau, Andrew, Elgar, Greg, Foulger, Rebecca E., Furió-Tarí, Pedro, Hackett, Joanne, Halai, Dina, Hamblin, Angela, Henderson, Shirley, Holman, James, Hubbard, Tim J.P., Jackson, Rob, Jones, Louise J., Kayikci, Melis, Lahnstein, Lea, Lawson, Kay, Leigh, Sarah E.A., Leong, Ivonne U.S., Lopez, Javier F., Maleady-Crowe, Fiona, Mason, Joanne, Mueller, Michael, Murugaesu, Nirupa, Odhams, Chris A., Perez-Gil, Daniel, Pullinger, John, Rahim, Tahrima, Riesgo-Ferreiro, Pablo, Rogers, Tim, Ryten, Mina, Savage, Kevin, Sawant, Kushmita, Siddiq, Afshan, Sieghart, Alexander, Smedley, Damian, Sosinsky, Alona, Spooner, William, Stevens, Helen E., Stuckey, Alexander, Sultana, Razvan, Thompson, Simon R., Tregidgo, Carolyn, Walsh, Emma, Watters, Sarah A., Welland, Matthew J., Williams, Eleanor, Witkowska, Katarzyna, Wood, Suzanne M., Zarowiecki, Magdalena, Ibañez, Kristina, Polke, James, Hagelstrom, R Tanner, Dolzhenko, Egor, Pasko, Dorota, Thomas, Ellen Rachel Amy, Daugherty, Louise C, Kasperaviciute, Dalia, Smith, Katherine R, Deans, Zandra C, Hill, Sue, Fowler, Tom, Scott, Richard H, Hardy, John, Houlden, Henry, Rendon, Augusto, Caulfield, Mark J, Eberle, Michael A, Taft, Ryan J, and Tucci, Arianna
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- 2022
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3. REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
- Author
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Dolzhenko, Egor, Weisburd, Ben, Ibañez, Kristina, Rajan-Babu, Indhu-Shree, Anyansi, Christine, Bennett, Mark F., Billingsley, Kimberley, Carroll, Ashley, Clamons, Samuel, Danzi, Matt C., Deshpande, Viraj, Ding, Jinhui, Fazal, Sarah, Halman, Andreas, Jadhav, Bharati, Qiu, Yunjiang, Richmond, Phillip A., Saunders, Christopher T., Scheffler, Konrad, van Vugt, Joke J. F. A., Zwamborn, Ramona R. A. J., Chong, Samuel S., Friedman, Jan M., Tucci, Arianna, Rehm, Heidi L., and Eberle, Michael A.
- Published
- 2022
- Full Text
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4. Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis
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Adeleye, Adelani, Alba, Camille, Bacikova, Dagmar, Hupalo, Daniel N., Martinez, Elisa McGrath, Pollard, Harvey B., Sukumar, Gauthaman, Soltis, Anthony R., Tuck, Meila, Zhang, Xijun, Wilkerson, Matthew D., Smith, Bradley N., Ticozzi, Nicola, Fallini, Claudia, Gkazi, Athina Soragia, Topp, Simon D., Kost, Jason, Scotter, Emma L., Kenna, Kevin P., Miller, Jack W., Tiloca, Cinzia, Vance, Caroline, Danielson, Eric W., Troakes, Claire, Colombrita, Claudia, Al-Sarraj, Safa, Lewis, Elizabeth A., King, Andrew, Calini, Daniela, Pensato, Viviana, Castellotti, Barbara, de Belleroche, Jacqueline, Baas, Frank, ten Asbroek, Anneloor L.M.A., Sapp, Peter C., McKenna-Yasek, Diane, McLaughlin, Russell L., Polak, Meraida, Asress, Seneshaw, Esteban-Pérez, Jesús, Muñoz-Blanco, José Luis, Stevic, Zorica, D’Alfonso, Sandra, Mazzini, Letizia, Comi, Giacomo P., Del Bo, Roberto, Ceroni, Mauro, Gagliardi, Stella, Querin, Giorgia, Bertolin, Cinzia, van Rheenen, Wouter, Diekstra, Frank P., Rademakers, Rosa, van Blitterswijk, Marka, Boylan, Kevin B., Lauria, Giuseppe, Duga, Stefano, Corti, Stefania, Cereda, Cristina, Corrado, Lucia, Sorarù, Gianni, Williams, Kelly L., Nicholson, Garth A., Blair, Ian P., Leblond-Manry, Claire, Rouleau, Guy A., Hardiman, Orla, Morrison, Karen E., Veldink, Jan H., van den Berg, Leonard H., Al-Chalabi, Ammar, Pall, Hardev, Shaw, Pamela J., Turner, Martin R., Talbot, Kevin, Taroni, Franco, García-Redondo, Alberto, Wu, Zheyang, Gellera, Cinzia, Ratti, Antonia, Brown, Robert H., Jr., Shaw, Christopher E., Ambrose, John C., Arumugam, Prabhu, Baple, Emma L., Bleda, Marta, Boardman-Pretty, Freya, Boissiere, Jeanne M., Boustred, Christopher R., Brittain, H., Caulfield, Mark J., Chan, Georgia C., Craig, Clare E.H., Daugherty, Louise C., de Burca, Anna, Devereau, Andrew, Elgar, Greg, Foulger, Rebecca E., Fowler, Tom, Furió-Tarí, Pedro, Hackett, Joanne M., Halai, Dina, Hamblin, Angela, Henderson, Shirley, Holman, James E., Hubbard, Tim J.P., Jackson, Rob, Jones, Louise J., Kasperaviciute, Dalia, Kayikci, Melis, Lahnstein, Lea, Lawson, Kay, Leigh, Sarah E.A., Leong, Ivonne U.S., Lopez, Javier F., Maleady-Crowe, Fiona, Mason, Joanne, McDonagh, Ellen M., Moutsianas, Loukas, Mueller, Michael, Murugaesu, Nirupa, Need, Anna C., Odhams, Chris A., Patch, Christine, Perez-Gil, Daniel, Polychronopoulos, Dimitris, Pullinger, John, Rahim, Tahrima, Rendon, Augusto, Riesgo-Ferreiro, Pablo, Rogers, Tim, Savage, Kevin, Sawant, Kushmita, Scott, Richard H., Siddiq, Afshan, Sieghart, Alexander, Smedley, Damian, Smith, Katherine R., Sosinsky, Alona, Spooner, William, Stevens, Helen E., Stuckey, Alexander, Sultana, Razvan, Thomas, Ellen R.A., Thompson, Simon R., Tregidgo, Carolyn, Walsh, Emma, Watters, Sarah A., Welland, Matthew J., Williams, Eleanor, Witkowska, Katarzyna, Wood, Suzanne M., Zarowiecki, Magdalena, Arepalli, Sampath, Auluck, Pavan, Baloh, Robert H., Bowser, Robert, Brice, Alexis, Broach, James, Camu, William, Chiò, Adriano, Cooper-Knock, John, Corcia, Philippe, Drepper, Carsten, Drory, Vivian E., Dunckley, Travis L., Faghri, Faraz, Farren, Jennifer, Feldman, Eva, Floeter, Mary Kay, Fratta, Pietro, Gerhard, Glenn, Gibson, Summer B., Goutman, Stephen A., Heiman-Patterson, Terry D., Hernandez, Dena G., Hoover, Ben, Jansson, Lilja, Kamel, Freya, Kirby, Janine, Kowall, Neil W., Laaksovirta, Hannu, Landi, Francesco, Le Ber, Isabelle, Lumbroso, Serge, MacGowan, Daniel JL., Maragakis, Nicholas J., Mora, Gabriele, Mouzat, Kevin, Myllykangas, Liisa, Nalls, Mike A., Orrell, Richard W., Ostrow, Lyle W., Pamphlett, Roger, Pioro, Erik, Pulst, Stefan M., Ravits, John M., Renton, Alan E., Robberecht, Wim, Robey, Ian, Rogaeva, Ekaterina, Rothstein, Jeffrey D., Sendtner, Michael, Sidle, Katie C., Simmons, Zachary, Stone, David J., Tienari, Pentti J., Trojanowski, John Q., Troncoso, Juan C., Valori, Miko, Van Damme, Philip, Van Den Bosch, Ludo, Zinman, Lorne, Albani, Diego, Borroni, Barbara, Padovani, Alessandro, Bruni, Amalia, Clarimon, Jordi, Dols-Icardo, Oriol, Illán-Gala, Ignacio, Lleó, Alberto, Danek, Adrian, Galimberti, Daniela, Scarpini, Elio, Serpente, Maria, Graff, Caroline, Chiang, Huei-Hsin, Khoshnood, Behzad, Öijerstedt, Linn, Morris, Christopher M., Nacmias, Benedetta, Sorbi, Sandro, Nielsen, Jorgen E., Hjermind, Lynne E., Novelli, Valeria, Puca, Annibale A., Pastor, Pau, Alvarez, Ignacio, Diez-Fairen, Monica, Aguilar, Miquel, Perneczky, Robert, Diehl-Schimd, Janine, Rossi, Mina, Ruiz, Agustin, Boada, Mercè, Hernández, Isabel, Moreno-Grau, Sonia, Schlachetzki, Johannes C., Aarsland, Dag, Albert, Marilyn S., Attems, Johannes, Barrett, Matthew J., Beach, Thomas G., Bekris, Lynn M., Bennett, David A., Besser, Lilah M., Bigio, Eileen H., Black, Sandra E., Boeve, Bradley F., Bohannan, Ryan C., Brett, Francesca, Brunetti, Maura, Caraway, Chad A., Palma, Jose-Alberto, Calvo, Andrea, Canosa, Antonio, Dickson, Dennis, Duyckaerts, Charles, Faber, Kelley, Ferman, Tanis, Flanagan, Margaret E., Floris, Gianluca, Foroud, Tatiana M., Fortea, Juan, Gan-Or, Ziv, Gentleman, Steve, Ghetti, Bernardino, Gibbs, Jesse Raphael, Goate, Alison, Goldstein, David, González-Aramburu, Isabel, Graff-Radford, Neill R., Hodges, Angela K., Hu, Heng-Chen, Hupalo, Daniel, Infante, Jon, Iranzo, Alex, Kaiser, Scott M., Kaufmann, Horacio, Keith, Julia, Kim, Ronald C., Klein, Gregory, Krüger, Rejko, Kukull, Walter, Kuzma, Amanda, Lage, Carmen, Lesage, Suzanne, Leverenz, James B., Logroscino, Giancarlo, Lopez, Grisel, Love, Seth, Mao, Qinwen, Marti, Maria Jose, Martinez-McGrath, Elisa, Masellis, Mario, Masliah, Eliezer, May, Patrick, McKeith, Ian, Mesulam, Marek-Marsel, Monuki, Edwin S., Newell, Kathy L., Norcliffe-Kaufmann, Lucy, Palmer, Laura, Perkins, Matthew, Pletnikova, Olga, Molina-Porcel, Laura, Reynolds, Regina H., Rodríguez-Rodríguez, Eloy, Rohrer, Jonathan D., Sanchez-Juan, Pascual, Scherzer, Clemens R., Serrano, Geidy E., Shakkottai, Vikram, Sidransky, Ellen, Tayebi, Nahid, Thomas, Alan J., Tilley, Bension S., Walton, Ronald L., Woltjer, Randy, Wszolek, Zbigniew K., Xiromerisiou, Georgia, Zecca, Chiara, Phatnani, Hemali, Kwan, Justin, Sareen, Dhruv, Broach, James R., Arcila-Londono, Ximena, Lee, Edward B., Shneider, Neil A., Fraenkel, Ernest, Zaitlen, Noah, Berry, James D., Malaspina, Andrea, Cox, Gregory A., Thompson, Leslie M., Finkbeiner, Steve, Dardiotis, Efthimios, Miller, Timothy M., Chandran, Siddharthan, Pal, Suvankar, Hornstein, Eran, MacGowan, Daniel J., Heiman-Patterson, Terry, Hammell, Molly G., Patsopoulos, Nikolaos.A., Butovsky, Oleg, Dubnau, Joshua, Nath, Avindra, Harms, Matt, Aronica, Eleonora, Poss, Mary, Phillips-Cremins, Jennifer, Crary, John, Atassi, Nazem, Lange, Dale J., Adams, Darius J., Stefanis, Leonidas, Gotkine, Marc, Babu, Suma, Raj, Towfique, Paganoni, Sabrina, Shalem, Ophir, Smith, Colin, Zhang, Bin, Harris, Brent, Broce, Iris, Drory, Vivian, Ravits, John, McMillan, Corey, Menon, Vilas, Wu, Lani, Altschuler, Steven, Amar, Khaled, Archibald, Neil, Bandmann, Oliver, Capps, Erica, Church, Alistair, Coebergh, Jan, Costantini, Alyssa, Critchley, Peter, Ghosh, Boyd CP., Hu, Michele T.M., Kobylecki, Christopher, Leigh, P. Nigel, Mann, Carl, Massey, Luke A., Morris, Huw R., Nath, Uma, Pavese, Nicola, Paviour, Dominic, Sharma, Jagdish, Vaughan, Jenny, Dewan, Ramita, Chia, Ruth, Ding, Jinhui, Hickman, Richard A., Stein, Thor D., Abramzon, Yevgeniya, Ahmed, Sarah, Sabir, Marya S., Portley, Makayla K., Tucci, Arianna, Ibáñez, Kristina, Shankaracharya, F.N.U., Keagle, Pamela, Rossi, Giacomina, Caroppo, Paola, Tagliavini, Fabrizio, Waldo, Maria L., Johansson, Per M., Nilsson, Christer F., Rowe, James B., Benussi, Luisa, Binetti, Giuliano, Ghidoni, Roberta, Jabbari, Edwin, Viollet, Coralie, Glass, Jonathan D., Singleton, Andrew B., Silani, Vincenzo, Ross, Owen A., Ryten, Mina, Torkamani, Ali, Tanaka, Toshiko, Ferrucci, Luigi, Resnick, Susan M., Pickering-Brown, Stuart, Brady, Christopher B., Kowal, Neil, Hardy, John A., Van Deerlin, Vivianna, Vonsattel, Jean Paul, Harms, Matthew B., Ferrari, Raffaele, Landers, John E., Gibbs, J. Raphael, Dalgard, Clifton L., Scholz, Sonja W., and Traynor, Bryan J.
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- 2021
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5. CLAPO syndrome: identification of somatic activating PIK3CA mutations and delineation of the natural history and phenotype
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Rodriguez-Laguna, Lara, Ibañez, Kristina, Gordo, Gema, Garcia-Minaur, Sixto, Santos-Simarro, Fernando, Agra, Noelia, Vallespín, Elena, Fernández-Montaño, Victoria E., Martín-Arenas, Rubén, del Pozo, Ángela, González-Pecellín, Héctor, Mena, Rocío, Rueda-Arenas, Inmaculada, Gomez, María V., Villaverde, Cristina, Bustamante, Ana, Ayuso, Carmen, Ruiz-Perez, Víctor L., Nevado, Julián, Lapunzina, Pablo, Lopez-Gutierrez, Juan C., and Martinez-Glez, Victor
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- 2018
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6. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels
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Martin, Antonio Rueda, Williams, Eleanor, Foulger, Rebecca E., Leigh, Sarah, Daugherty, Louise C., Niblock, Olivia, Leong, Ivone U. S., Smith, Katherine R., Gerasimenko, Oleg, Haraldsdottir, Eik, Thomas, Ellen, Scott, Richard H., Baple, Emma, Tucci, Arianna, Brittain, Helen, de Burca, Anna, Ibañez, Kristina, Kasperaviciute, Dalia, Smedley, Damian, Caulfield, Mark, Rendon, Augusto, and McDonagh, Ellen M.
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- 2019
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7. Deletion at 6q24.2–26 predicts longer survival of high-grade serous epithelial ovarian cancer patients
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Kamieniak, Marta M., Rico, Daniel, Milne, Roger L., Muñoz-Repeto, Ivan, Ibáñez, Kristina, Grillo, Miguel A., Domingo, Samuel, Borrego, Salud, Cazorla, Alicia, García-Bueno, José M., Hernando, Susana, García-Donas, Jesús, Hernández-Agudo, Elena, y Cajal, Teresa Ramón, Robles-Díaz, Luis, Márquez-Rodas, Ivan, Cusidó, Maite, Sáez, Raquel, Lacambra-Calvet, Carmen, Osorio, Ana, Urioste, Miguel, Cigudosa, Juan C., Paz-Ares, Luis, Palacios, José, Benítez, Javier, and García, María J.
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- 2015
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8. Functional genomics provide key insights to improve the diagnostic yield of hereditary ataxia.
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Chen, Zhongbo, Tucci, Arianna, Cipriani, Valentina, Gustavsson, Emil K, Ibañez, Kristina, Reynolds, Regina H, Zhang, David, Vestito, Letizia, García, Alejandro Cisterna, Sethi, Siddharth, Brenton, Jonathan W, García-Ruiz, Sonia, Fairbrother-Browne, Aine, Gil-Martinez, Ana-Luisa, Consortium, Genomics England Research, Wood, Nick, Hardy, John A, Smedley, Damian, Houlden, Henry, and Botía, Juan
- Subjects
FRIEDREICH'S ataxia ,SPINOCEREBELLAR ataxia ,FUNCTIONAL genomics ,MICROSATELLITE repeats ,GENE expression ,WHOLE genome sequencing - Abstract
Improvements in functional genomic annotation have led to a critical mass of neurogenetic discoveries. This is exemplified in hereditary ataxia, a heterogeneous group of disorders characterised by incoordination from cerebellar dysfunction. Associated pathogenic variants in more than 300 genes have been described, leading to a detailed genetic classification partitioned by age-of-onset. Despite these advances, up to 75% of patients with ataxia remain molecularly undiagnosed even following whole genome sequencing, as exemplified in the 100 000 Genomes Project. This study aimed to understand whether we can improve our knowledge of the genetic architecture of hereditary ataxia by leveraging functional genomic annotations, and as a result, generate insights and strategies that raise the diagnostic yield. To achieve these aims, we used publicly-available multi-omics data to generate 294 genic features, capturing information relating to a gene's structure, genetic variation, tissue-specific, cell-type-specific and temporal expression, as well as protein products of a gene. We studied these features across genes typically causing childhood-onset, adult-onset or both types of disease first individually, then collectively. This led to the generation of testable hypotheses which we investigated using whole genome sequencing data from up to 2182 individuals presenting with ataxia and 6658 non-neurological probands recruited in the 100 000 Genomes Project. Using this approach, we demonstrated a high short tandem repeat (STR) density within childhood-onset genes suggesting that we may be missing pathogenic repeat expansions within this cohort. This was verified in both childhood- and adult-onset ataxia patients from the 100 000 Genomes Project who were unexpectedly found to have a trend for higher repeat sizes even at naturally-occurring STRs within known ataxia genes, implying a role for STRs in pathogenesis. Using unsupervised analysis, we found significant similarities in genomic annotation across the gene panels, which suggested adult- and childhood-onset patients should be screened using a common diagnostic gene set. We tested this within the 100 000 Genomes Project by assessing the burden of pathogenic variants among childhood-onset genes in adult-onset patients and vice versa. This demonstrated a significantly higher burden of rare, potentially pathogenic variants in conventional childhood-onset genes among individuals with adult-onset ataxia. Our analysis has implications for the current clinical practice in genetic testing for hereditary ataxia. We suggest that the diagnostic rate for hereditary ataxia could be increased by removing the age-of-onset partition, and through a modified screening for repeat expansions in naturally-occurring STRs within known ataxia-associated genes, in effect treating these regions as candidate pathogenic loci. [ABSTRACT FROM AUTHOR]
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- 2023
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9. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study
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Ibañez, Kristina, primary, Polke, James, additional, Hagelstrom, R Tanner, additional, Dolzhenko, Egor, additional, Pasko, Dorota, additional, Thomas, Ellen Rachel Amy, additional, Daugherty, Louise C, additional, Kasperaviciute, Dalia, additional, Smith, Katherine R, additional, Deans, Zandra C, additional, Hill, Sue, additional, Fowler, Tom, additional, Scott, Richard H, additional, Hardy, John, additional, Chinnery, Patrick F, additional, Houlden, Henry, additional, Rendon, Augusto, additional, Caulfield, Mark J, additional, Eberle, Michael A, additional, Taft, Ryan J, additional, Tucci, Arianna, additional, McDonagh, Ellen M, additional, Rueda, Antonio, additional, Polychronopoulos, Dimitris, additional, Chan, Georgia, additional, Angus-Leppan, Heather, additional, Bhatia, Kailash P, additional, Davison, James E, additional, Festenstein, Richard, additional, Fratta, Pietro, additional, Giunti, Paola, additional, Howard, Robin, additional, Venkata, Laxmi, additional, Laurá, Matilde, additional, McEntagart, Meriel, additional, Menzies, Lara, additional, Morris, Huw, additional, Reilly, Mary M, additional, Robinson, Robert, additional, Rosser, Elisabeth, additional, Faravelli, Francesca, additional, Schrag, Anette, additional, Schott, Jonathan M, additional, Warner, Thomas T, additional, Wood, Nicholas W, additional, Bourn, David, additional, Eggleton, Kelly, additional, Labrum, Robyn, additional, Twiss, Philip, additional, Abbs, Stephen, additional, Santos, Liana, additional, Almheiri, Ghareesa, additional, Sheikh, Isabella, additional, Vandrovcova, Jana, additional, Patch, Christine, additional, Taylor Tavares, Ana Lisa, additional, Hyder, Zerin, additional, Need, Anna, additional, Brittain, Helen, additional, Baple, Emma, additional, Moutsianas, Loukas, additional, Deshpande, Viraj, additional, Perry, Denise L, additional, Ajay, Subramanian S., additional, Chawla, Aditi, additional, Rajan, Vani, additional, Oprych, Kathryn, additional, Douglas, Angela, additional, Wilson, Gill, additional, Ellard, Sian, additional, Temple, I Karen, additional, Mumford, Andrew, additional, McMullan, Dom, additional, Naresh, Kikkeri, additional, Flinter, Frances A, additional, Taylor, Jenny C, additional, Greenhalgh, Lynn, additional, Newman, William, additional, Brennan, Paul, additional, Sayer, John A, additional, Raymond, F Lucy, additional, Chitty, Lyn S, additional, Ambrose, John C., additional, Arumugam, Prabhu, additional, Bleda, Marta, additional, Boardman-Pretty, Freya, additional, Boissiere, Jeanne M., additional, Boustred, Christopher R., additional, Craig, Clare E.H., additional, de Burca, Anna, additional, Devereau, Andrew, additional, Elgar, Greg, additional, Foulger, Rebecca E., additional, Furió-Tarí, Pedro, additional, Hackett, Joanne, additional, Halai, Dina, additional, Hamblin, Angela, additional, Henderson, Shirley, additional, Holman, James, additional, Hubbard, Tim J.P., additional, Jackson, Rob, additional, Jones, Louise J., additional, Kayikci, Melis, additional, Lahnstein, Lea, additional, Lawson, Kay, additional, Leigh, Sarah E.A., additional, Leong, Ivonne U.S., additional, Lopez, Javier F., additional, Maleady-Crowe, Fiona, additional, Mason, Joanne, additional, Mueller, Michael, additional, Murugaesu, Nirupa, additional, Odhams, Chris A., additional, Perez-Gil, Daniel, additional, Pullinger, John, additional, Rahim, Tahrima, additional, Riesgo-Ferreiro, Pablo, additional, Rogers, Tim, additional, Ryten, Mina, additional, Savage, Kevin, additional, Sawant, Kushmita, additional, Siddiq, Afshan, additional, Sieghart, Alexander, additional, Smedley, Damian, additional, Sosinsky, Alona, additional, Spooner, William, additional, Stevens, Helen E., additional, Stuckey, Alexander, additional, Sultana, Razvan, additional, Thompson, Simon R., additional, Tregidgo, Carolyn, additional, Walsh, Emma, additional, Watters, Sarah A., additional, Welland, Matthew J., additional, Williams, Eleanor, additional, Witkowska, Katarzyna, additional, Wood, Suzanne M., additional, and Zarowiecki, Magdalena, additional
- Published
- 2022
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10. Additional file 5 of REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
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Dolzhenko, Egor, Weisburd, Ben, Ibañez, Kristina, Rajan-Babu, Indhu-Shree, Anyansi, Christine, Bennett, Mark F., Billingsley, Kimberley, Carroll, Ashley, Clamons, Samuel, Danzi, Matt C., Deshpande, Viraj, Ding, Jinhui, Fazal, Sarah, Halman, Andreas, Jadhav, Bharati, Qiu, Yunjiang, Richmond, Phillip A., Saunders, Christopher T., Scheffler, Konrad, van Vugt, Joke J. F. A., Zwamborn, Ramona R. A. J., Chong, Samuel S., Friedman, Jan M., Tucci, Arianna, Rehm, Heidi L., and Eberle, Michael A.
- Abstract
Additional file 5: Figure S2. Read pileups in a region surrounding DMPK repeat expansion generated by (A) JBrowse, (B) IGV, and (C) REViewer.
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- 2022
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11. Additional file 1 of REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
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Dolzhenko, Egor, Weisburd, Ben, Ibañez, Kristina, Rajan-Babu, Indhu-Shree, Anyansi, Christine, Bennett, Mark F., Billingsley, Kimberley, Carroll, Ashley, Clamons, Samuel, Danzi, Matt C., Deshpande, Viraj, Ding, Jinhui, Fazal, Sarah, Halman, Andreas, Jadhav, Bharati, Qiu, Yunjiang, Richmond, Phillip A., Saunders, Christopher T., Scheffler, Konrad, van Vugt, Joke J. F. A., Zwamborn, Ramona R. A. J., Chong, Samuel S., Friedman, Jan M., Tucci, Arianna, Rehm, Heidi L., and Eberle, Michael A.
- Abstract
Additional file 1: Supplementary methods. Description of the concordance study dataset; Description of the wrapper script; Evaluation of manual review performance; Comparison with haplotype-resolved assemblies, Comparison with other visualization software; REViewer allele structure of FMR1 reference samples; Comparison of STR genotypes extracted from long-read genome assembly.
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- 2022
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12. Additional file 4 of REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
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Dolzhenko, Egor, Weisburd, Ben, Ibañez, Kristina, Rajan-Babu, Indhu-Shree, Anyansi, Christine, Bennett, Mark F., Billingsley, Kimberley, Carroll, Ashley, Clamons, Samuel, Danzi, Matt C., Deshpande, Viraj, Ding, Jinhui, Fazal, Sarah, Halman, Andreas, Jadhav, Bharati, Qiu, Yunjiang, Richmond, Phillip A., Saunders, Christopher T., Scheffler, Konrad, van Vugt, Joke J. F. A., Zwamborn, Ramona R. A. J., Chong, Samuel S., Friedman, Jan M., Tucci, Arianna, Rehm, Heidi L., and Eberle, Michael A.
- Abstract
Additional file 4: Figure S1. REViewer pileup plots for some NA12878 STRs: (A) ATXN10, (B) RFC1, (C) CNPB.
- Published
- 2022
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13. Use of whole genome sequencing to determine genetic basis of suspected mitochondrial disorders: cohort study
- Author
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Schon, Katherine R, Horvath, Rita, Wei, Wei, Calabrese, Claudia, Tucci, Arianna, Ibañez, Kristina, Ratnaike, Thiloka, Pitceathly, Robert D S, Bugiardini, Enrico, Quinlivan, Rosaline, Hanna, Michael G, Clement, Emma, Ashton, Emma, Sayer, John A, Brennan, Paul, Josifova, Dragana, Izatt, Louise, Fratter, Carl, Nesbitt, Victoria, Barrett, Timothy, McMullen, Dominic J, Smith, Audrey, Deshpande, Charulata, Smithson, Sarah F, Festenstein, Richard, Canham, Natalie, Caulfield, Mark, Houlden, Henry, Rahman(, Shamima, Chinnery, Patrick F, Genomics England Research Consortium, Ambrose, John C, Arumugam, Prabhu, Bevers, Roel, Bleda, Marta, Boardman-Pretty, Freya, Boustred, Christopher R, Brittain, Helen, Caulfield, Mark J, Chan, Georgia C, Elgar, Greg, Fowler, Tom, Giess, Adam, Hamblin, Angela, Henderson, Shirley, Hubbard, Tim J P, Jackson, Rob, Jones, Louise J, Kasperaviciute, Dalia, Kayikci, Melis, Kousathanas, Athanasios, Lahnstein, Lea, Leigh, Sarah E A, Leong, Ivonne U S, Lopez, Javier F, Maleady-Crowe, Fiona, McEntegart, Meriel, Minneci, Federico, Moutsianas, Loukas, Mueller, Michael, Murugaesu, Nirupa, Need, Anna C, O’Donovan, Peter, Odhams, Chris A, Patch, Christine, Buonerimo Pereira, Mariana, Perez-Gil, Daniel, Pullinger, John, Rahim, Tahrima, Rendon, Augusto, Rogers, Tim, Savage, Kevin, Sawant, Kushmita, Scott, Richard H, Siddiq, Afshan, Sieghart, Alexander, Smith, Samuel C, Sosinsky, Alona, Stuckey, Alexander, Tanguy, Mélanie, Taylor Tavares, Ana Lisa, Thomas, Ellen R A, Thompson, Simon R, Welland, Matthew J, Williams, Eleanor, Witkowska, Katarzyna, Wood, Suzanne M, Schon, Katherine R [0000-0001-8054-8954], Houlden, Henry [0000-0002-2866-7777], Rahman(, Shamima [0000-0003-2088-730X], Chinnery, Patrick F [0000-0002-7065-6617], and Apollo - University of Cambridge Repository
- Subjects
Adult ,Genetic Markers ,Male ,medicine.medical_specialty ,Mitochondrial DNA ,Mitochondrial Diseases ,Adolescent ,Mitochondrial disease ,Bioinformatics ,DNA, Mitochondrial ,Genome ,Young Adult ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,Genetic Testing ,Copy-number variation ,Medical diagnosis ,Child ,Aged ,030304 developmental biology ,Aged, 80 and over ,Whole genome sequencing ,0303 health sciences ,Whole Genome Sequencing ,business.industry ,Research ,Infant, Newborn ,Infant ,General Medicine ,Middle Aged ,medicine.disease ,3. Good health ,Phenotype ,Child, Preschool ,Mutation ,Medical genetics ,Microsatellite ,Female ,business ,030217 neurology & neurosurgery ,Follow-Up Studies - Abstract
ObjectiveTo determine whether whole genome sequencing can be used to define the molecular basis of suspected mitochondrial disease.DesignCohort study.SettingNational Health Service, England, including secondary and tertiary care.Participants345 patients with suspected mitochondrial disorders recruited to the 100 000 Genomes Project in England between 2015 and 2018.InterventionShort read whole genome sequencing was performed. Nuclear variants were prioritised on the basis of gene panels chosen according to phenotypes, ClinVar pathogenic/likely pathogenic variants, and the top 10 prioritised variants from Exomiser. Mitochondrial DNA variants were called using an in-house pipeline and compared with a list of pathogenic variants. Copy number variants and short tandem repeats for 13 neurological disorders were also analysed. American College of Medical Genetics guidelines were followed for classification of variants.Main outcome measureDefinite or probable genetic diagnosis.ResultsA definite or probable genetic diagnosis was identified in 98/319 (31%) families, with an additional 6 (2%) possible diagnoses. Fourteen of the diagnoses (4% of the 319 families) explained only part of the clinical features. A total of 95 different genes were implicated. Of 104 families given a diagnosis, 39 (38%) had a mitochondrial diagnosis and 65 (63%) had a non-mitochondrial diagnosis.ConclusionWhole genome sequencing is a useful diagnostic test in patients with suspected mitochondrial disorders, yielding a diagnosis in a further 31% after exclusion of common causes. Most diagnoses were non-mitochondrial disorders and included developmental disorders with intellectual disability, epileptic encephalopathies, other metabolic disorders, cardiomyopathies, and leukodystrophies. These would have been missed if a targeted approach was taken, and some have specific treatments.
- Published
- 2021
14. Use of whole genome sequencing to determine genetic basis of suspected mitochondrial disorders: cohort study
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Schon, Katherine R, primary, Horvath, Rita, additional, Wei, Wei, additional, Calabrese, Claudia, additional, Tucci, Arianna, additional, Ibañez, Kristina, additional, Ratnaike, Thiloka, additional, Pitceathly, Robert D S, additional, Bugiardini, Enrico, additional, Quinlivan, Rosaline, additional, Hanna, Michael G, additional, Clement, Emma, additional, Ashton, Emma, additional, Sayer, John A, additional, Brennan, Paul, additional, Josifova, Dragana, additional, Izatt, Louise, additional, Fratter, Carl, additional, Nesbitt, Victoria, additional, Barrett, Timothy, additional, McMullen, Dominic J, additional, Smith, Audrey, additional, Deshpande, Charulata, additional, Smithson, Sarah F, additional, Festenstein, Richard, additional, Canham, Natalie, additional, Caulfield, Mark, additional, Houlden, Henry, additional, Rahman(, Shamima, additional, and Chinnery, Patrick F, additional
- Published
- 2021
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- View/download PDF
15. A New Overgrowth Syndrome is due to Mutations in RNF125
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Tenorio, Jair, Mansilla, Alicia, Valencia, María, Martínez-Glez, Víctor, Romanelli, Valeria, Arias, Pedro, Castrejón, Nerea, Poletta, Fernando, Guillén-Navarro, Encarna, Gordo, Gema, Mansilla, Elena, García-Santiago, Fé, González-Casado, Isabel, Vallespín, Elena, Palomares, María, Mori, María A., Santos-Simarro, Fernando, García-Miñaur, Sixto, Fernández, Luis, Mena, Rocío, Benito-Sanz, Sara, del Pozo, Ángela, Silla, Juan Carlos, Ibañez, Kristina, López-Granados, Eduardo, Martín-Trujillo, Alex, Montaner, David, Heath, Karen E., Campos-Barros, Ángel, Dopazo, Joaquín, Nevado, Julián, Monk, David, Ruiz-Pérez, Víctor L., and Lapunzina, Pablo
- Published
- 2014
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16. Somatic activating mutations in PIK3CA cause generalized lymphatic anomaly
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Rodriguez-Laguna, Lara, Agra, Noelia, Ibañez, Kristina, Oliva-Molina, Gloria, Gordo, Gema, Khurana, Noor, Hominick, Devon, Beato, María, Colmenero, Isabel, Herranz, Gonzalo, Torres Canizalez, Juan M, Rodríguez Pena, Rebeca, Vallespín, Elena, Martín-Arenas, Rubén, Del Pozo, Ángela, Villaverde, Cristina, Bustamante, Ana, Ayuso, Carmen, Lapunzina, Pablo, Lopez-Gutierrez, Juan C, Dellinger, Michael T, and Martinez-Glez, Victor
- Subjects
nutritional and metabolic diseases ,lipids (amino acids, peptides, and proteins) ,neoplasms - Abstract
Generalized lymphatic anomaly (GLA) is a vascular disorder characterized by diffuse or multifocal lymphatic malformations (LMs). The etiology of GLA is poorly understood. We identified four distinct somatic PIK3CA variants (Glu542Lys, Gln546Lys, His1047Arg, and His1047Leu) in tissue samples from five out of nine patients with GLA. These same PIK3CA variants occur in PIK3CA-related overgrowth spectrum and cause hyperactivation of the PI3K-AKT-mTOR pathway. We found that the mTOR inhibitor, rapamycin, prevented lymphatic hyperplasia and dysfunction in mice that expressed an active form of PIK3CA (His1047Arg) in their lymphatics. We also found that rapamycin reduced pain in patients with GLA. In conclusion, we report that somatic activating PIK3CA mutations can cause GLA, and we provide preclinical and clinical evidence to support the use of rapamycin for the treatment of this disabling and deadly disease.
- Published
- 2019
17. Pitfalls of trio-based exome sequencing: imprinted genes and parental mosaicism—MAGEL2 as an example
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Palomares-Bralo, María, Vallespín, Elena, del Pozo, Ángela, Ibañez, Kristina, Silla, Juan Carlos, Galán, Enrique, Gordo, Gema, Martínez-Glez, Víctor, Alba-Valdivia, Lázaro I, Heath, Karen E, García-Miñaúr, Sixto, Lapunzina, Pablo, and Santos-Simarro, Fernando
- Published
- 2017
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18. Somatic activating mutations in PIK3CA cause generalized lymphatic anomaly
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Rodriguez-Laguna, Lara, primary, Agra, Noelia, additional, Ibañez, Kristina, additional, Oliva-Molina, Gloria, additional, Gordo, Gema, additional, Khurana, Noor, additional, Hominick, Devon, additional, Beato, María, additional, Colmenero, Isabel, additional, Herranz, Gonzalo, additional, Torres Canizalez, Juan M., additional, Rodríguez Pena, Rebeca, additional, Vallespín, Elena, additional, Martín-Arenas, Rubén, additional, del Pozo, Ángela, additional, Villaverde, Cristina, additional, Bustamante, Ana, additional, Ayuso, Carmen, additional, Lapunzina, Pablo, additional, Lopez-Gutierrez, Juan C., additional, Dellinger, Michael T., additional, and Martinez-Glez, Victor, additional
- Published
- 2018
- Full Text
- View/download PDF
19. CLAPO syndrome: Identification of somatic activating PIK3CA mutations and delineation of the natural history and phenotype
- Author
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Rodriguez-Laguna, Lara, primary, Ibañez, Kristina, additional, Gordo, Gema, additional, Garcia-Minaur, Sixto, additional, Santos-Simarro, Fernando, additional, Agra, Noelia, additional, Vallespín, Elena, additional, Fernández-Montaño, Victoria E, additional, Martín-Arenas, Rubén, additional, del Pozo, Ángela, additional, Gonzalez-Pecellín, Héctor, additional, Mena, Rocío, additional, Rueda-Arenas, Inmaculada, additional, Gomez, María V., additional, Villaverde, Cristina, additional, Bustamante, Ana, additional, Ayuso, Carmen, additional, Ruiz-Perez, Víctor L., additional, Nevado, Julián, additional, Lapunzina, Pablo, additional, Lopez-Gutierrez, Juan C., additional, and Martinez-Glez, Victor, additional
- Published
- 2017
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20. A Population‐Wide Exploration of the THAP11 CAG Repeat Size and Structure in the 100,000 Genomes Project and UK Biobank.
- Author
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Clarkson, Chris, Chen, Zhongbo, Rocca, Clarissa, Jadhav, Bharati, Ibañez, Kristina, Ryten, Mina, Sharp, Andrew J., Houlden, Henry, and Tucci, Arianna
- Subjects
- *
FRIEDREICH'S ataxia , *MOVEMENT disorders , *SPINOCEREBELLAR ataxia , *NEURODEGENERATION , *DATABASES - Abstract
Background Objective Methods Results Conclusions A CAG repeat expansion in THAP11 was recently found to be associated with spinocerebellar ataxia in two Chinese families. Expanded repeats ranged from 45 to 100 units, with CAA sequence interruptions in the 5′ region and an uninterrupted CAG tract in the 3′ tail.Here, we assess the population distribution of the THAP11 repeat, and its contribution to neurological diseases.We interrogated data from 54,788 individuals from Genomics England, 10,686 patients from the UCL Queen Square Institute of Neurology in‐house database (UCL IoN), and 424,340 individuals from the UK Biobank.We identified expanded repeats in four individuals with learning difficulties without ataxia and in three individuals in UK Biobank, one with hereditary ataxia, one with hereditary neuropathy, and one with neurodegenerative disease. We showed a linear relationship between the number of CAA interruptions and overall repeat length.These results indicate that THAP11 expansions are rare in the British population and that sequence structures predisposed to expansions may be more common in non‐British ancestries. © 2024 The Author(s).
Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. [ABSTRACT FROM AUTHOR]- Published
- 2024
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21. Increased frequency of repeat expansion mutations across different populations.
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Ibañez K, Jadhav B, Zanovello M, Gagliardi D, Clarkson C, Facchini S, Garg P, Martin-Trujillo A, Gies SJ, Deforie VG, Dalmia A, Hensman Moss DJ, Vandrovcova J, Rocca C, Moutsianas L, Marini-Bettolo C, Walker H, Turner C, Shoai M, Long JD, Fratta P, Langbehn DR, Tabrizi SJ, Caulfield MJ, Cortese A, Escott-Price V, Hardy J, Houlden H, Sharp AJ, and Tucci A
- Abstract
Repeat expansion disorders (REDs) are a devastating group of predominantly neurological diseases. Together they are common, affecting 1 in 3,000 people worldwide with population-specific differences. However, prevalence estimates of REDs are hampered by heterogeneous clinical presentation, variable geographic distributions, and technological limitations leading to under-ascertainment. Here, leveraging whole genome sequencing data from 82,176 individuals from different populations, we found an overall disease allele frequency of REDs of 1 in 283 individuals. Modelling disease prevalence using genetic data, age at onset and survival, we show that the expected number of people with REDs would be two to three times higher than currently reported figures, indicating under-diagnosis and/or incomplete penetrance. While some REDs are population-specific, e.g. Huntington disease-like 2 in Africans, most REDs are represented in all broad genetic ancestries (i.e. Europeans, Africans, Americans, East Asians, and South Asians), challenging the notion that some REDs are found only in specific populations. These results have worldwide implications for local and global health communities in the diagnosis and counselling of REDs., Competing Interests: Competing Interests Statement The authors declare no competing interests
- Published
- 2024
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22. Somatic activating mutations in PIK3CA cause generalized lymphatic anomaly.
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Rodriguez-Laguna L, Agra N, Ibañez K, Oliva-Molina G, Gordo G, Khurana N, Hominick D, Beato M, Colmenero I, Herranz G, Torres Canizalez JM, Rodríguez Pena R, Vallespín E, Martín-Arenas R, Del Pozo Á, Villaverde C, Bustamante A, Ayuso C, Lapunzina P, Lopez-Gutierrez JC, Dellinger MT, and Martinez-Glez V
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- Adolescent, Adult, Amino Acid Substitution, Child, Child, Preschool, Female, Humans, Male, Proto-Oncogene Proteins c-akt genetics, Proto-Oncogene Proteins c-akt metabolism, Signal Transduction drug effects, Signal Transduction genetics, TOR Serine-Threonine Kinases genetics, TOR Serine-Threonine Kinases metabolism, Class I Phosphatidylinositol 3-Kinases genetics, Class I Phosphatidylinositol 3-Kinases metabolism, Lymphangioleiomyomatosis diagnostic imaging, Lymphangioleiomyomatosis drug therapy, Lymphangioleiomyomatosis enzymology, Lymphangioleiomyomatosis genetics, Lymphatic System abnormalities, Lymphatic System diagnostic imaging, Lymphatic System enzymology, Mutation, Missense, Sirolimus administration & dosage
- Abstract
Generalized lymphatic anomaly (GLA) is a vascular disorder characterized by diffuse or multifocal lymphatic malformations (LMs). The etiology of GLA is poorly understood. We identified four distinct somatic PIK3CA variants (Glu542Lys, Gln546Lys, His1047Arg, and His1047Leu) in tissue samples from five out of nine patients with GLA. These same PIK3CA variants occur in PIK3CA -related overgrowth spectrum and cause hyperactivation of the PI3K-AKT-mTOR pathway. We found that the mTOR inhibitor, rapamycin, prevented lymphatic hyperplasia and dysfunction in mice that expressed an active form of PIK3CA (His1047Arg) in their lymphatics. We also found that rapamycin reduced pain in patients with GLA. In conclusion, we report that somatic activating PIK3CA mutations can cause GLA, and we provide preclinical and clinical evidence to support the use of rapamycin for the treatment of this disabling and deadly disease., (© 2018 Rodriguez-Laguna et al.)
- Published
- 2019
- Full Text
- View/download PDF
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