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1. Author Correction: Analysis and visualisation of electronic health records data to identify undiagnosed patients with rare genetic diseases

Author

Moynihan, Daniel, Monaco, Sean, Ting, Teck Wah, Narasimhalu, Kaavya, Hsieh, Jenny, Kam, Sylvia, Lim, Jiin Ying, Lim, Weng Khong, Davila, Sonia, Bylstra, Yasmin, Balakrishnan, Iswaree Devi, Heng, Mark, Chia, Elian, Yeo, Khung Keong, Goh, Bee Keow, Gupta, Ritu, Tan, Tele, Baynam, Gareth, and Jamuar, Saumya Shekhar

Published
2024
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3. Host gene expression signatures to identify infection type and organ dysfunction in children evaluated for sepsis: a multicentre cohort study

Author

Levin, Michael, Coin, Lachlan, Gormley, Stuart, Hamilton, Shea, Hoggart, Clive, Kaforou, Myrsini, Sancho-Shimizu, Vanessa, Wright, Victoria, Abdulla, Amina, Agapow, Paul, Bartlett, Maeve, Eleftherohorinou, Hariklia, Galassini, Rachel, Inwald, David, Mashbat, Meg, Menikou, Stephanie, Mustafa, Sobia, Nadel, Simon, Rahman, Rahmeen, Shailes, Hannah, Thakker, Clare, Bokhandi, S., Power, Sue, Barham, Heather, Pathan, N., Ridout, Jenna, White, Deborah, Thurston, Sarah, Faust, S., Patel, S., McCorkell, Jenni, Davies, P., Crate, Lindsey, Navarra, Helen, Carter, Stephanie, Ramaiah, R., Patel, Rekha, Tuffrey, Catherine, Gribbin, Andrew, McCready, Sharon, Peters, Mark, Hardy, Katie, Standing, Fran, O'Neill, Lauren, Abelake, Eugenia, Deep, Akash, Nsirim, Eniola, Pollard, Andrew, Willis, Louise, Young, Zoe, Royad, C., White, Sonia, Fortune, Peter-Marc, Hudnott, Phil, Martinón-Torres, Federico, Salas, Antonio, Álvez González, Fernando, Barral-Arca, Ruth, Cebey-López, Miriam, Curras-Tuala, María José, García, Natalia, García Vicente, Luisa, Gómez-Carballa, Alberto, Gómez Rial, Jose, Grela Beiroa, Andrea, Justicia Grande, Antonio, Leboráns Iglesias, Pilar, Martínez Santos, Alba Elena, Martinón-Torres, Nazareth, Martinón Sánchez, José María, Morillo Gutiérrez, Beatriz, Mosquera Pérez, Belén, Obando Pacheco, Pablo, Pardo-Seco, Jacobo, Pischedda, Sara, Rivero-Calle, Irene, Rodríguez-Tenreiro, Carmen, Redondo-Collazo, Lorenzo, Salas Ellacuriaga, Antonio, Fernández, Sonia Serén, del Sol Porto Silva, María, Vega, Ana, Vilanova Trillo, Lucía, Reyes, Susana Beatriz, Cruz León León, María, Navarro Mingorance, Álvaro, Gabaldó Barrio, Xavier, Oñate Vergara, Eider, Concha Torre, Andrés, Vivanco, Ana, Fernández, Reyes, Giménez Sánchez, Francisco, Sánchez Forte, Miguel, Rojo, Pablo, Contreras, J. Ruiz, Palacios, Alba, Epalza Ibarrondo, Cristina, Fernández Cooke, Elizabeth, Navarro, Marisa, Álvarez Álvarez, Cristina, José Lozano, María, Carreras, Eduardo, Brió Sanagustín, Sonia, Neth, Olaf, Martínez Padilla, Mª del Carmen, Prieto Tato, Luis Manuel, Guillén, Sara, Fernández Silveira, Laura, Moreno, David, de Groot, R., Tutu van Furth, A.M., van der Flier, M., Boeddha, N.P., Driessen, G.J.A., Emonts, M., Hazelzet, J.A., Kuijpers, T.W., Pajkrt, D., Sanders, E.A.M., van de Beek, D., van der Ende, A., Philipsen, H.L.A., Adeel, A.O.A., Breukels, M.A., Brinkman, D.M.C., de Korte, C.C.M.M., de Vries, E., de Waal, W.J., Dekkers, R., Dings-Lammertink, A., Doedens, R.A., Donker, A.E., Dousma, M., Faber, T.E., Gerrits, G.P.J.M., Gerver, J.A.M., Heidema, J., Homan-van der Veen, J., Jacobs, M.A.M., Jansen, N.J.G., Kawczynski, P., Klucovska, K., Kneyber, M.C.J., Koopman-Keemink, Y., Langenhorst, V.J., Leusink, J., Loza, B.F., Merth, I.T., Miedema, C.J., Neeleman, C., Noordzij, J.G., Obihara, C.C., van Overbeek- van Gils, A.L.T., Poortman, G.H., Potgieter, S.T., Potjewijd, J., Rosias, P.P.R., Sprong, T., ten Tussher, G.W., Thio, B.J., Tramper-Stranders, G.A., van Deuren, M., van der Meer, H., van Kuppevelt, A.J.M., van Wermeskerken, A.M., Verwijs, W.A., Wolfs, T.F.W., Schlapbach, Luregn J., Agyeman, Philipp, Aebi, Christoph, Giannoni, Eric, Stocker, Martin, Posfay-Barbe, Klara M., Heininger, Ulrich, Bernhard-Stirnemann, Sara, Niederer-Loher, Anita, Kahlert, Christian, Hasters, Paul, Relly, Christa, Baer, Walter, Berger, Christoph, Carrol, Enitan D., Paulus, Stéphane, Frederick, Hannah, Jennings, Rebecca, Johnston, Joanne, Kenwright, Rhian, Fink, Colin G, Pinnock, Elli, Emonts, Marieke, Agbeko, Rachel, Anderson, Suzanne, Secka, Fatou, Bojang, Kalifa, Sarr, Isatou, Kebbeh, Ngange, Sey, Gibbi, Saidykhan, Momodou, Cole, Fatoumata, Thomas, Gilleh, Antonio, Martin, Zenz, Werner, Kohlfürst, Daniela S., Binder, Alexander, Schweintzger, Nina A., Sagmeister, Manfred, Baumgart, Hinrich, Baumgartner, Markus, Behrends, Uta, Biebl, Ariane, Birnbacher, Robert, Blanke, Jan-Gerd, Boelke, Carsten, Breuling, Kai, Brunner, Jürgen, Buller, Maria, Dahlem, Peter, Dietrich, Beate, Eber, Ernst, Elias, Johannes, Emhofer, Josef, Etschmaier, Rosa, Farr, Sebastian, Girtler, Ylenia, Grigorow, Irina, Heimann, Konrad, Ihm, Ulrike, Jaros, Zdenek, Kalhoff, Hermann, Kaulfersch, Wilhelm, Kemen, Christoph, Klocker, Nina, Köster, Bernhard, Kohlmaier, Benno, Komini, Eleni, Kramer, Lydia, Neubert, Antje, Ortner, Daniel, Pescollderungg, Lydia, Pfurtscheller, Klaus, Reiter, Karl, Ristic, Goran, Rödl, Siegfried, Sellner, Andrea, Sonnleitner, Astrid, Sperl, Matthias, Stelzl, Wolfgang, Till, Holger, Trobisch, Andreas, Vierzig, Anne, Vogel, Ulrich, Weingarten, Christina, Welke, Stefanie, Wimmer, Andreas, Wintergerst, Uwe, Wüller, Daniel, Zaunschirm, Andrew, Ziuraite, Ieva, Žukovskaja, Veslava, Hibberd, Martin L., Davila, Sonia, Delany, Isabel, Schlapbach, Luregn J, Raman, Sainath, Sharp, Nathalie, Phillips, Natalie, Irwin, Adam, Balch, Ross, Harley, Amanda, Johnson, Kerry, Sever, Zoe, George, Shane, Grimwood, Keith, Snelling, Peter J, Chavan, Arjun, Kitcatt, Eleanor, Lawton, Luke, Hempenstall, Allison, Pilot, Pelista, Gibbons, Kristen S, Le Marsney, Renate, Blumenthal, Antje, Ganesamoorthy, Devika, Pardo, Carolyn, Kling, Jessica, McPherson, Stephen, MacDonald, Anna D, Bialasiewicz, Seweryn, Pham, Trang, Wilson, Clare, Sharp, Natalie, Kling, Jessica C, McPherson, Stephen J, Herberg, Jethro A, and Coin, Lachlan J M

Published
2024
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4. Contribution of common and rare variants to Asian neovascular age-related macular degeneration subtypes

Author

Fan, Qiao, Li, Hengtong, Wang, Xiaomeng, Tham, Yih-Chung, Teo, Kelvin Yi Chong, Yasuda, Masayuki, Lim, Weng Khong, Kwan, Yuet Ping, Teo, Jing Xian, Chen, Ching-Jou, Chen, Li Jia, Ahn, Jeeyun, Davila, Sonia, Miyake, Masahiro, Tan, Patrick, Park, Kyu Hyung, Pang, Chi Pui, Khor, Chiea Chuan, Wong, Tien Yin, Yanagi, Yasuo, Cheung, Chui Ming Gemmy, and Cheng, Ching-Yu

Published
2023
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5. The Singapore National Precision Medicine Strategy

Author

Wong, Eleanor, Bertin, Nicolas, Hebrard, Maxime, Tirado-Magallanes, Roberto, Bellis, Claire, Lim, Weng Khong, Chua, Chee Yong, Tong, Philomena Mei Lin, Chua, Raymond, Mak, Kenneth, Lim, Tit Meng, Cheong, Wei Yang, Thien, Kwee Eng, Goh, Khean Teik, Chai, Jin-Fang, Lee, Jimmy, Sung, Joseph Jao-Yiu, Wong, Tien Yin, Chin, Calvin Woon Loong, Gluckman, Peter D., Goh, Liuh Ling, Ban, Kenneth Hon Kim, Tan, Tin Wee, Sim, Xueling, Cheng, Ching-Yu, Davila, Sonia, Karnani, Neerja, Leong, Khai Pang, Liu, Jianjun, Prabhakar, Shyam, Maurer-Stroh, Sebastian, Verma, Chandra Shekhar, Krishnaswamy, Pavitra, Goh, Rick Siow Mong, Chia, Irenaeus, Ho, Clarissa, Low, Doreen, Virabhak, Suchin, Yong, Jacklyn, Zheng, Weiling, Seow, Shih Wee, Seck, Yee Kwang, Koh, Mingshi, Chambers, John C., Tai, E. Shyong, and Tan, Patrick

Published
2023
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6. A five-safes approach to a secure and scalable genomics data repository

Author

Shih, Chih Chuan, Chen, Jieqi, Lee, Ai Shan, Bertin, Nicolas, Hebrard, Maxime, Khor, Chiea Chuen, Li, Zheng, Juan Tan, Joanna Hui, Meah, Wee Yang, Peh, Su Qin, Mok, Shi Qi, Sim, Kar Seng, Liu, Jianjun, Wang, Ling, Wong, Eleanor, Li, Jingmei, Tin, Aung, Cheng, Ching-Yu, Heng, Chew-Kiat, Yuan, Jian-Min, Koh, Woon-Puay, Saw, Seang Mei, Friedlander, Yechiel, Sim, Xueling, Chai, Jin Fang, Chong, Yap Seng, Davila, Sonia, Goh, Liuh Ling, Lee, Eng Sing, Wong, Tien Yin, Karnani, Neerja, Leong, Khai Pang, Yeo, Khung Keong, Chambers, John C., Lim, Su Chi, Goh, Rick Siow Mong, Tan, Patrick, and Dorajoo, Rajkumar

Published
2023
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7. Extensive Ethnic Variation and Linkage Disequilibrium at the FCGR2/3 Locus: Different Genetic Associations Revealed in Kawasaki Disease.

Author

Nagelkerke, Sietse Q, Tacke, Carline E, Breunis, Willemijn B, Tanck, Michael WT, Geissler, Judy, Png, Eileen, Hoang, Long T, van der Heijden, Joris, Naim, Ahmad NM, Yeung, Rae SM, Levin, Michael L, Wright, Victoria J, Burgner, David P, Ponsonby, Anne-Louise, Ellis, Justine A, Cimaz, Rolando, Shimizu, Chisato, Burns, Jane C, Fijnvandraat, Karin, van der Schoot, C Ellen, van den Berg, Timo K, de Boer, Martin, Davila, Sonia, Hibberd, Martin L, Kuijpers, Taco W, and International Kawasaki Disease Genetics Consortium

Subjects
International Kawasaki Disease Genetics Consortium, Humans, Mucocutaneous Lymph Node Syndrome, Genetic Predisposition to Disease, Receptors, IgG, Odds Ratio, Case-Control Studies, Gene Expression Profiling, Gene Frequency, Genotype, Haplotypes, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Alleles, Ethnic Groups, Genome-Wide Association Study, Genetic Loci, Genetic Association Studies, DNA Copy Number Variations, FCGR polymorphism, Fc-gamma receptor, Kawasaki disease, immunogenetics, linkage disequilibrium, Receptors, IgG, Polymorphism, Single Nucleotide, Immunology, Medical Microbiology
Abstract

The human Fc-gamma receptors (FcγRs) link adaptive and innate immunity by binding immunoglobulin G (IgG). All human low-affinity FcγRs are encoded by the FCGR2/3 locus containing functional single nucleotide polymorphisms (SNPs) and gene copy number variants. This locus is notoriously difficult to genotype and high-throughput methods commonly used focus on only a few SNPs. We performed multiplex ligation-dependent probe amplification for all relevant genetic variations at the FCGR2/3 locus in >4,000 individuals to define linkage disequilibrium (LD) and allele frequencies in different populations. Strong LD and extensive ethnic variation in allele frequencies was found across the locus. LD was strongest for the FCGR2C-ORF haplotype (rs759550223+rs76277413), which leads to expression of FcγRIIc. In Europeans, the FCGR2C-ORF haplotype showed strong LD with, among others, rs201218628 (FCGR2A-Q27W, r 2 = 0.63). LD between these two variants was weaker (r 2 = 0.17) in Africans, whereas the FCGR2C-ORF haplotype was nearly absent in Asians (minor allele frequency

Published
2019

8. Analysis of clinically relevant variants from ancestrally diverse Asian genomes

Author

Chan, Sock Hoai, Bylstra, Yasmin, Teo, Jing Xian, Kuan, Jyn Ling, Bertin, Nicolas, Gonzalez-Porta, Mar, Hebrard, Maxime, Tirado-Magallanes, Roberto, Tan, Joanna Hui Juan, Jeyakani, Justin, Li, Zhihui, Chai, Jin Fang, Chong, Yap Seng, Davila, Sonia, Goh, Liuh Ling, Lee, Eng Sing, Wong, Eleanor, Wong, Tien Yin, Prabhakar, Shyam, Liu, Jianjun, Cheng, Ching-Yu, Eisenhaber, Birgit, Karnani, Neerja, Leong, Khai Pang, Sim, Xueling, Yeo, Khung Keong, Chambers, John C., Tai, E-Shyong, Tan, Patrick, Jamuar, Saumya S., Ngeow, Joanne, and Lim, Weng Khong

Published
2022
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10. Data Mining of Electronic Health Records to Identify Undiagnosed Patients with Rare Genetic Diseases

Author

Moynihan, Daniel, primary, Monaco, Sean, additional, Ting, Teck Wah, additional, Narasimhalu, Kaavya, additional, Hsieh, Jenny, additional, Kam, Sylvia, additional, Lim, Jiin Ying, additional, Lim, Weng Khong, additional, Davila, Sonia, additional, Bylstra, Yasmin, additional, Balakrishnan, Iswaree Devi, additional, Heng, Mark, additional, Chia, Elian, additional, Yeo, Khung Keong, additional, Goh, Bee Keow, additional, Gupta, Ritu, additional, Tan, Tele, additional, Baynam, Gareth, additional, and Jamuar, Saumya Shekhar, additional

Published
2023
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11. Low frequency variants associated with leukocyte telomere length in the Singapore Chinese population

Author

Chang, Xuling, Gurung, Resham L., Wang, Ling, Jin, Aizhen, Li, Zheng, Wang, Renwei, Beckman, Kenneth B., Adams-Haduch, Jennifer, Meah, Wee Yang, Sim, Kar Seng, Lim, Weng Khong, Davila, Sonia, Tan, Patrick, Teo, Jing Xian, Yeo, Khung Keong, M., Yiamunaa, Liu, Sylvia, Lim, Su Chi, Liu, Jianjun, van Dam, Rob M., Friedlander, Yechiel, Koh, Woon-Puay, Yuan, Jian-Min, Khor, Chiea Chuen, Heng, Chew-Kiat, and Dorajoo, Rajkumar

Published
2021
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14. Host gene expression signatures to identify infection type and organ dysfunction in children evaluated for sepsis: a multicentre cohort study

Author

Schlapbach, Luregn J, Ganesamoorthy, Devika, Wilson, Clare, Raman, Sainath, George, Shane, Snelling, Peter J, Phillips, Natalie, Irwin, Adam, Sharp, Natalie, Le Marsney, Renate, Chavan, Arjun, Hempenstall, Allison, Bialasiewicz, Seweryn, MacDonald, Anna D, Grimwood, Keith, Kling, Jessica C, McPherson, Stephen J, Blumenthal, Antje, Kaforou, Myrsini, Levin, Michael, Herberg, Jethro A, Gibbons, Kristen S, Coin, Lachlan J M, Levin, Michael, Coin, Lachlan, Gormley, Stuart, Hamilton, Shea, Hoggart, Clive, Kaforou, Myrsini, Sancho-Shimizu, Vanessa, Wright, Victoria, Abdulla, Amina, Agapow, Paul, Bartlett, Maeve, Eleftherohorinou, Hariklia, Galassini, Rachel, Inwald, David, Mashbat, Meg, Menikou, Stephanie, Mustafa, Sobia, Nadel, Simon, Rahman, Rahmeen, Shailes, Hannah, Thakker, Clare, Bokhandi, S., Power, Sue, Barham, Heather, Pathan, N., Ridout, Jenna, White, Deborah, Thurston, Sarah, Faust, S., Patel, S., McCorkell, Jenni, Davies, P., Crate, Lindsey, Navarra, Helen, Carter, Stephanie, Ramaiah, R., Patel, Rekha, Tuffrey, Catherine, Gribbin, Andrew, McCready, Sharon, Peters, Mark, Hardy, Katie, Standing, Fran, O'Neill, Lauren, Abelake, Eugenia, Deep, Akash, Nsirim, Eniola, Pollard, Andrew, Willis, Louise, Young, Zoe, Royad, C., White, Sonia, Fortune, Peter-Marc, Hudnott, Phil, Martinón-Torres, Federico, Salas, Antonio, Álvez González, Fernando, Barral-Arca, Ruth, Cebey-López, Miriam, Curras-Tuala, María José, García, Natalia, García Vicente, Luisa, Gómez-Carballa, Alberto, Gómez Rial, Jose, Grela Beiroa, Andrea, Justicia Grande, Antonio, Leboráns Iglesias, Pilar, Martínez Santos, Alba Elena, Martinón-Torres, Nazareth, Martinón Sánchez, José María, Morillo Gutiérrez, Beatriz, Mosquera Pérez, Belén, Obando Pacheco, Pablo, Pardo-Seco, Jacobo, Pischedda, Sara, Rivero-Calle, Irene, Rodríguez-Tenreiro, Carmen, Redondo-Collazo, Lorenzo, Salas Ellacuriaga, Antonio, Fernández, Sonia Serén, del Sol Porto Silva, María, Vega, Ana, Vilanova Trillo, Lucía, Reyes, Susana Beatriz, Cruz León León, María, Navarro Mingorance, Álvaro, Gabaldó Barrio, Xavier, Oñate Vergara, Eider, Concha Torre, Andrés, Vivanco, Ana, Fernández, Reyes, Giménez Sánchez, Francisco, Sánchez Forte, Miguel, Rojo, Pablo, Contreras, J. Ruiz, Palacios, Alba, Epalza Ibarrondo, Cristina, Fernández Cooke, Elizabeth, Navarro, Marisa, Álvarez Álvarez, Cristina, José Lozano, María, Carreras, Eduardo, Brió Sanagustín, Sonia, Neth, Olaf, Martínez Padilla, Mª del Carmen, Prieto Tato, Luis Manuel, Guillén, Sara, Fernández Silveira, Laura, Moreno, David, de Groot, R., Tutu van Furth, A.M., van der Flier, M., Boeddha, N.P., Driessen, G.J.A., Emonts, M., Hazelzet, J.A., Kuijpers, T.W., Pajkrt, D., Sanders, E.A.M., van de Beek, D., van der Ende, A., Philipsen, H.L.A., Adeel, A.O.A., Breukels, M.A., Brinkman, D.M.C., de Korte, C.C.M.M., de Vries, E., de Waal, W.J., Dekkers, R., Dings-Lammertink, A., Doedens, R.A., Donker, A.E., Dousma, M., Faber, T.E., Gerrits, G.P.J.M., Gerver, J.A.M., Heidema, J., Homan-van der Veen, J., Jacobs, M.A.M., Jansen, N.J.G., Kawczynski, P., Klucovska, K., Kneyber, M.C.J., Koopman-Keemink, Y., Langenhorst, V.J., Leusink, J., Loza, B.F., Merth, I.T., Miedema, C.J., Neeleman, C., Noordzij, J.G., Obihara, C.C., van Overbeek- van Gils, A.L.T., Poortman, G.H., Potgieter, S.T., Potjewijd, J., Rosias, P.P.R., Sprong, T., ten Tussher, G.W., Thio, B.J., Tramper-Stranders, G.A., van Deuren, M., van der Meer, H., van Kuppevelt, A.J.M., van Wermeskerken, A.M., Verwijs, W.A., Wolfs, T.F.W., Schlapbach, Luregn J., Agyeman, Philipp, Aebi, Christoph, Giannoni, Eric, Stocker, Martin, Posfay-Barbe, Klara M., Heininger, Ulrich, Bernhard-Stirnemann, Sara, Niederer-Loher, Anita, Kahlert, Christian, Hasters, Paul, Relly, Christa, Baer, Walter, Berger, Christoph, Carrol, Enitan D., Paulus, Stéphane, Frederick, Hannah, Jennings, Rebecca, Johnston, Joanne, Kenwright, Rhian, Fink, Colin G, Pinnock, Elli, Emonts, Marieke, Agbeko, Rachel, Anderson, Suzanne, Secka, Fatou, Bojang, Kalifa, Sarr, Isatou, Kebbeh, Ngange, Sey, Gibbi, Saidykhan, Momodou, Cole, Fatoumata, Thomas, Gilleh, Antonio, Martin, Zenz, Werner, Kohlfürst, Daniela S., Binder, Alexander, Schweintzger, Nina A., Sagmeister, Manfred, Baumgart, Hinrich, Baumgartner, Markus, Behrends, Uta, Biebl, Ariane, Birnbacher, Robert, Blanke, Jan-Gerd, Boelke, Carsten, Breuling, Kai, Brunner, Jürgen, Buller, Maria, Dahlem, Peter, Dietrich, Beate, Eber, Ernst, Elias, Johannes, Emhofer, Josef, Etschmaier, Rosa, Farr, Sebastian, Girtler, Ylenia, Grigorow, Irina, Heimann, Konrad, Ihm, Ulrike, Jaros, Zdenek, Kalhoff, Hermann, Kaulfersch, Wilhelm, Kemen, Christoph, Klocker, Nina, Köster, Bernhard, Kohlmaier, Benno, Komini, Eleni, Kramer, Lydia, Neubert, Antje, Ortner, Daniel, Pescollderungg, Lydia, Pfurtscheller, Klaus, Reiter, Karl, Ristic, Goran, Rödl, Siegfried, Sellner, Andrea, Sonnleitner, Astrid, Sperl, Matthias, Stelzl, Wolfgang, Till, Holger, Trobisch, Andreas, Vierzig, Anne, Vogel, Ulrich, Weingarten, Christina, Welke, Stefanie, Wimmer, Andreas, Wintergerst, Uwe, Wüller, Daniel, Zaunschirm, Andrew, Ziuraite, Ieva, Žukovskaja, Veslava, Hibberd, Martin L., Davila, Sonia, Delany, Isabel, Schlapbach, Luregn J, Raman, Sainath, Sharp, Nathalie, Phillips, Natalie, Irwin, Adam, Balch, Ross, Harley, Amanda, Johnson, Kerry, Sever, Zoe, George, Shane, Grimwood, Keith, Snelling, Peter J, Chavan, Arjun, Kitcatt, Eleanor, Lawton, Luke, Hempenstall, Allison, Pilot, Pelista, Gibbons, Kristen S, Le Marsney, Renate, Blumenthal, Antje, Ganesamoorthy, Devika, Pardo, Carolyn, Kling, Jessica, McPherson, Stephen, MacDonald, Anna D, Bialasiewicz, Seweryn, Pham, Trang, and Coin, Lachlan

Abstract

Sepsis is defined as dysregulated host response to infection that leads to life-threatening organ dysfunction. Biomarkers characterising the dysregulated host response in sepsis are lacking. We aimed to develop host gene expression signatures to predict organ dysfunction in children with bacterial or viral infection.

Published
2024
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15. Cluster analysis and visualisation of electronic health records data to identify undiagnosed patients with rare genetic diseases.

Author

Moynihan, Daniel, Monaco, Sean, Ting, Teck Wah, Narasimhalu, Kaavya, Hsieh, Jenny, Kam, Sylvia, Lim, Jiin Ying, Lim, Weng Khong, Davila, Sonia, Bylstra, Yasmin, Balakrishnan, Iswaree Devi, Heng, Mark, Chia, Elian, Yeo, Khung Keong, Goh, Bee Keow, Gupta, Ritu, Tan, Tele, Baynam, Gareth, and Jamuar, Saumya Shekhar

Abstract

Rare genetic diseases affect 5–8% of the population but are often undiagnosed or misdiagnosed. Electronic health records (EHR) contain large amounts of data, which provide opportunities for analysing and mining. Data mining, in the form of cluster analysis and visualisation, was performed on a database containing deidentified health records of 1.28 million patients across 3 major hospitals in Singapore, in a bid to improve the diagnostic process for patients who are living with an undiagnosed rare disease, specifically focusing on Fabry Disease and Familial Hypercholesterolaemia (FH). On a baseline of 4 patients, we identified 2 additional patients with potential diagnosis of Fabry disease, suggesting a potential 50% increase in diagnosis. Similarly, we identified > 12,000 individuals who fulfil the clinical and laboratory criteria for FH but had not been diagnosed previously. This proof-of-concept study showed that it is possible to perform mining on EHR data albeit with some challenges and limitations. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Replication and meta-analysis of GWAS identified susceptibility loci in Kawasaki disease confirm the importance of B lymphoid tyrosine kinase (BLK) in disease susceptibility.

Author

Chang, Chia-Jung, Kuo, Ho-Chang, Chang, Jeng-Sheng, Lee, Jong-Keuk, Tsai, Fuu-Jen, Khor, Chiea Chuen, Chang, Li-Ching, Chen, Shih-Ping, Ko, Tai-Ming, Liu, Yi-Min, Chen, Ying-Ju, Hong, Young Mi, Jang, Gi Young, Hibberd, Martin L, Kuijpers, Taco, Burgner, David, Levin, Michael, Burns, Jane C, Davila, Sonia, International Kawasaki Disease Genetics Consortium, Korean Kawasaki Disease Genetics Consortium, Taiwan Kawasaki Disease Genetics Consortium, Chen, Yuan-Tsong, Chen, Chien-Hsiun, Wu, Jer-Yuarn, and Lee, Yi-Ching

Subjects
International Kawasaki Disease Genetics Consortium, Korean Kawasaki Disease Genetics Consortium, Taiwan Kawasaki Disease Genetics Consortium, B-Lymphocytes, Cell Line, Transformed, Humans, Mucocutaneous Lymph Node Syndrome, Genetic Predisposition to Disease, src-Family Kinases, Cohort Studies, Reproducibility of Results, Gene Expression Regulation, Enzymologic, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Asian Continental Ancestry Group, European Continental Ancestry Group, Taiwan, Promoter Regions, Genetic, Genome-Wide Association Study, Genetic Loci, Republic of Korea, General Science & Technology
Abstract

The BLK and CD40 loci have been associated with Kawasaki disease (KD) in two genome-wide association studies (GWAS) conducted in a Taiwanese population of Han Chinese ancestry (Taiwanese) and in Japanese cohorts. Here we build on these findings with replication studies of the BLK and CD40 loci in populations of Korean and European descent. The BLK region was significantly associated with KD susceptibility in both populations. Within the BLK gene the rs2736340-located linkage disequilibrium (LD ) comprising the promoter and first intron was strongly associated with KD, with the combined results of Asian studies including Taiwanese, Japanese, and Korean populations (2,539 KD patients and 7,021 controls) providing very compelling evidence of association (rs2736340, OR = 1.498, 1.354-1.657; P = 4.74×10(-31)). We determined the percentage of B cells present in the peripheral blood mononuclear cell (PBMC) population and the expression of BLK in the peripheral blood leukocytes (leukocytes) of KD patients during the acute and convalescent stages. The percentage of B cells in the PBMC population and the expression of BLK in leukocytes were induced in patients in the acute stage of KD. In B cell lines derived from KD patients, and in purified B cells from KD patients obtained during the acute stage, those with the risk allele of rs2736340 expressed significantly lower levels of BLK. These results suggest that peripheral B cells play a pathogenic role during the acute stage of KD. Decreased BLK expression in peripheral blood B cells may alter B cell function and predispose individuals to KD. These associative data suggest a role for B cells during acute KD. Understanding the functional implications may facilitate the development of B cell-mediated therapy for KD.

Published
2013

17. ALPK1 missense pathogenic variant in five families leads to ROSAH syndrome, an ocular multisystem autosomal dominant disorder

Author

Williams, Lloyd B., Javed, Asif, Sabri, Amin, Morgan, Denise J., Huff, Chad D., Grigg, John R., Heng, Xiu Ting, Khng, Alexis J., Hollink, Iris H. I. M., Morrison, Margaux A., Owen, Leah A., Anderson, Katherine, Kinard, Krista, Greenlees, Rebecca, Novacic, Danica, Nida Sen, H., Zein, Wadih M., Rodgers, George M., Vitale, Albert T., Haider, Neena B., Hillmer, Axel M., Ng, Pauline C., Shankaracharya, Cheng, Anson, Zheng, Linda, Gillies, Mark C., van Slegtenhorst, Marjon, van Hagen, P. Martin, Missotten, Tom O. A. R., Farley, Gary L., Polo, Michael, Malatack, James, Curtin, Julie, Martin, Frank, Arbuckle, Susan, Alexander, Stephen I., Chircop, Megan, Davila, Sonia, Digre, Kathleen B., Jamieson, Robyn V., and DeAngelis, Margaret M.

Published
2019
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18. Matrix metalloproteinase haplotypes associated with coronary artery aneurysm formation in patients with Kawasaki disease

Author

Shimizu, Chisato, Matsubara, Tomoyo, Onouchi, Yoshihiro, Jain, Sonia, Sun, Shelly, Nievergelt, Caroline M, Shike, Hiroko, Brophy, Victoria H, Takegawa, Tsuyoshi, Furukawa, Susumu, Akagi, Teiji, Newburger, Jane W, Baker, Annette L, Burgner, David, Hibberd, Martin L, Davila, Sonia, Levin, Michael, Mamtani, Manju, He, Weijing, Ahuja, Sunil K, and Burns, Jane C

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Heart Disease, Heart Disease - Coronary Heart Disease, Autoimmune Disease, Cardiovascular, Clinical Research, Atherosclerosis, 2.1 Biological and endogenous factors, Aetiology, Case-Control Studies, Child, Coronary Aneurysm, Female, Haplotypes, Humans, Male, Matrix Metalloproteinases, Mucocutaneous Lymph Node Syndrome, Multigene Family, Polymorphism, Single Nucleotide, Clinical Sciences, Genetics & Heredity, Clinical sciences
Abstract

Aneurysms of the vascular wall represent a final common pathway for a number of inflammatory processes, including atherosclerosis and idiopathic vasculitis syndromes. Kawasaki disease (KD) is an acute, self-limited vasculitis in children and the leading cause of acquired coronary artery aneurysms. We sought to identify shared molecular mechanisms of aneurysm formation by genotyping eight polymorphisms in matrix metalloproteinase (MMP)-1, 3, 7, 12 and 13 in the gene cluster on Chr.11q22, whose gene products have been implicated in aneurysm formation or are known to have elastase activity. We genotyped 482 US-UK KD patients (aneurysm+: n=111, aneurysm-: n=371) and tested our findings in an independent cohort of 200 Japanese KD patients (aneurysm+: n=58, aneurysm-: n=142). Analysis of the five MMP genes identified modest trends in allele and genotype frequencies for MMP-3 rs3025058 (-/T) and haplotypes containing MMP-3 rs3025058 (-/T) and MMP-12 rs2276109 (A/G) (nominal P=2 to 4 × 10(-5)) that conferred increased risk of aneurysm formation in US-UK subjects. This finding was validated in Japanese subjects and suggests the importance of this locus in aneurysm formation in children with KD. The region encompassing these risk haplotypes is a prime candidate for resequencing to look for rare genetic variation that may influence aneurysm formation.

Published
2010

19. A genome-wide association study identifies novel and functionally related susceptibility Loci for Kawasaki disease.

Author

Burgner, David, Davila, Sonia, Breunis, Willemijn B, Ng, Sarah B, Li, Yi, Bonnard, Carine, Ling, Ling, Wright, Victoria J, Thalamuthu, Anbupalam, Odam, Miranda, Shimizu, Chisato, Burns, Jane C, Levin, Michael, Kuijpers, Taco W, Hibberd, Martin L, and International Kawasaki Disease Genetics Consortium

Subjects
International Kawasaki Disease Genetics Consortium, Humans, Mucocutaneous Lymph Node Syndrome, Genetic Predisposition to Disease, Oligonucleotide Array Sequence Analysis, Chi-Square Distribution, Case-Control Studies, Chromosome Mapping, Gene Expression, Gene Frequency, Haplotypes, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genes, Databases, Genetic, Adult, Child, Ethnic Groups, Gene Regulatory Networks, Genome-Wide Association Study, Databases, Genetic, Polymorphism, Single Nucleotide, Genetics, Developmental Biology
Abstract

Kawasaki disease (KD) is a pediatric vasculitis that damages the coronary arteries in 25% of untreated and approximately 5% of treated children. Epidemiologic data suggest that KD is triggered by unidentified infection(s) in genetically susceptible children. To investigate genetic determinants of KD susceptibility, we performed a genome-wide association study (GWAS) in 119 Caucasian KD cases and 135 matched controls with stringent correction for possible admixture, followed by replication in an independent cohort and subsequent fine-mapping, for a total of 893 KD cases plus population and family controls. Significant associations of 40 SNPs and six haplotypes, identifying 31 genes, were replicated in an independent cohort of 583 predominantly Caucasian KD families, with NAALADL2 (rs17531088, p(combined) = 1.13 x 10(-6)) and ZFHX3 (rs7199343, p(combined) = 2.37 x 10(-6)) most significantly associated. Sixteen associated variants with a minor allele frequency of >0.05 that lay within or close to known genes were fine-mapped with HapMap tagging SNPs in 781 KD cases, including 590 from the discovery and replication stages. Original or tagging SNPs in eight of these genes replicated the original findings, with seven genes having further significant markers in adjacent regions. In four genes (ZFHX3, NAALADL2, PPP1R14C, and TCP1), the neighboring markers were more significantly associated than the originally associated variants. Investigation of functional relationships between the eight fine-mapped genes using Ingenuity Pathway Analysis identified a single functional network (p = 10(-13)) containing five fine-mapped genes-LNX1, CAMK2D, ZFHX3, CSMD1, and TCP1-with functional relationships potentially related to inflammation, apoptosis, and cardiovascular pathology. Pair-wise blood transcript levels were measured during acute and convalescent KD for all fine-mapped genes, revealing a consistent trend of significantly reduced transcript levels prior to treatment. This is one of the first GWAS in an infectious disease. We have identified novel, plausible, and functionally related variants associated with KD susceptibility that may also be relevant to other cardiovascular diseases.

Published
2009

20. Genetic association and expression studies indicate a role of toll-like receptor 8 in pulmonary tuberculosis.

Author

Davila, Sonia, Hibberd, Martin L, Hari Dass, Ranjeeta, Wong, Hazel EE, Sahiratmadja, Edhyana, Bonnard, Carine, Alisjahbana, Bachti, Szeszko, Jeffrey S, Balabanova, Yanina, Drobniewski, Francis, van Crevel, Reinout, van de Vosse, Esther, Nejentsev, Sergey, Ottenhoff, Tom HM, and Seielstad, Mark

Subjects
Cell Line, Chromosomes, Human, X, Humans, Tuberculosis, Pulmonary, Genetic Predisposition to Disease, RNA, Messenger, Case-Control Studies, Gene Expression, Sex Characteristics, Gene Frequency, Haplotypes, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Adolescent, Adult, Aged, Aged, 80 and over, Middle Aged, Indonesia, Female, Male, Toll-Like Receptor 8, and over, Chromosomes, Human, X, Polymorphism, Single Nucleotide, RNA, Messenger, Tuberculosis, Pulmonary, Genetics, Developmental Biology
Abstract

Despite high rates of exposure, only 5-10% of people infected with Mycobacterium tuberculosis will develop active tuberculosis (TB) disease, suggesting a significant role for genetic variation in the human immune response to this infection. Here, we studied TB association and expression of 18 genes involved in the Toll-like receptor (TLR) pathways. Initially, we genotyped 149 sequence polymorphisms in 375 pulmonary TB patients and 387 controls from Indonesia. We found that four polymorphisms in the TLR8 gene on chromosome X showed evidence of association with TB susceptibility in males, including a non-synonymous polymorphism rs3764880 (Met1Val; P = 0.007, odds ratio (OR) = 1.8, 95% c.i. = 1.2-2.7). We genotyped these four TLR8 polymorphisms in an independent collection of 1,837 pulmonary TB patients and 1,779 controls from Russia and again found evidence of association in males (for rs3764880 P = 0.03, OR = 1.2, 95% c.i. = 1.02-1.48). Combined evidence for association is P = 1.2x10(-3)-6x10(-4). In addition, a quantitative PCR analysis indicated that TLR8 transcript levels are significantly up-regulated in patients during the acute phase of disease (P = 9.36x10(-5)), relative to baseline levels following successful chemotherapy. A marked increase in TLR8 protein expression was also observed directly in differentiated macrophages upon infection with M. bovis bacille Calmette-Guérin (BCG). Taken together, our results provide evidence, for the first time, of a role for the TLR8 gene in susceptibility to pulmonary TB across different populations.

Published
2008

23. Variation in CFHR3 determines susceptibility to meningococcal disease by controlling factor H concentrations

Author

Kumar, Vikrant, Pouw, Richard B, Autio, Matias I, Sagmeister, Manfred G, Phua, Zai Yang, Borghini, Lisa, Wright, Victoria J, Hoggart, Clive, Pan, Bangfen, Tan, Antson Kiat Yee, Binder, Alexander, Brouwer, Mieke C, Pinnock, Ellie, De Groot, Ronald, Hazelzet, Jan, Emonts, Marieke, Van Der Flier, Michiel, Reiter, Karl, Nöthen, Markus M, Hoffmann, Per, EUCLIDS consortium, Schlapbach, Luregn J, Bellos, Evangelos, Anderson, Suzanne, Secka, Fatou, Martinón-Torres, Federico, Salas, Antonio, Fink, Colin, Carrol, Enitan D, Pollard, Andrew J, Coin, Lachlan J, Zenz, Werner, Wouters, Diana, Ang, Lay Teng, Hibberd, Martin L, Levin, Michael, Kuijpers, Taco W, Davila, Sonia, consortium, EUCLIDS, Pediatrics, Paediatric Infectious Diseases / Rheumatology / Immunology, Landsteiner Laboratory, and ARD - Amsterdam Reproduction and Development

Subjects
CFHR3, Genotype, Meningococcal disease, infectious disease, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Complement, in-depth sequencing, Blood Proteins, Complement System Proteins, Neisseria meningitidis, factor H, QR, Meningococcal Infections, Factor H-related protein, genotyping, Complement Factor H, Genetics, Humans, CFH, Genetic Predisposition to Disease, Genetics (clinical), RC
Abstract

Neisseria meningitidis protects itself from complement-mediated killing by binding complement factor H (FH). Previous studies associated susceptibility to meningococcal disease (MD) with variation in CFH, but the causal variants and underlying mechanism remained unknown. Here we attempted to define the association more accurately by sequencing the CFH-CFHR locus and imputing missing genotypes in previously obtained GWAS datasets of MD-affected individuals of European ancestry and matched controls. We identified a CFHR3 SNP that provides protection from MD (rs75703017, p value = 1.1 × 10−16) by decreasing the concentration of FH in the blood (p value = 1.4 × 10−11). We subsequently used dual-luciferase studies and CRISPR gene editing to establish that deletion of rs75703017 increased FH expression in hepatocyte by preventing promotor inhibition. Our data suggest that reduced concentrations of FH in the blood confer protection from MD; with reduced access to FH, N. meningitidis is less able to shield itself from complement-mediated killing.

Published
2022

25. Genomic landscape of drug binding and pharmacogenetic variation across diverse populations using SNPdrug3D

Author

Maurer-Stroh, Sebastian, primary, Malik, Ashar, additional, Kenanov, Dimitar, additional, Chong, Cheng-Shoong, additional, Ozturk, Mert Burak, additional, Hebrard, Maxime, additional, Ho, Ying Swan, additional, Wang, Zhenxun, additional, Limviphuvadh, Vachiranee, additional, Miyajima, Jhoann, additional, Magallanes, Roberto, additional, Sim, Xueling, additional, Chai, Jin Fang, additional, Davila, Sonia, additional, Yeo, Khung Keong, additional, Leong, Khai Pang, additional, Goh, Liuh Ling, additional, Karnani, Neerja, additional, Eriksson, Johan Gunnar, additional, Cheng, Ching-Yu, additional, Wong, Tien, additional, Loh, Marie, additional, Dalan, Rinkoo, additional, Khor, Chiea Chuen, additional, Chew, Guo-Liang, additional, Lim, Weng Khong, additional, Ngeow, Joanne, additional, Chambers, John, additional, Tai, E Shyong, additional, Bertin, Nicolas, additional, Tan, Chris Soon Heng, additional, Koh, Judice, additional, Tan, Patrick, additional, and Verma, Chandra, additional

Published
2023
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27. Identification of regulatory variants associated with genetic susceptibility to meningococcal disease

Author

Borghini, Lisa, Png, Eileen, Binder, Alexander, Wright, Victoria J., Pinnock, Ellie, de Groot, Ronald, Hazelzet, Jan, Emonts, Marieke, Van der Flier, Michiel, Schlapbach, Luregn J., Anderson, Suzanne, Secka, Fatou, Salas, Antonio, Fink, Colin, Carrol, Enitan D., Pollard, Andrew J., Coin, Lachlan J., Kuijpers, Taco W., Martinon-Torres, Federico, Zenz, Werner, Levin, Michael, Hibberd, Martin L., Davila, Sonia, and EUCLIDS consortium

Published
2019
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29. RAPTOR: A Five-Safes approach to a secure, cloud native and serverless genomics data repository

Author

Shih, Chih Chuan, primary, Chen, Jieqi, additional, Lee, Ai Shan, additional, Bertin, Nicolas, additional, Hebrard, Maxime, additional, Khor, Chiea Chuen, additional, Li, Zheng, additional, Tan, Joanna Hui Juan, additional, Meah, Wee Yang, additional, Peh, Su Qin, additional, Mok, Shi Qi, additional, Sim, Kar Seng, additional, Liu, Jianjun, additional, Wang, Ling, additional, Wong, Eleanor, additional, Li, Jingmei, additional, Tin, Aung, additional, Cheng, Ching-Yu, additional, Heng, Chew-Kiat, additional, Yuan, Jian-Min, additional, Koh, Woon-Puay, additional, Saw, Seang Mei, additional, Friedlander, Yechiel, additional, Sim, Xueling, additional, Chai, Jin Fang, additional, Chong, Yap Seng, additional, Davila, Sonia, additional, Goh, Liuh Ling, additional, Lee, Eng Sing, additional, Wong, Tien Yin, additional, Karnani, Neerja, additional, Leong, Khai Pang, additional, Yeo, Khung Keong, additional, Chambers, John C, additional, Lim, Su Chi, additional, Goh, Rick Siow Mong, additional, Tan, Patrick, additional, and Dorajoo, Rajkumar, additional

Published
2022
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30. High-Resolution Digital Phenotypes From Consumer Wearables and Their Applications in Machine Learning of Cardiometabolic Risk Markers: Cohort Study

Author

Zhou, Weizhuang, primary, Chan, Yu En, additional, Foo, Chuan Sheng, additional, Zhang, Jingxian, additional, Teo, Jing Xian, additional, Davila, Sonia, additional, Huang, Weiting, additional, Yap, Jonathan, additional, Cook, Stuart, additional, Tan, Patrick, additional, Chin, Calvin Woon-Loong, additional, Yeo, Khung Keong, additional, Lim, Weng Khong, additional, and Krishnaswamy, Pavitra, additional

Published
2022
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31. Phagosomal RNA sensing through TLR8 controls susceptibility to tuberculosis

Author

Maserumule, Charlotte, primary, Passemar, Charlotte, additional, Oh, Olivia S H, additional, Hegyi, Kriztina, additional, Brown, Karen, additional, Weimann, Aaron, additional, Dinan, Adam, additional, Davila, Sonia, additional, Klapholz, Catherine, additional, Bryant, Josephine, additional, Verma, Deepshikha, additional, Gadwa, Jacob, additional, Krishnananthasivam, Shivankari, additional, Vongtongsalee, Kridakorn, additional, Kendall, Edward, additional, Trelles, Andres, additional, Hibberd, Martin L, additional, Prados-Rosales, Rafael, additional, Andi, Kaliappan, additional, Kumar, S Siva, additional, Ordway, Diane, additional, MacAry, Paul A, additional, and Floto, R. Andres, additional

Published
2022
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32. Angiomotin mutation causes glomerulopathy and renal cysts by upregulating hepatocyte nuclear factor transcriptional activity

Author

Zhang, Yaochun, primary, Lu, Liangjian, additional, Hu, Zhenhua, additional, Dai, Yu, additional, Ahmad, Nurul Jannah Binti, additional, Ng, Jun Li, additional, Chan, Chang Yien, additional, Hossain, Md. Zakir, additional, Loh, Alwin Hwai Liang, additional, Ward, Jerrold M., additional, Tan, Puay Hoon, additional, Davila, Sonia, additional, Kumar, Vikrant, additional, Hunziker, Walter, additional, Lin, Haishu, additional, Yap, Hui Kim, additional, and Ng, Kar Hui, additional

Published
2022
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34. Acute to Subacute Atraumatic Entrapment Neuropathies in Patients With CMT1A: A Report of a Distinct Phenotypic Variant of CMT1A

Author

Chen, Zhiyong, primary, Saini, Monica, additional, Neo, Shermyn X. M., additional, Ng, Peng-Soon, additional, Koh, Jasmine S., additional, Prasad, Kalpana, additional, Verma, Kamal, additional, Davila, Sonia, additional, Lim, Weng Khong, additional, Phua, Ziqun, additional, Li, Michelle M., additional, Kang, Corrine, additional, Tay, Karine S. S., additional, and Chai, Josiah Y. H., additional

Published
2022
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36. High-Resolution Digital Phenotypes from Consumer Wearables Enhance Prediction of Cardiometabolic Risk Markers

Author

Zhou, Weizhuang, primary, Chan, Yu En, additional, Foo, Chuan Sheng, additional, Zhang, Jingxian, additional, Teo, Jing Xian, additional, Davila, Sonia, additional, Huang, Weiting, additional, Yap, Jonathan, additional, Cook, Stuart Alexander, additional, Tan, Patrick, additional, Chin, Calvin Woon-Loong, additional, Yeo, Khung Keong, additional, Lim, Weng Khong, additional, and Krishnaswamy, Pavitra, additional

Published
2021
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38. Additional file 1 of Family history assessment significantly enhances delivery of precision medicine in the genomics era

Author

Bylstra, Yasmin, Weng Khong Lim, Kam, Sylvia, Koei Wan Tham, R. Ryanne Wu, Teo, Jing Xian, Davila, Sonia, Jyn Ling Kuan, Sock Hoai Chan, Bertin, Nicolas, Yang, Cheng Xi, Rozen, Steve, Teh, Bin Tean, Khung Keong Yeo, Cook, Stuart Alexander, Saumya Shekhar Jamuar, Ginsburg, Geoffrey S., Orlando, Lori A., and Tan, Patrick

Abstract

Additional file 1: Table S1. Cancer gene panel. Fig. S1. Variant curation and classification flowchart. Fig. S2. Cancer prevalence amongst the 73 increased FH risk participants. Table S2. Overview of LP/P variants found in the FH not available and FH available groups. Table S3. LP/P variants found in the FH not available group. Table S4. Clinically actionable variants and associated family history in the increased FH risk cohort. Table S5. Variants of unknown significance and associated family history in the increased FH cohort.

Published
2021
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41. HPV Could be a Potential Factor of Survival in Laryngeal Cancer: a Preliminary Study in Mexican Patients

Author

Peralta, Raul, Garcia, Paola, Valdivia, Alejandra, Lopez, Arianna, Apresa, Teresa, Hernandez, Dulce M., Gallegos, Francisco, Alvarado-Cabrero, Isabel, Vargas-De-Leon, Cruz, Davila, Sonia, Romero, Pablo, and Salcedo, Mauricio

Subjects
Male, HPV, EGFR, Papillomavirus Infections, Middle Aged, Prognosis, ErbB Receptors, Survival Rate, DNA, Viral, Carcinoma, Squamous Cell, laryngeal cancer, Humans, Female, Laryngeal Neoplasms, Mexico, Papillomaviridae, Research Article, Follow-Up Studies
Abstract

Introduction: In Head and Neck (HN) cancer, the High-Risk Human Papillomavirus (hr HPV) infection has been associated in about 40% of these tumors. The hr HPV infection is one of the etiological factors of several epithelial tumors; however, its association with the prognosis has not yet been established for patients with Laryngeal Squamous Cell Carcinoma (LSCC). On the other hand, Epidermal Growth Factor Receptor (EGFR) is a molecular marker widely studied in cancer and its overexpression has been associated with poor prognosis in some types of cancer, including the HN cancer. In the present study, we analyzed EGFR expression and HPV detection in a cohort of Mexican patients with LSCC and define their association with clinical-pathological and survival parameters. Methods: EGFR expression analysis was performed by immunohistochemistry assay. A tissue array was constructed based on 30 paraffin-embedded tissue samples. HPV detection was performed by PCR. The results were then compared with the clinical-pathological variables and outcome measures (Kaplan Meier and Cox analysis). Results: High expression of EGFR was observed in 43% of the samples and 20% of HPV detection. The statistical analyses provided evidence of disassociation between clinical-pathological parameters and EGFR expression, but there was an association with poor prognosis. Interestingly, HPV detection is slightly associated with good prognosis. Conclusion: Both, EGFR overexpression and HPV presence could be associated with an unfavorable prognosis in patients with LSCC, independently of other clinical-pathological factors.

Published
2018

42. Mutations in PRKCSH cause isolated autosomal dominant polycystic liver disease

Author

Li, Airong, Davila, Sonia, Furu, Laszlo, Qian, Qi, Tian, Xin, Kamath, Patrick S., King, Bernard F., Torres, Vicente E., and Somlo, Stefan

Subjects
Cysts -- Physiological aspects, Cysts -- Genetic aspects, Liver diseases -- Physiological aspects, Liver diseases -- Genetic aspects, Biological sciences
Published
2003

45. Family History Assessment Significantly Enhances Delivery of Precision Medicine in the Genomics Era

Author

Bylstra, Yasmin, primary, Lim, Weng Khong, additional, Kam, Sylvia, additional, Tham, Koei Wan, additional, Wu, R. Ryanne, additional, Teo, Jing Xian, additional, Davila, Sonia, additional, Kuan, Jyn Ling, additional, Chan, Sock Hoai, additional, Bertin, Nicolas, additional, Yang, ChengXi, additional, Rozen, Steve, additional, Teh, Bin Tean, additional, Yeo, Khung Keong, additional, Cook, Stuart Alexander, additional, Orlando, Lori A., additional, Jamuar, Saumya Shekhar, additional, Ginsburg, Geoffrey S., additional, and Tan, Patrick, additional

Published
2020
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46. Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore

Author

Wu, Degang, primary, Dou, Jinzhuang, additional, Chai, Xiaoran, additional, Bellis, Claire, additional, Wilm, Andreas, additional, Shih, Chih Chuan, additional, Soon, Wendy Wei Jia, additional, Bertin, Nicolas, additional, Lin, Clarabelle Bitong, additional, Khor, Chiea Chuen, additional, DeGiorgio, Michael, additional, Cheng, Shanshan, additional, Bao, Li, additional, Karnani, Neerja, additional, Hwang, William Ying Khee, additional, Davila, Sonia, additional, Tan, Patrick, additional, Shabbir, Asim, additional, Moh, Angela, additional, Tan, Eng-King, additional, Foo, Jia Nee, additional, Goh, Liuh Ling, additional, Leong, Khai Pang, additional, Foo, Roger S.Y., additional, Lam, Carolyn Su Ping, additional, Richards, Arthur Mark, additional, Cheng, Ching-Yu, additional, Aung, Tin, additional, Wong, Tien Yin, additional, Ng, Huck Hui, additional, Liu, Jianjun, additional, Wang, Chaolong, additional, Ackers-Johnson, Matthew Andrew, additional, Aliwarga, Edita, additional, Ban, Kenneth Hon Kim, additional, Bertrand, Denis, additional, Chambers, John C., additional, Chan, Dana Leng Hui, additional, Chan, Cheryl Xue Li, additional, Chee, Miao Li, additional, Chee, Miao Ling, additional, Chen, Pauline, additional, Chen, Yunxin, additional, Chew, Elaine Guo Yan, additional, Chew, Wen Jie, additional, Chiam, Lynn Hui Yun, additional, Chong, Jenny Pek Ching, additional, Chua, Ivan, additional, Cook, Stuart A., additional, Dai, Wei, additional, Dorajoo, Rajkumar, additional, Foo, Chuan-Sheng, additional, Goh, Rick Siow Mong, additional, Hillmer, Axel M., additional, Irwan, Ishak D., additional, Jaufeerally, Fazlur, additional, Javed, Asif, additional, Jeyakani, Justin, additional, Koh, John Tat Hung, additional, Koh, Jia Yu, additional, Krishnaswamy, Pavitra, additional, Kuan, Jyn Ling, additional, Kumari, Neelam, additional, Lee, Ai Shan, additional, Lee, Seow Eng, additional, Lee, Sheldon, additional, Lee, Yen Ling, additional, Leong, See Ting, additional, Li, Zheng, additional, Li, Peter Yiqing, additional, Liew, Jun Xian, additional, Liew, Oi Wah, additional, Lim, Su Chi, additional, Lim, Weng Khong, additional, Lim, Chia Wei, additional, Lim, Tingsen Benson, additional, Lim, Choon Kiat, additional, Loh, Seet Yoong, additional, Lok, Au Wing, additional, Chin, Calvin W.L., additional, Majithia, Shivani, additional, Maurer-Stroh, Sebastian, additional, Meah, Wee Yang, additional, Mok, Shi Qi, additional, Nargarajan, Niranjan, additional, Ng, Pauline, additional, Ng, Sarah B., additional, Ng, Zhenyuan, additional, Ng, Jessica Yan Xia, additional, Ng, Ebonne, additional, Ng, Shi Ling, additional, Nusinovici, Simon, additional, Ong, Chin Thing, additional, Pan, Bangfen, additional, Pedergnana, Vincent, additional, Poh, Stanley, additional, Prabhakar, Shyam, additional, Prakash, Kumar M., additional, Quek, Ivy, additional, Sabanayagam, Charumathi, additional, See, Wei Qiang, additional, Sia, Yee Yen, additional, Sim, Xueling, additional, Sim, Wey Cheng, additional, So, Jimmy, additional, Soon, Dinna K.N., additional, Tai, E. Shyong, additional, Tan, Nicholas Y., additional, Tan, Louis C.S., additional, Tan, Hong Chang, additional, Tan, Wilson Lek Wen, additional, Tandiono, Moses, additional, Tay, Amanda, additional, Thakur, Sahil, additional, Tham, Yih Chung, additional, Tiang, Zenia, additional, Toh, Grace Li-Xian, additional, Tsai, Pi Kuang, additional, Veeravalli, Lavanya, additional, Verma, Chandra S., additional, Wang, Ling, additional, Wang, Min Rui, additional, Wong, Wing-Cheong, additional, Xie, Zhicheng, additional, Yeo, Khung Keong, additional, Zhang, Liang, additional, Zhai, Weiwei, additional, and Zhao, Yi, additional

Published
2019
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49. MOVERS

Author

Wenk, Markus and Davila, Sonia

Published
2004

50. Additional file 7: of Changes in H3K27ac following lipopolysaccharide stimulation of nasopharyngeal epithelial cells

Author

Borghini, Lisa, Hibberd, Martin, and Davila, Sonia

Abstract

RELA activation following LPS treatment and binding at super-enhancers. A: Detroit 562 cells were treated with LPS at 1 μg/mL or fresh medium (no treatment) for 2 h and nuclear protein were extracted to be used in NFkB p65 transcription factor assay. No binding sites (no BS), wild type NFkB binding sites (WT BS) or mutant NFkB binding sites (mutant BS) were added in solution into the wells to check for RELA specificity. B: The cells were treated similarly and RELA activation was investigated at different time points for an extended period of time. The two curves correspond to independent experiments (dup = duplicate). C: Distribution of the RELA signal in Control-only (grey) and LPS-only (orange) Super-enhancers identified from the H3K27ac ChIP-seq data. (PDF 318 kb)

Published
2018
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