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1. The Human Phenotype Ontology in 2021

Author

Köhler, Sebastian, Gargano, Michael, Matentzoglu, Nicolas, Carmody, Leigh C, Lewis-Smith, David, Vasilevsky, Nicole A, Danis, Daniel, Balagura, Ganna, Baynam, Gareth, Brower, Amy M, Callahan, Tiffany J, Chute, Christopher G, Est, Johanna L, Galer, Peter D, Ganesan, Shiva, Griese, Matthias, Haimel, Matthias, Pazmandi, Julia, Hanauer, Marc, Harris, Nomi L, Hartnett, Michael J, Hastreiter, Maximilian, Hauck, Fabian, He, Yongqun, Jeske, Tim, Kearney, Hugh, Kindle, Gerhard, Klein, Christoph, Knoflach, Katrin, Krause, Roland, Lagorce, David, McMurry, Julie A, Miller, Jillian A, Munoz-Torres, Monica C, Peters, Rebecca L, Rapp, Christina K, Rath, Ana M, Rind, Shahmir A, Rosenberg, Avi Z, Segal, Michael M, Seidel, Markus G, Smedley, Damian, Talmy, Tomer, Thomas, Yarlalu, Wiafe, Samuel A, Xian, Julie, Yüksel, Zafer, Helbig, Ingo, Mungall, Christopher J, Haendel, Melissa A, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Neurosciences, Neurodegenerative, Animals, Biological Ontologies, Computational Biology, Databases, Factual, Disease, Disease Models, Animal, Genome, Genotype, Humans, Infant, Newborn, International Cooperation, Internet, Neonatal Screening, Pharmacogenetics, Phenotype, Software, Terminology as Topic, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

Published
2021

6. Contributors

Author

Aaen, Gregory S., primary, Abend, Nicholas Scott, additional, Abou-Hamden, Amal, additional, Allen, Jeffrey C., additional, Amato, Anthony A., additional, Amlie-Lefond, Catherine, additional, Ashwal, Stephen, additional, Bailey, Russell C., additional, Bale, James F., additional, Banwell, Brenda, additional, Barañano, Kristin W., additional, Barkovich, A. James, additional, Barohn, Richard J., additional, Bartels, Ute K., additional, Bartnik-Olson, Brenda, additional, Barzilai, Ori, additional, Bassuk, Alexander, additional, Bearden, David R., additional, Ben-Sira, Liat, additional, Bernard, Timothy J., additional, Berry-Kravis, Elizabeth, additional, Beslow, Lauren A., additional, Biegel, Jaclyn A., additional, Billinghurst, Lori, additional, Birnbaum, Angela K., additional, Blackburn, Joanna S., additional, Bobowski, Nuala, additional, Boire, Adrienne, additional, Bönnemann, Carsten G., additional, Bonifacio, Sonia L., additional, Bonthius, Daniel J., additional, Borcherding, Breck, additional, Branchford, Brian R., additional, Brandsema, John, additional, Brennan, Kathryn M., additional, Brenton, J. Nicholas, additional, Brooks-Kayal, Amy R., additional, Brown, Lawrence W., additional, Buchalter, Jeffrey, additional, Camfield, Carol S., additional, Camfield, Peter R., additional, Campoy, Cristina, additional, Carpenter, Jessica L., additional, Chang, Taeun, additional, Chau, Vann, additional, Chi, Susan N., additional, Chiriboga, Claudia A., additional, Cho, Yoon-Jae, additional, Christian, Cindy W., additional, Chrestian, Nicholas, additional, Cilio, Maria Roberta, additional, Clark, Robin D., additional, Cohen, Bruce H., additional, Cohn, Ronald D., additional, Connolly, Anne M., additional, Constable, Todd, additional, Constantini, Shlomi, additional, Conway, Jeannine M., additional, Coulter, David L., additional, Cowan, Tina M., additional, Dale, Russell C., additional, Darbro, Benjamin, additional, Darras, Basil T., additional, Dastgir, Jahannaz, additional, De Meirleir, Linda, additional, De Vivo, Darryl C., additional, de Vries, Linda S., additional, Deisch, Jeremy K., additional, Deltenre, Paul, additional, Desai, Jay, additional, Descartes, Maria, additional, deVeber, Gabrielle, additional, Dhamne, Sameer C., additional, Diaz, Jullianne, additional, DiMauro, Salvatore, additional, Dobyns, William B., additional, Doherty, Dan, additional, Donner, Elizabeth J., additional, Dosenbach, Nico U.F., additional, Dowling, James J., additional, Drake, James M., additional, Ejerskov, Cecile, additional, Engel, Andrew G., additional, Enns, Gregory M., additional, Escolano-Margarit, María Victoria, additional, Etzion, Iris, additional, Fatemi, S. Ali, additional, Fehlings, Darcy L., additional, Feinberg, Michelle Lauren, additional, Ferriero, Donna M., additional, Filipek, Pauline A., additional, Finkel, Richard S., additional, Fisher, Paul G., additional, Flanigan, Kevin, additional, Foreman, Nicholas K., additional, Franco, Israel, additional, Frank, Yitzchak, additional, Fredrick, Douglas R., additional, Freeze, Hudson H., additional, Fuente-Mora, Cristina, additional, Furman, Joseph M., additional, Gallagher, Renata C., additional, Garel, Catherine, additional, Gertsch, Emily, additional, Gilbert, Donald L., additional, Gilles, Elizabeth E., additional, Giza, Christopher C., additional, Glaser, Carol A., additional, Glass, Hannah C., additional, Glauser, Tracy, additional, Glykys, Joseph, additional, Goldstein, Amy, additional, Gonorazky, Hernan Dario, additional, Gonzalez, Rodolfo, additional, Goodkin, Howard P., additional, Graham, John M., additional, Greninger, Alexander L., additional, Gronseth, Gary, additional, Gropman, Andrea L., additional, Grundy, Richard, additional, Guerrini, Renzo, additional, Gupta, Nalin, additional, Hahn, Jin S., additional, Hamblin, Milton H., additional, Hani, Abeer J., additional, Hanmantgad, Sharyu, additional, Harbert, Mary J., additional, Harini, Chellamani, additional, Harriott, Andrea M., additional, Heatwole, Chad, additional, Hershey, Andrew D., additional, Hirtz, Deborah G., additional, Holmes, Gregory L., additional, Holshouser, Barbara A., additional, Hurwitz, Kathleen A., additional, Hwang, Eugene, additional, Ichord, Rebecca N., additional, Jafar-Nejad, Paymaan, additional, Jain, Sejal V., additional, Jordan, Lori, additional, Kabbouche, Marielle A., additional, Kacperski, Joanne, additional, Kang, Peter B., additional, Kariannis, Matthias A., additional, Kaufmann, Horacio, additional, Kaye, Harper L., additional, Keating, Robert, additional, Kennedy, Colin R., additional, Khakoo, Yasmin, additional, Kirton, Adam, additional, Kissel, John T., additional, Knupp, Kelly G., additional, Korf, Bruce R., additional, Kossoff, Eric H., additional, Kothare, Sanjeev V., additional, Kupfer, Oren, additional, LaFrance, W. Curt, additional, Latal, Beatrice, additional, Leber, Steven M., additional, Lee, Jean-Pyo, additional, Leppik, Ilo E., additional, Lerman-Sagie, Tally, additional, Lerner, Jason T., additional, Leventer, Richard J., additional, Licht, Daniel J., additional, Lichter-Konecki, Uta, additional, Lidar, Zvi, additional, Liem, Djin Gie, additional, Loddenkemper, Tobias, additional, Long, Roger K., additional, Luc, Quyen N., additional, Mackay, Mark, additional, Majnemer, Annette, additional, Makhani, Naila, additional, Malinger, Gustavo, additional, Mandelbaum, David E., additional, Maricich, Stephen M., additional, Maski, Kiran P., additional, Mathur, Mudit, additional, Matthews, Dennis J., additional, McMahon, Kelly, additional, DeMara-Hoth, Megan B., additional, Mendelsohn, Bryce, additional, Mennella, Julie A., additional, Ment, Laura R., additional, Mercuri, Eugenio, additional, Michelson, David J., additional, Mikati, Mohamad A., additional, Mikhail, Fady M., additional, Miller, Steven Paul, additional, Milunsky, Jeff M., additional, Mink, Jonathan W., additional, Mirzaa, Ghayda M., additional, Mitchell, Wendy G., additional, Mohan, Michael A., additional, Mohassel, Payam, additional, Moharir, Mahendranath, additional, Monani, Umrao R., additional, Monje Deisseroth, Michelle, additional, Moodley, Manikum, additional, Mower, Andrew, additional, Moxley, Richard T., additional, Mueller, Sabine, additional, Muotri, Alysson R., additional, Nagamani, Sandesh C.S., additional, Narayanan, Mohan J., additional, Narayanan, Vinodh, additional, Nass, Ruth D., additional, Neul, Jeffrey L., additional, Nevo, Yoram, additional, Ng, Bobby G., additional, Nickels, Katherine C., additional, Nimmo, Graeme A.M., additional, Noetzel, Michael J., additional, Norcliffe-Kaufmann, Lucy, additional, Nordli, Douglas R., additional, Nowak-Göttl, Ulrike, additional, O'Brien, Hope L., additional, Oleszek, Joyce, additional, Oskoui, Maryam, additional, Paciorkowski, Alex R., additional, Packer, Roger J., additional, Packman, Seymour, additional, Palma, Jose-Alberto, additional, Pardo, Andrea C., additional, Parsons, Julie A., additional, Partridge, John Colin, additional, Pastores, Gregory M., additional, Patterson, Marc C., additional, Pearce, William J., additional, Pearl, Phillip L., additional, Penner, Melanie, additional, Percival, Leila, additional, Pereira, Marcia, additional, Pfister, Stefan M., additional, Phillips, John, additional, Plecko, Barbara, additional, Plioplys, Sigita, additional, Poduri, Annapurna, additional, Poisson, Sharon, additional, Pomeroy, Scott L., additional, Poretti, Andrea, additional, Powers, Scott W., additional, Pranzatelli, Michael R., additional, Przekop, Allison, additional, Rabie, Malcolm, additional, Rangasamy, Sampathkumar, additional, Raymond, Gerald V., additional, Reddy, Alyssa T., additional, Rendleman, Rebecca L., additional, Rho, Jong M., additional, Rodan, Lance H., additional, Roddy, Sarah M., additional, Rogers, Elizabeth E., additional, Rosenthal, Stephen M., additional, Rosman, N. Paul, additional, Ross, M. Elizabeth, additional, Rotenberg, Alexander, additional, Rust, Robert S., additional, Sanchez, Cheryl P., additional, Sanchez, Pedro, additional, Sánchez Fernández, Iván, additional, Sands, Tristan T., additional, Sanger, Terence D., additional, Sannagowdara, Kumar, additional, Scheinost, Dustin, additional, Scher, Mark S., additional, Schor, Nina F., additional, Schrauwen, Isabelle, additional, Segal, Michael M., additional, Seinfeld, Syndi, additional, Selcen, Duygu, additional, Seltzer, Laurie E., additional, Semrud-Clikeman, Margaret, additional, Shaw, Dennis W., additional, Shaywitz, Bennett A., additional, Shaywitz, Sally E., additional, Shellhaas, Renée A., additional, Sherr, Elliott H., additional, Sheth, Rita D., additional, Shevell, Michael I., additional, Shinnar, Shlomo, additional, Shofty, Ben, additional, Shu, Stanford K., additional, Shy, Michael E., additional, Silveira Moriyama, Laura, additional, Silvestri, Nicholas J., additional, Sims, Katherine B., additional, Singer, Harvey S., additional, Singhal, Nilika Shah, additional, Smith, Craig M., additional, Smith, Edward, additional, Smith, Stephen A., additional, Snyder, Evan Y., additional, Soul, Janet, additional, Spalink, Christy L., additional, Spencer, Karen A., additional, Stafstrom, Carl E., additional, Steinfeld, Robert, additional, Strober, Jonathan B., additional, Sullivan, Joseph, additional, Swaiman, Kenneth F., additional, Swoboda, Kathryn J., additional, Tate, Elizabeth D., additional, Tatum, William O., additional, Tein, Ingrid, additional, Tekulve, Kristyn, additional, Tenney, Jeffrey R., additional, Thiele, Elizabeth A., additional, Thompson-Stone, Robert, additional, Tochen, Laura, additional, Tormoehlen, Laura M., additional, Tran, Lily, additional, Trauner, Doris A., additional, Turnacioglu, Sinan O., additional, Ullrich, Nicole J., additional, Urion, David K., additional, Van Camp, Guy, additional, Van Hirtum-Das, Michèle, additional, van Karnebeek, Clara D.M., additional, Van Maldergem, Lionel, additional, Vanderver, Adeline, additional, Vitanza, Nicholas A., additional, von Rhein, Michael, additional, von Scheven, Emily, additional, Wagner, Ann, additional, Wainwright, Mark S., additional, Walker, Melissa A., additional, Walkup, John T., additional, Walsh, Laurence, additional, Walters-Sen, Lauren C., additional, Wang, Raymond Y., additional, Warner, Thomas T., additional, Whelan, Harry T., additional, Weinberg, Geoffrey A., additional, Wells, Elizabeth M., additional, Wheless, James W., additional, Wirrell, Elaine C., additional, Wisoff, Jeffrey H., additional, Wolf, Nicole I., additional, Wolfe, Gil I., additional, Wright, F. Virginia, additional, Wycliffe, Nathaniel D., additional, Yang, Michele L., additional, Yuskaitis, Christopher J., additional, Zoghbi, Huda Y., additional, and Zupanc, Mary L., additional

Published
2017
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10. User testing of a diagnostic decision support system with machine-assisted chart review to facilitate clinical genomic diagnosis

Author

Kulchak Rahm, Alanna, primary, Walton, Nephi A, additional, Feldman, Lynn K, additional, Jenkins, Conner, additional, Jenkins, Troy, additional, Person, Thomas N, additional, Peterson, Joeseph, additional, Reynolds, Jonathon C, additional, Robinson, Peter N, additional, Woltz, Makenzie A, additional, Williams, Marc S, additional, and Segal, Michael M, additional

Published
2021
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12. Contributors

Author

Abou-Hamden, Amal, primary, Amato, Anthony A., additional, Ashwal, Stephen, additional, Axelrod, Felicia B., additional, Bale, James F., additional, Banwell, Brenda, additional, Baranano, Kristin W., additional, Barkovich, A. James, additional, Barohn, Richard J., additional, Batshaw, Mark L., additional, Ben-Sira, Liat, additional, Birnbaum, Angela K., additional, Boustany, Rose-Mary N., additional, Brooks-Kayal, Amy, additional, Brown, Lawrence W., additional, Camfield, Carol S., additional, Camfield, Peter R., additional, Casselbrant, Margaretha L., additional, Chiriboga, Claudia A., additional, Christian, Susan L., additional, Cilio, Maria Roberta, additional, Connolly, Anne M., additional, Conway, Jeannine M., additional, Cornes, Susannah, additional, Coulter, David L., additional, Cowan, Tina M., additional, Das, Soma, additional, De Vivo, Darryl C., additional, de Vries, Linda S., additional, Desai, Jay, additional, Descartes, Maria, additional, deVeber, Gabrielle, additional, DiMauro, Salvatore, additional, Dobyns, William B., additional, Dong, Qing, additional, Drake, James M., additional, Duhaime, Ann-Christine, additional, du Plessis, Adre J., additional, El-Bitar, Mohamad K., additional, Enns, Gregory M., additional, Escolar, Diana M., additional, Evans, Owen B., additional, Fatemi, S. Ali, additional, Ferriero, Donna M., additional, Filipek, Pauline A., additional, Frank, Yitzchak, additional, Fredrick, Douglas R., additional, Freeze, Hudson H., additional, Friedman, Neil R., additional, Furman, Joseph M., additional, Garg, Bhuwan P., additional, Ghosh, Debabrata, additional, Gilles, Elizabeth E., additional, Giza, Christopher C., additional, Glaser, Carol A., additional, Gleeson, Joseph G., additional, Graham, John M., additional, Gressens, Pierre, additional, Guerrini, Renzo, additional, Gupta, Nalin, additional, Hahn, Jin S., additional, Harini, Chellamani, additional, Heatwole, Chad, additional, Hirtz, Deborah G., additional, Holmes, Gregory L., additional, Holshouser, Barbara A., additional, Ichord, Rebecca N., additional, Jafar-Nejad, Paymaan, additional, Jensen, Frances E., additional, Johnston, Michael V., additional, Jordan, Lori, additional, Khakoo, Yasmin, additional, Khasraw, Mustafa, additional, Kirton, Adam, additional, Kissel, John T., additional, Klein, Ophir, additional, Knupp, Kelly, additional, Korf, Bruce R., additional, Kotagal, Suresh, additional, Leber, Steven, additional, Leppik, Ilo E., additional, Lerman-Sagie, Tally, additional, Lerner, Jason T., additional, Leshner, Robert T., additional, Leventer, Richard J., additional, Lewis, Donald W., additional, Lewis, Paul F., additional, Lichter-Konecki, Uta, additional, Limperopoulos, Catherine, additional, Louie, Janice K., additional, Luc, Quyen N., additional, MacDonald, Tobey J., additional, Makhani, Naila, additional, Malinger, Gustavo, additional, Mandelbaum, David E., additional, Marcuccilli, Charles J., additional, Maricich, Stephen M., additional, Martin, Lee J., additional, Mennella, Julie A., additional, Ment, Laura R., additional, Michelson, David J., additional, Mikhail, Fady M., additional, Millen, Kathleen J., additional, Miller, Steven P., additional, Mink, Jonathan W., additional, Mirzaa, Ghayda, additional, Mitchell, Wendy G., additional, Moodley, Manikum, additional, Morton, Lawrence D., additional, Moxley, Richard T., additional, Muppidi, Srikanth, additional, Nash, Kendall, additional, Nass, Ruth, additional, Noetzel, Michael J., additional, Nordli, Douglas R., additional, Northington, Frances J., additional, Ouvrier, Robert, additional, Packer, Roger J., additional, Packman, Seymour, additional, Parsons, Julie A., additional, Partridge, John C., additional, Pastores, Gregory M., additional, Patterson, Marc C., additional, Pellock, John M., additional, Perkin, Ronald M., additional, Rapin, Isabelle, additional, Raymond, Gerald V., additional, Rendleman, Rebecca, additional, Rho, Jong M., additional, Roddy, Sarah M., additional, Rosenthal, Stephen M., additional, Rosman, N. Paul, additional, Ross, M. Elizabeth, additional, Rust, Robert S., additional, Sanchez-Lara, Pedro A., additional, Sanger, Terence D., additional, Sanmaneechai, Oranee, additional, Schaad, Urs B., additional, Scher, Mark S., additional, Schor, Nina F., additional, Segal, Michael M., additional, Shaywitz, Bennett A., additional, Shaywitz, Sally E., additional, Sherr, Elliott H., additional, Shevell, Michael I., additional, Shinnar, Shlomo, additional, Shu, Stanford K., additional, Silverstein, Faye S., additional, Singer, Harvey S., additional, Sladky, John T., additional, Smith, Stephen A., additional, Soul, Janet S., additional, Stafstrom, Carl E., additional, Strober, Jonathan B., additional, Sullivan, Joseph, additional, Swaiman, Kenneth F., additional, Sweney, Matthew T., additional, Swoboda, Kathryn J., additional, Täuber, Martin G., additional, Taylor, Donald A., additional, Tein, Ingrid, additional, Thiele, Elizabeth A., additional, Trauner, Doris A., additional, Tuchman, Roberto, additional, Vanderver, Adeline, additional, Hirtum-Das, Michéle Van, additional, Vedanarayanan, V. Venkataraman, additional, Vexler, Zinaida S., additional, Vezina, Gilbert, additional, Scheven, Emily von, additional, Wagner, Ann, additional, Wainwright, Mark S., additional, Walkup, John T., additional, Walsh, Laurence E., additional, Wang, Ching H., additional, Wheless, James W., additional, Wolf, Nicole I., additional, Wolfe, Gil I., additional, Wu, Yvonne W., additional, Wycliffe, Nathaniel D., additional, Yager, Jerome Y., additional, Zimmer, Jennifer A., additional, Zoghbi, Huda Y., additional, and Zupanc, Mary L., additional

Published
2012
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15. The Human Phenotype Ontology in 2021

Author

Köhler, Sebastian, primary, Gargano, Michael, additional, Matentzoglu, Nicolas, additional, Carmody, Leigh C, additional, Lewis-Smith, David, additional, Vasilevsky, Nicole A, additional, Danis, Daniel, additional, Balagura, Ganna, additional, Baynam, Gareth, additional, Brower, Amy M, additional, Callahan, Tiffany J, additional, Chute, Christopher G, additional, Est, Johanna L, additional, Galer, Peter D, additional, Ganesan, Shiva, additional, Griese, Matthias, additional, Haimel, Matthias, additional, Pazmandi, Julia, additional, Hanauer, Marc, additional, Harris, Nomi L, additional, Hartnett, Michael J, additional, Hastreiter, Maximilian, additional, Hauck, Fabian, additional, He, Yongqun, additional, Jeske, Tim, additional, Kearney, Hugh, additional, Kindle, Gerhard, additional, Klein, Christoph, additional, Knoflach, Katrin, additional, Krause, Roland, additional, Lagorce, David, additional, McMurry, Julie A, additional, Miller, Jillian A, additional, Munoz-Torres, Monica C, additional, Peters, Rebecca L, additional, Rapp, Christina K, additional, Rath, Ana M, additional, Rind, Shahmir A, additional, Rosenberg, Avi Z, additional, Segal, Michael M, additional, Seidel, Markus G, additional, Smedley, Damian, additional, Talmy, Tomer, additional, Thomas, Yarlalu, additional, Wiafe, Samuel A, additional, Xian, Julie, additional, Yüksel, Zafer, additional, Helbig, Ingo, additional, Mungall, Christopher J, additional, Haendel, Melissa A, additional, and Robinson, Peter N, additional

Published
2020
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16. User Testing of a Diagnostic Decision Support System with Machine-assisted Chart Review to Facilitate Clinical Genomic Diagnosis

Author

Rahm, Alanna Kulchak, primary, Walton, Nephi A., additional, Feldman, Lynn K., additional, Jenkins, Conner, additional, Jenkins, Troy, additional, Person, Thomas N., additional, Peterson, Joseph, additional, Reynolds, Jonathon C., additional, Robinson, Peter N., additional, Woltz, Makenzie A., additional, Williams, Marc S., additional, and Segal, Michael M., additional

Published
2020
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17. The Human Phenotype Ontology in 2021

Author

Köhler, Sebastian, Gargano, Michael, Matentzoglu, Nicolas, Carmody, Leigh C, Lewis-Smith, David, Vasilevsky, Nicole A, Danis, Daniel, Balagura, Ganna, Baynam, Gareth, Brower, Amy M, Callahan, Tiffany J, Chute, Christopher G, Est, Johanna L, Galer, Peter D, Ganesan, Shiva, Griese, Matthias, Haimel, Matthias, Pazmandi, Julia, Hanauer, Marc, Harris, Nomi L, Hartnett, Michael J, Hastreiter, Maximilian, Hauck, Fabian, He, Yongqun, Jeske, Tim, Kearney, Hugh, Kindle, Gerhard, Klein, Christoph, Knoflach, Katrin, Krause, Roland, Lagorce, David, McMurry, Julie A, Miller, Jillian A, Munoz-Torres, Monica C, Peters, Rebecca L, Rapp, Christina K, Rath, Ana M, Rind, Shahmir A, Rosenberg, Avi Z, Segal, Michael M, Seidel, Markus G, Smedley, Damian, Talmy, Tomer, Thomas, Yarlalu, Wiafe, Samuel A, Xian, Julie, Yüksel, Zafer, Helbig, Ingo, Mungall, Christopher J, Haendel, Melissa A, and Robinson, Peter N

Subjects
endocrine system, Genotype, International Cooperation, Neurodegenerative, Databases, Neonatal Screening, Terminology as Topic, Information and Computing Sciences, Animals, Humans, Disease, Factual, Internet, Genome, Animal, fungi, Computational Biology, Infant, Biological Sciences, Newborn, equipment and supplies, body regions, Phenotype, Networking and Information Technology R&D, Networking and Information Technology R&D (NITRD), Biological Ontologies, Pharmacogenetics, Disease Models, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], Software, Environmental Sciences, Developmental Biology
Abstract

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

Published
2020

22. Hypothalamic or central obesity is associated with an early rise in plasma insulin concentration

Author

Segal, Michael M., Bell, Jennifer, and Abrams, Gary M.

Subjects
Hypothalamus -- Abnormalities, Obesity in children -- Physiological aspects, Encephalomyelitis -- Complications, Hypothalamo-hypophyseal system -- Abnormalities, Neuroendocrinology -- Case studies, Health
Abstract

In experimental animals, a brain lesion in the ventromedial hypothalamus results in a syndrome of overeating and obesity. Similar syndromes may be observed in humans, but in people obesity due to a hypothalamic lesion, at least an obvious hypothalamic lesion, is not common. The evaluation of patients with hypothalamic obesity, however, suggests that the insulin responses of these patients are similar to those observed for other sorts of obesity. Most studies are performed after the patient has reached the plateau of obesity, when there is little evidence of the physiological and endocrine changes which occur early in the onset of obesity. The authors report the case of a seven-year-old boy recovering from a case of meningoencephalitis (inflammation of the brain and surrounding membrane) of undetermined cause. Even while the patient was being examined by the neurologist, he exhibited a preoccupation with food. One week after discharge for the encephalitis, the patient returned, complaining of constant eating and drinking. He had gained 7.5 kilograms (about 17 pounds) during that week. In addition, he reported eating vegetables he had previously disliked. Early testing revealed that the boy had normal glucose tolerance but strikingly high levels of insulin. Two months later the patient showed signs of insulin resistance and of a diabetic pattern of response to carbohydrates. The authors suggest that the early elevation of insulin may be a key factor in causing the obesity and not merely another consequence of obesity. It is worth noting that animals with ventromedial hypothalamic lesions sometimes show inappropriate rage reactions. Similar rage reactions were not seen in the patient, but it was noted that the patient did become enraged when denied access to food. (Consumer Summary produced by Reliance Medical Information, Inc.)

Published
1991

23. Experience with Integrating Diagnostic Decision Support Software with Electronic Health Records: Benefits versus Risks of Information Sharing

Author

Segal, Michael M., primary, Rahm, Alanna K., additional, Hulse, Nathan C., additional, Wood, Grant, additional, Williams, Janet L., additional, Feldman, Lynn, additional, Moore, Gregory J., additional, Gehrum, David, additional, Yefko, Michelle, additional, Mayernick, Steven, additional, Gildersleeve, Roger, additional, Sunderland, Margie C., additional, Bleyl, Steven B., additional, Haug, Peter, additional, and Williams, Marc S., additional

Published
2017
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24. Evidence-based decision support for pediatric rheumatology reduces diagnostic errors.

Author

Segal, Michael M., Athreya, Balu, Son, Mary Beth F., Tirosh, Irit, Hausmann, Jonathan S., Ang, Elizabeth YN., Zurakowski, David, Feldman, Lynn K., Sundel, Robert P., Segal, Michael M., Athreya, Balu, Son, Mary Beth F., Tirosh, Irit, Hausmann, Jonathan S., Ang, Elizabeth YN., Zurakowski, David, Feldman, Lynn K., and Sundel, Robert P.

Abstract

BACKGROUND: The number of trained specialists world-wide is insufficient to serve all children with pediatric rheumatologic disorders, even in the countries with robust medical resources. We evaluated the potential of diagnostic decision support software (DDSS) to alleviate this shortage by assessing the ability of such software to improve the diagnostic accuracy of non-specialists. METHODS: Using vignettes of actual clinical cases, clinician testers generated a differential diagnosis before and after using diagnostic decision support software. The evaluation used the SimulConsult® DDSS tool, based on Bayesian pattern matching with temporal onset of each finding in each disease. The tool covered 5405 diseases (averaging 22 findings per disease). Rheumatology content in the database was developed using both primary references and textbooks. The frequency, timing, age of onset and age of disappearance of findings, as well as their incidence, treatability, and heritability were taken into account in order to guide diagnostic decision making. These capabilities allowed key information such as pertinent negatives and evolution over time to be used in the computations. Efficacy was measured by comparing whether the correct condition was included in the differential diagnosis generated by clinicians before using the software ("unaided"), versus after use of the DDSS ("aided"). RESULTS: The 26 clinicians demonstrated a significant reduction in diagnostic errors following introduction of the software, from 28% errors while unaided to 15% using decision support (p < 0.0001). Improvement was greatest for emergency medicine physicians (p = 0.013) and clinicians in practice for less than 10 years (p = 0.012). This error reduction occurred despite the fact that testers employed an "open book" approach to generate their initial lists of potential diagnoses, spending an average of 8.6 min using printed and electronic sources of medical information before using the diagnostic softwa

Published
2016

29. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

Author

Brownstein, Catherine A., Beggs, Alan H., Homer, Nils, Merriman, Barry, Yu, Timothy W., Flannery, Katherine C., DeChene, Elizabeth T., Towne, Meghan C., Savage, Sarah K., Price, Emily N., Holm, Ingrid A., Luquette, Lovelace J., Lyon, Elaine, Majzoub, Joseph, Neupert, Peter, McCallie, David, Jr., Szolovits, Peter, Willard, Huntington F., Mendelsohn, Nancy J., Temme, Renee, Finkel, Richard S., Yum, Sabrina W., Medne, Livija, Sunyaev, Shamil R., Adzhubey, Ivan, Cassa, Christopher A., de Bakker, Paul I. W., Duzkale, Hatice, Dworzynski, Piotr, Fairbrother, William, Francioli, Laurent, Funke, Birgit H., Giovanni, Monica A., Handsaker, Robert E., Lage, Kasper, Lebo, Matthew S., Lek, Monkol, Leshchiner, Ignaty, MacArthur, Daniel G., McLaughlin, Heather M., Murray, Michael F., Pers, Tune H., Polak, Paz P., Raychaudhuri, Soumya, Rehm, Heidi L., Soemedi, Rachel, Stitziel, Nathan O., Vestecka, Sara, Supper, Jochen, Gugenmus, Claudia, Klocke, Bernward, Hahn, Alexander, Schubach, Max, Menzel, Mortiz, Biskup, Saskia, Freisinger, Peter, Deng, Mario, Braun, Martin, Perner, Sven, Smith, Richard J. H., Andorf, Janeen L., Huang, Jian, Ryckman, Kelli, Sheffield, Val C., Stone, Edwin M., Bair, Thomas, Black-Ziegelbein, E. Ann, Braun, Terry A., Darbro, Benjamin, DeLuca, Adam P., Kolbe, Diana L., Scheetz, Todd E., Shearer, Aiden E., Sompallae, Rama, Wang, Kai, Bassuk, Alexander G., Edens, Erik, Mathews, Katherine, Moore, Steven A., Shchelochkov, Oleg A., Trapane, Pamela, Bossler, Aaron, Campbell, Colleen A., Heusel, Jonathan W., Kwitek, Anne, Maga, Tara, Panzer, Karin, Wassink, Thomas, Van Daele, Douglas, Azaiez, Hela, Booth, Kevin, Meyer, Nic, Segal, Michael M., Williams, Marc S., Tromp, Gerard, White, Peter, Corsmeier, Donald, Fitzgerald-Butt, Sara, Herman, Gail, Lamb-Thrush, Devon, McBride, Kim L., Newsom, David, Pierson, Christopher R., Rakowsky, Alexander T., Maver, Ales, Lovrecic, Luca, Palandacic, Anja, Peterlin, Borut, Torkamani, Ali, Wedell, Anna, Huss, Mikael, Alexeyenko, Andrey, Lindvall, Jessica M., Magnusson, Mans, Nilsson, Daniel, Stranneheim, Henrik, Taylan, Fulya, Gilissen, Christian, Hoischen, Alexander, van Bon, Bregje, Yntema, Helger, Nelen, Marcel, Zhang, Weidong, Sager, Jason, Zhang, Lu, Blair, Kathryn, Kural, Deniz, Cariaso, Michael, Lennon, Greg G., Javed, Asif, Agrawal, Saloni, Ng, Pauline C., Sandhu, Komal S., Krishna, Shuba, Veeramachaneni, Vamsi, Isakov, Ofer, Halperin, Eran, Friedman, Eitan, Shomron, Noam, Glusman, Gustavo, Roach, Jared C., Caballero, Juan, Cox, Hannah C., Mauldin, Denise, Ament, Seth A., Rowen, Lee, Richards, Daniel R., San Lucas, F. Anthony, Gonzalez-Garay, Manuel L., Caskey, C. Thomas, Bai, Yu, Huang, Ying, Fang, Fang, Zhang, Yan, Wang, Zhengyuan, Barrera, Jorge, Garcia-Lobo, Juan M., Gonzalez-Lamuno, Domingo, Llorca, Javier, Rodriguez, Maria C., Varela, Ignacio, Reese, Martin G., De la Vega, Francisco M., Kiruluta, Edward, Cargill, Michele, Hart, Reece K., Sorenson, Jon M., Lyon, Gholson J., Stevenson, David A., Bray, Bruce E., Moore, Barry M., Eilbeck, Karen, Yandell, Mark, Zhao, Hongyu, Hou, Lin, Chen, Xiaowei, Yan, Xiting, Chen, Mengjie, Li, Cong, Yang, Can, Gunel, Murat, Li, Peining, Kong, Yong, Alexander, Austin C., Albertyn, Zayed I., Boycott, Kym M., Bulman, Dennis E., Gordon, Paul M. K., Innes, A. Micheil, Knoppers, Bartha M., Majewski, Jacek, Marshall, Christian R., Parboosingh, Jillian S., Sawyer, Sarah L., Samuels, Mark E., Schwartzentruber, Jeremy, Kohane, Isaac S., Margulies, David M., Brownstein, Catherine A., Beggs, Alan H., Homer, Nils, Merriman, Barry, Yu, Timothy W., Flannery, Katherine C., DeChene, Elizabeth T., Towne, Meghan C., Savage, Sarah K., Price, Emily N., Holm, Ingrid A., Luquette, Lovelace J., Lyon, Elaine, Majzoub, Joseph, Neupert, Peter, McCallie, David, Jr., Szolovits, Peter, Willard, Huntington F., Mendelsohn, Nancy J., Temme, Renee, Finkel, Richard S., Yum, Sabrina W., Medne, Livija, Sunyaev, Shamil R., Adzhubey, Ivan, Cassa, Christopher A., de Bakker, Paul I. W., Duzkale, Hatice, Dworzynski, Piotr, Fairbrother, William, Francioli, Laurent, Funke, Birgit H., Giovanni, Monica A., Handsaker, Robert E., Lage, Kasper, Lebo, Matthew S., Lek, Monkol, Leshchiner, Ignaty, MacArthur, Daniel G., McLaughlin, Heather M., Murray, Michael F., Pers, Tune H., Polak, Paz P., Raychaudhuri, Soumya, Rehm, Heidi L., Soemedi, Rachel, Stitziel, Nathan O., Vestecka, Sara, Supper, Jochen, Gugenmus, Claudia, Klocke, Bernward, Hahn, Alexander, Schubach, Max, Menzel, Mortiz, Biskup, Saskia, Freisinger, Peter, Deng, Mario, Braun, Martin, Perner, Sven, Smith, Richard J. H., Andorf, Janeen L., Huang, Jian, Ryckman, Kelli, Sheffield, Val C., Stone, Edwin M., Bair, Thomas, Black-Ziegelbein, E. Ann, Braun, Terry A., Darbro, Benjamin, DeLuca, Adam P., Kolbe, Diana L., Scheetz, Todd E., Shearer, Aiden E., Sompallae, Rama, Wang, Kai, Bassuk, Alexander G., Edens, Erik, Mathews, Katherine, Moore, Steven A., Shchelochkov, Oleg A., Trapane, Pamela, Bossler, Aaron, Campbell, Colleen A., Heusel, Jonathan W., Kwitek, Anne, Maga, Tara, Panzer, Karin, Wassink, Thomas, Van Daele, Douglas, Azaiez, Hela, Booth, Kevin, Meyer, Nic, Segal, Michael M., Williams, Marc S., Tromp, Gerard, White, Peter, Corsmeier, Donald, Fitzgerald-Butt, Sara, Herman, Gail, Lamb-Thrush, Devon, McBride, Kim L., Newsom, David, Pierson, Christopher R., Rakowsky, Alexander T., Maver, Ales, Lovrecic, Luca, Palandacic, Anja, Peterlin, Borut, Torkamani, Ali, Wedell, Anna, Huss, Mikael, Alexeyenko, Andrey, Lindvall, Jessica M., Magnusson, Mans, Nilsson, Daniel, Stranneheim, Henrik, Taylan, Fulya, Gilissen, Christian, Hoischen, Alexander, van Bon, Bregje, Yntema, Helger, Nelen, Marcel, Zhang, Weidong, Sager, Jason, Zhang, Lu, Blair, Kathryn, Kural, Deniz, Cariaso, Michael, Lennon, Greg G., Javed, Asif, Agrawal, Saloni, Ng, Pauline C., Sandhu, Komal S., Krishna, Shuba, Veeramachaneni, Vamsi, Isakov, Ofer, Halperin, Eran, Friedman, Eitan, Shomron, Noam, Glusman, Gustavo, Roach, Jared C., Caballero, Juan, Cox, Hannah C., Mauldin, Denise, Ament, Seth A., Rowen, Lee, Richards, Daniel R., San Lucas, F. Anthony, Gonzalez-Garay, Manuel L., Caskey, C. Thomas, Bai, Yu, Huang, Ying, Fang, Fang, Zhang, Yan, Wang, Zhengyuan, Barrera, Jorge, Garcia-Lobo, Juan M., Gonzalez-Lamuno, Domingo, Llorca, Javier, Rodriguez, Maria C., Varela, Ignacio, Reese, Martin G., De la Vega, Francisco M., Kiruluta, Edward, Cargill, Michele, Hart, Reece K., Sorenson, Jon M., Lyon, Gholson J., Stevenson, David A., Bray, Bruce E., Moore, Barry M., Eilbeck, Karen, Yandell, Mark, Zhao, Hongyu, Hou, Lin, Chen, Xiaowei, Yan, Xiting, Chen, Mengjie, Li, Cong, Yang, Can, Gunel, Murat, Li, Peining, Kong, Yong, Alexander, Austin C., Albertyn, Zayed I., Boycott, Kym M., Bulman, Dennis E., Gordon, Paul M. K., Innes, A. Micheil, Knoppers, Bartha M., Majewski, Jacek, Marshall, Christian R., Parboosingh, Jillian S., Sawyer, Sarah L., Samuels, Mark E., Schwartzentruber, Jeremy, Kohane, Isaac S., and Margulies, David M.

Abstract

Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups., QC 20140819

Published
2014
Full Text
View/download PDF

30. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

Author

Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Szolovits, Peter, Brownstein, Catherine A., Beggs, Alan H., Homer, Nils, Merriman, Barry, Yu, Timothy W., Flannery, Katherine C., DeChene, Elizabeth T., Towne, Meghan C., Savage, Sarah K., Price, Emily N., Holm, Ingrid A., Luquette, Lovelace J., Lyon, Elaine, Majzoub, Joseph, Neupert, Peter, McCallie Jr., David, Willard, Huntington F., Mendelsohn, Nancy J., Temme, Renee, Finkel, Richard S., Yum, Sabrina W., Medne, Livija, Sunyaev, Shamil R., Adzhubey, Ivan, Cassa, Christopher A., de Bakker, Paul I. W., Duzkale, Hatice, Dworzyński, Piotr, Fairbrother, William G., Francioli, Laurent, Funke, Birgit H., Giovanni, Monica A., Handsaker, Robert E., Lage, Kasper, Lebo, Matthew S., Lek, Monkol, Leshchiner, Ignaty, MacArthur, Daniel G., McLaughlin, Heather M., Murray, Michael F., Pers, Tune H., Polak, Paz P., Raychaudhuri, Soumya, Rehm, Heidi L., Soemedi, Rachel, Stitziel, Nathan O., Vestecka, Sara, Supper, Jochen, Gugenmus, Claudia, Klocke, Bernward, Hahn, Alexander, Schubach, Max, Menzel, Mortiz, Biskup, Saskia, Freisinger, Peter, Deng, Mario, Braun, Martin, Perner, Sven, Smith, Richard J. H., Andorf, Janeen L., Huang, Jian, Ryckman, Kelli, Sheffield, Val C., Stone, Edwin M., Bair, Thomas, Black-Ziegelbein, E. A., Braun, Terry A., Darbro, Benjamin, DeLuca, Adam P., Kolbe, Diana L., Scheetz, Todd E., Shearer, Aiden E., Sompallae, Rama, Wang, Kai, Bassuk, Alexander G., Edens, Erik, Mathews, Katherine, Moore, Steven A., Shchelochkov, Oleg A., Trapane, Pamela, Bossler, Aaron, Campbell, Colleen A., Heusel, Jonathan W., Kwitek, Anne, Maga, Tara, Panzer, Karin, Wassink, Thomas, Van Daele, Douglas, Azaiez, Hela, Booth, Kevin, Meyer, Nic, Segal, Michael M., Williams, Marc S., Tromp, Gerard, White, Peter, Corsmeier, Donald, Fitzgerald-Butt, Sara, Herman, Gail, Lamb-Thrush, Devon, McBride, Kim L., Newsom, David, Pierson, Christopher R., Rakowsky, Alexander T., Maver, Ales, Lovrečić, Luca, Palandacic, Anja, Peterlin, Borut, Torkamani, Ali, Wedell, Anna, Huss, Mikael, Alexeyenko, Andrey, Lindvall, Jessica M., Magnusson, Mans, Nilsson, Daniel, Stranneheim, Henrik, Taylan, Fulya, Gilissen, Christian, Hoischen, Alexander, van Bon, Bregje, Yntema, Helger, Nelen, Marcel, Zhang, Weidong, Sager, Jason, Zhang, Lu, Blair, Kathryn, Kural, Deniz, Cariaso, Michael, Lennon, Greg G., Javed, Asif, Agrawal, Saloni, Ng, Pauline C., Sandhu, Komal S., Krishna, Shuba, Veeramachaneni, Vamsi, Isakov, Ofer, Halperin, Eran, Friedman, Eitan, Shomron, Noam, Glusman, Gustavo, Roach, Jared C., Caballero, Juan, Cox, Hannah C., Mauldin, Denise, Ament, Seth A., Rowen, Lee, Richards, Daniel R., Lucas, F Anthony S., Gonzalez-Garay, Manuel L., Caskey, C. T., Bai, Yu, Huang, Ying, Fang, Fang, Zhang, Yan, Wang, Zhengyuan, Barrera, Jorge, Garcia-Lobo, Juan M., González-Lamuno, Domingo, Llorca, Javier, Rodriguez, Maria C., Varela, Ignacio, Reese, Martin G., De La Vega, Francisco M., Kiruluta, Edward, Cargill, Michele, Hart, Reece K., Sorenson, Jon M., Lyon, Gholson J., Stevenson, David A., Bray, Bruce E., Moore, Barry M., Eilbeck, Karen, Yandell, Mark, Zhao, Hongyu, Hou, Lin, Chen, Xiaowei, Yan, Xiting, Chen, Mengjie, Li, Cong, Yang, Can, Gunel, Murat, Li, Peining, Kong, Yong, Alexander, Austin C., Albertyn, Zayed I., Boycott, Kym M., Bulman, Dennis E., Gordon, Paul M. K., Innes, A. M., Knoppers, Bartha M., Majewski, Jacek, Marshall, Christian R., Parboosingh, Jillian S., Sawyer, Sarah L., Samuels, Mark E., Schwartzentruber, Jeremy, Kohane, Isaac, Margulies, David M., Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Szolovits, Peter, Brownstein, Catherine A., Beggs, Alan H., Homer, Nils, Merriman, Barry, Yu, Timothy W., Flannery, Katherine C., DeChene, Elizabeth T., Towne, Meghan C., Savage, Sarah K., Price, Emily N., Holm, Ingrid A., Luquette, Lovelace J., Lyon, Elaine, Majzoub, Joseph, Neupert, Peter, McCallie Jr., David, Willard, Huntington F., Mendelsohn, Nancy J., Temme, Renee, Finkel, Richard S., Yum, Sabrina W., Medne, Livija, Sunyaev, Shamil R., Adzhubey, Ivan, Cassa, Christopher A., de Bakker, Paul I. W., Duzkale, Hatice, Dworzyński, Piotr, Fairbrother, William G., Francioli, Laurent, Funke, Birgit H., Giovanni, Monica A., Handsaker, Robert E., Lage, Kasper, Lebo, Matthew S., Lek, Monkol, Leshchiner, Ignaty, MacArthur, Daniel G., McLaughlin, Heather M., Murray, Michael F., Pers, Tune H., Polak, Paz P., Raychaudhuri, Soumya, Rehm, Heidi L., Soemedi, Rachel, Stitziel, Nathan O., Vestecka, Sara, Supper, Jochen, Gugenmus, Claudia, Klocke, Bernward, Hahn, Alexander, Schubach, Max, Menzel, Mortiz, Biskup, Saskia, Freisinger, Peter, Deng, Mario, Braun, Martin, Perner, Sven, Smith, Richard J. H., Andorf, Janeen L., Huang, Jian, Ryckman, Kelli, Sheffield, Val C., Stone, Edwin M., Bair, Thomas, Black-Ziegelbein, E. A., Braun, Terry A., Darbro, Benjamin, DeLuca, Adam P., Kolbe, Diana L., Scheetz, Todd E., Shearer, Aiden E., Sompallae, Rama, Wang, Kai, Bassuk, Alexander G., Edens, Erik, Mathews, Katherine, Moore, Steven A., Shchelochkov, Oleg A., Trapane, Pamela, Bossler, Aaron, Campbell, Colleen A., Heusel, Jonathan W., Kwitek, Anne, Maga, Tara, Panzer, Karin, Wassink, Thomas, Van Daele, Douglas, Azaiez, Hela, Booth, Kevin, Meyer, Nic, Segal, Michael M., Williams, Marc S., Tromp, Gerard, White, Peter, Corsmeier, Donald, Fitzgerald-Butt, Sara, Herman, Gail, Lamb-Thrush, Devon, McBride, Kim L., Newsom, David, Pierson, Christopher R., Rakowsky, Alexander T., Maver, Ales, Lovrečić, Luca, Palandacic, Anja, Peterlin, Borut, Torkamani, Ali, Wedell, Anna, Huss, Mikael, Alexeyenko, Andrey, Lindvall, Jessica M., Magnusson, Mans, Nilsson, Daniel, Stranneheim, Henrik, Taylan, Fulya, Gilissen, Christian, Hoischen, Alexander, van Bon, Bregje, Yntema, Helger, Nelen, Marcel, Zhang, Weidong, Sager, Jason, Zhang, Lu, Blair, Kathryn, Kural, Deniz, Cariaso, Michael, Lennon, Greg G., Javed, Asif, Agrawal, Saloni, Ng, Pauline C., Sandhu, Komal S., Krishna, Shuba, Veeramachaneni, Vamsi, Isakov, Ofer, Halperin, Eran, Friedman, Eitan, Shomron, Noam, Glusman, Gustavo, Roach, Jared C., Caballero, Juan, Cox, Hannah C., Mauldin, Denise, Ament, Seth A., Rowen, Lee, Richards, Daniel R., Lucas, F Anthony S., Gonzalez-Garay, Manuel L., Caskey, C. T., Bai, Yu, Huang, Ying, Fang, Fang, Zhang, Yan, Wang, Zhengyuan, Barrera, Jorge, Garcia-Lobo, Juan M., González-Lamuno, Domingo, Llorca, Javier, Rodriguez, Maria C., Varela, Ignacio, Reese, Martin G., De La Vega, Francisco M., Kiruluta, Edward, Cargill, Michele, Hart, Reece K., Sorenson, Jon M., Lyon, Gholson J., Stevenson, David A., Bray, Bruce E., Moore, Barry M., Eilbeck, Karen, Yandell, Mark, Zhao, Hongyu, Hou, Lin, Chen, Xiaowei, Yan, Xiting, Chen, Mengjie, Li, Cong, Yang, Can, Gunel, Murat, Li, Peining, Kong, Yong, Alexander, Austin C., Albertyn, Zayed I., Boycott, Kym M., Bulman, Dennis E., Gordon, Paul M. K., Innes, A. M., Knoppers, Bartha M., Majewski, Jacek, Marshall, Christian R., Parboosingh, Jillian S., Sawyer, Sarah L., Samuels, Mark E., Schwartzentruber, Jeremy, Kohane, Isaac, and Margulies, David M.

Abstract

Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups., Boston Children's Hospital (Manton Center for Orphan Disease Research), Harvard Medical School (Center for Biomedical Infomatics)

Published
2014

33. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

Author

Brownstein, Catherine A, primary, Beggs, Alan H, additional, Homer, Nils, additional, Merriman, Barry, additional, Yu, Timothy W, additional, Flannery, Katherine C, additional, DeChene, Elizabeth T, additional, Towne, Meghan C, additional, Savage, Sarah K, additional, Price, Emily N, additional, Holm, Ingrid A, additional, Luquette, Lovelace J, additional, Lyon, Elaine, additional, Majzoub, Joseph, additional, Neupert, Peter, additional, McCallie Jr, David, additional, Szolovits, Peter, additional, Willard, Huntington F, additional, Mendelsohn, Nancy J, additional, Temme, Renee, additional, Finkel, Richard S, additional, Yum, Sabrina W, additional, Medne, Livija, additional, Sunyaev, Shamil R, additional, Adzhubey, Ivan, additional, Cassa, Christopher A, additional, de Bakker, Paul IW, additional, Duzkale, Hatice, additional, Dworzyński, Piotr, additional, Fairbrother, William, additional, Francioli, Laurent, additional, Funke, Birgit H, additional, Giovanni, Monica A, additional, Handsaker, Robert E, additional, Lage, Kasper, additional, Lebo, Matthew S, additional, Lek, Monkol, additional, Leshchiner, Ignaty, additional, MacArthur, Daniel G, additional, McLaughlin, Heather M, additional, Murray, Michael F, additional, Pers, Tune H, additional, Polak, Paz P, additional, Raychaudhuri, Soumya, additional, Rehm, Heidi L, additional, Soemedi, Rachel, additional, Stitziel, Nathan O, additional, Vestecka, Sara, additional, Supper, Jochen, additional, Gugenmus, Claudia, additional, Klocke, Bernward, additional, Hahn, Alexander, additional, Schubach, Max, additional, Menzel, Mortiz, additional, Biskup, Saskia, additional, Freisinger, Peter, additional, Deng, Mario, additional, Braun, Martin, additional, Perner, Sven, additional, Smith, Richard JH, additional, Andorf, Janeen L, additional, Huang, Jian, additional, Ryckman, Kelli, additional, Sheffield, Val C, additional, Stone, Edwin M, additional, Bair, Thomas, additional, Black-Ziegelbein, E, additional, Braun, Terry A, additional, Darbro, Benjamin, additional, DeLuca, Adam P, additional, Kolbe, Diana L, additional, Scheetz, Todd E, additional, Shearer, Aiden E, additional, Sompallae, Rama, additional, Wang, Kai, additional, Bassuk, Alexander G, additional, Edens, Erik, additional, Mathews, Katherine, additional, Moore, Steven A, additional, Shchelochkov, Oleg A, additional, Trapane, Pamela, additional, Bossler, Aaron, additional, Campbell, Colleen A, additional, Heusel, Jonathan W, additional, Kwitek, Anne, additional, Maga, Tara, additional, Panzer, Karin, additional, Wassink, Thomas, additional, Van Daele, Douglas, additional, Azaiez, Hela, additional, Booth, Kevin, additional, Meyer, Nic, additional, Segal, Michael M, additional, Williams, Marc S, additional, Tromp, Gerard, additional, White, Peter, additional, Corsmeier, Donald, additional, Fitzgerald-Butt, Sara, additional, Herman, Gail, additional, Lamb-Thrush, Devon, additional, McBride, Kim L, additional, Newsom, David, additional, Pierson, Christopher R, additional, Rakowsky, Alexander T, additional, Maver, Aleš, additional, Lovrečić, Luca, additional, Palandačić, Anja, additional, Peterlin, Borut, additional, Torkamani, Ali, additional, Wedell, Anna, additional, Huss, Mikael, additional, Alexeyenko, Andrey, additional, Lindvall, Jessica M, additional, Magnusson, Måns, additional, Nilsson, Daniel, additional, Stranneheim, Henrik, additional, Taylan, Fulya, additional, Gilissen, Christian, additional, Hoischen, Alexander, additional, van Bon, Bregje, additional, Yntema, Helger, additional, Nelen, Marcel, additional, Zhang, Weidong, additional, Sager, Jason, additional, Zhang, Lu, additional, Blair, Kathryn, additional, Kural, Deniz, additional, Cariaso, Michael, additional, Lennon, Greg G, additional, Javed, Asif, additional, Agrawal, Saloni, additional, Ng, Pauline C, additional, Sandhu, Komal S, additional, Krishna, Shuba, additional, Veeramachaneni, Vamsi, additional, Isakov, Ofer, additional, Halperin, Eran, additional, Friedman, Eitan, additional, Shomron, Noam, additional, Glusman, Gustavo, additional, Roach, Jared C, additional, Caballero, Juan, additional, Cox, Hannah C, additional, Mauldin, Denise, additional, Ament, Seth A, additional, Rowen, Lee, additional, Richards, Daniel R, additional, Lucas, F Anthony, additional, Gonzalez-Garay, Manuel L, additional, Caskey, C, additional, Bai, Yu, additional, Huang, Ying, additional, Fang, Fang, additional, Zhang, Yan, additional, Wang, Zhengyuan, additional, Barrera, Jorge, additional, Garcia-Lobo, Juan M, additional, González-Lamuño, Domingo, additional, Llorca, Javier, additional, Rodriguez, Maria C, additional, Varela, Ignacio, additional, Reese, Martin G, additional, De La Vega, Francisco M, additional, Kiruluta, Edward, additional, Cargill, Michele, additional, Hart, Reece K, additional, Sorenson, Jon M, additional, Lyon, Gholson J, additional, Stevenson, David A, additional, Bray, Bruce E, additional, Moore, Barry M, additional, Eilbeck, Karen, additional, Yandell, Mark, additional, Zhao, Hongyu, additional, Hou, Lin, additional, Chen, Xiaowei, additional, Yan, Xiting, additional, Chen, Mengjie, additional, Li, Cong, additional, Yang, Can, additional, Gunel, Murat, additional, Li, Peining, additional, Kong, Yong, additional, Alexander, Austin C, additional, Albertyn, Zayed I, additional, Boycott, Kym M, additional, Bulman, Dennis E, additional, Gordon, Paul MK, additional, Innes, A, additional, Knoppers, Bartha M, additional, Majewski, Jacek, additional, Marshall, Christian R, additional, Parboosingh, Jillian S, additional, Sawyer, Sarah L, additional, Samuels, Mark E, additional, Schwartzentruber, Jeremy, additional, Kohane, Isaac S, additional, and Margulies, David M, additional

Published
2014
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34. Evidence-Based Decision Support for Neurological Diagnosis Reduces Errors and Unnecessary Workup

Author

Segal, Michael M., primary, Williams, Marc S., additional, Gropman, Andrea L., additional, Torres, Alcy R., additional, Forsyth, Rob, additional, Connolly, Anne M., additional, El-Hattab, Ayman W., additional, Perlman, Seth J., additional, Samanta, Debopam, additional, Parikh, Sumit, additional, Pavlakis, Steven G., additional, Feldman, Lynn K., additional, Betensky, Rebecca A., additional, and Gospe, Sidney M., additional

Published
2013
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37. Clinical Pertinence Metric Enables Hypothesis-Independent Genome-Phenome Analysis for Neurologic Diagnosis.

Author

Segal, Michael M., Abdellateef, Mostafa, El-Hattab, Ayman W., Hilbush, Brian S., De La Vega, Francisco M., Tromp, Gerard, Williams, Marc S., Betensky, Rebecca A., and Gleeson, Joseph

Subjects
*DIFFERENTIAL diagnosis, *DIAGNOSIS of neurological disorders, *NEUROLOGICAL disorders -- Genetic aspects, *NEUROLOGY, *HUMAN genome
Abstract

We describe an “integrated genome-phenome analysis” that combines both genomic sequence data and clinical information for genomic diagnosis. It is novel in that it uses robust diagnostic decision support and combines the clinical differential diagnosis and the genomic variants using a “pertinence” metric. This allows the analysis to be hypothesis-independent, not requiring assumptions about mode of inheritance, number of genes involved, or which clinical findings are most relevant. Using 20 genomic trios with neurologic disease, we find that pertinence scores averaging 99.9% identify the causative variant under conditions in which a genomic trio is analyzed and family-aware variant calling is done. The analysis takes seconds, and pertinence scores can be improved by clinicians adding more findings. The core conclusion is that automated genome-phenome analysis can be accurate, rapid, and efficient. We also conclude that an automated process offers a methodology for quality improvement of many components of genomic analysis. [ABSTRACT FROM PUBLISHER]

Published
2015
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40. Evidence-Based Decision Support for Neurological Diagnosis Reduces Errors and Unnecessary Workup.

Author

Segal, Michael M., Williams, Marc S., Gropman, Andrea L., Torres, Alcy R., Forsyth, Rob, Connolly, Anne M., El-Hattab, Ayman W., Perlman, Seth J., Samanta, Debopam, Parikh, Sumit, Pavlakis, Steven G., Feldman, Lynn K., Betensky, Rebecca A., and Gospe, Sidney M.

Subjects
*DIAGNOSTIC examinations, *ERRORS & omissions insurance, *NEUROSCIENCES, *NEUROLOGY, *VIGNETTES
Abstract

Using vignettes of real cases and the SimulConsult diagnostic decision support software, neurologists listed a differential diagnosis and workup before and after using the decision support. Using the software, there was a significant reduction in error, up to 75% for diagnosis and 56% for workup. This error reduction occurred despite the baseline being one in which testers were allowed to use narrative resources and Web searching. A key factor that improved performance was taking enough time (>2 minutes) to enter clinical findings into the software accurately. Under these conditions and for instances in which the diagnoses changed based on using the software, diagnostic accuracy improved in 96% of instances. There was a 6% decrease in the number of workup items accompanied by a 34% increase in relevance. The authors conclude that decision support for a neurological diagnosis can reduce errors and save on unnecessary testing. [ABSTRACT FROM PUBLISHER]

Published
2014
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42. Spilled some salt? Call OSHA

Author

Segal, Michael M.

Subjects
United States. Occupational Safety and Health Administration -- Laws, regulations and rules, Chemicals -- Labeling, Business, Business, general
Published
1991

43. Unisex insurance: a 'fairness' costly to women

Author

Stricker, Irwin J., Lautzenheiser, Barbara J., and Segal, Michael M.

Subjects
Sex discrimination against women -- Economic aspects, Discrimination in insurance -- Economic aspects
Published
1984

48. Explorations in Parallel Distributed Processing: A Handbook of Models, Programs, and Exercises

Author

Segal, Michael M.

Subjects
Explorations in Parallel Distributed Processing: A Handbook of Models, Programs, and Exercises (Book), Books -- Book reviews, Science and technology
Abstract

Explorations in Parallel Distributed Processing This publication, produced by one of the leading neural network groups and illustrating much of their work, is a landmark. The package consists of a [...]

Published
1988

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