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1. Minimum information and guidelines for reporting a Multiplexed Assay of Variant Effect

Author

Claussnitzer, Melina, Parikh, Victoria N., Wagner, Alex H., Arbesfeld, Jeremy A., Bult, Carol J., Firth, Helen V., Muffley, Lara A., Ba, Alex N. Nguyen, Riehle, Kevin, Roth, Frederick P., Tabet, Daniel, Bolognesi, Benedetta, Glazer, Andrew M., and Rubin, Alan F.

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

Multiplexed Assays of Variant Effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniques across diverse disciplines has led to a heterogeneous mix of data formats and descriptions, which complicates the downstream use of the resulting datasets. To address these issues and promote reproducibility and reuse of MAVE data, we define a set of minimum information standards for MAVE data and metadata and outline a controlled vocabulary aligned with established biomedical ontologies for describing these experimental designs.

Published
2023

3. GA4GH Phenopackets: A Practical Introduction

Author

Ladewig, Markus S, Jacobsen, Julius OB, Wagner, Alex H, Danis, Daniel, Kassaby, Baha El, Gargano, Michael, Groza, Tudor, Baudis, Michael, Steinhaus, Robin, Seelow, Dominik, Bechrakis, Nikolaos E, Mungall, Christopher J, Schofield, Paul N, Elemento, Olivier, Smith, Lindsay, McMurry, Julie A, Munoz‐Torres, Monica, Haendel, Melissa A, and Robinson, Peter N

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Health Services and Systems, Health Sciences, Biotechnology, Networking and Information Technology R&D (NITRD), Rare Diseases, Human Genome, Cancer, Generic health relevance, Good Health and Well Being, FAIR data, Global Alliance for Genomics and Health, Human Phenotype Ontology, Phenopacket Schema, deep phenotyping
Abstract

The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. A detailed example is presented that illustrates how to use the schema to represent the clinical course of a patient with retinoblastoma, including demographic information, the clinical diagnosis, phenotypic features and clinical measurements, an examination of the extirpated tumor, therapies, and the results of genomic analysis. The Phenopacket Schema, together with other GA4GH data and technical standards, will enable data exchange and provide a foundation for the computational analysis of disease and phenotype information to improve our ability to diagnose and conduct research on all types of disorders, including cancer and rare diseases.

Published
2023

4. Phenopacket-tools: Building and validating GA4GH Phenopackets

Author

Danis, Daniel, Jacobsen, Julius OB, Wagner, Alex H, Groza, Tudor, Beckwith, Martha A, Rekerle, Lauren, Carmody, Leigh C, Reese, Justin, Hegde, Harshad, Ladewig, Markus S, Seitz, Berthold, Munoz-Torres, Monica, Harris, Nomi L, Rambla, Jordi, Baudis, Michael, Mungall, Christopher J, Haendel, Melissa A, and Robinson, Peter N

Subjects
Information and Computing Sciences, Biological Sciences, Genetics, Precision Medicine, Biotechnology, Human Genome, 1.5 Resources and infrastructure (underpinning), 2.6 Resources and infrastructure (aetiology), Humans, Software, Genomics, Databases, Factual, Neoplasms, Gene Library, General Science & Technology
Abstract

The Global Alliance for Genomics and Health (GA4GH) is a standards-setting organization that is developing a suite of coordinated standards for genomics. The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information that characterizes an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including rare disease, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. We present phenopacket-tools, an open-source Java library and command-line application for construction, conversion, and validation of phenopackets. Phenopacket-tools simplifies construction of phenopackets by providing concise builders, programmatic shortcuts, and predefined building blocks (ontology classes) for concepts such as anatomical organs, age of onset, biospecimen type, and clinical modifiers. Phenopacket-tools can be used to validate the syntax and semantics of phenopackets as well as to assess adherence to additional user-defined requirements. The documentation includes examples showing how to use the Java library and the command-line tool to create and validate phenopackets. We demonstrate how to create, convert, and validate phenopackets using the library or the command-line application. Source code, API documentation, comprehensive user guide and a tutorial can be found at https://github.com/phenopackets/phenopacket-tools. The library can be installed from the public Maven Central artifact repository and the application is available as a standalone archive. The phenopacket-tools library helps developers implement and standardize the collection and exchange of phenotypic and other clinical data for use in phenotype-driven genomic diagnostics, translational research, and precision medicine applications.

Published
2023

5. A Simple Standard for Sharing Ontological Mappings (SSSOM)

Author

Matentzoglu, Nicolas, Balhoff, James P., Bello, Susan M., Bizon, Chris, Brush, Matthew, Callahan, Tiffany J., Chute, Christopher G, Duncan, William D., Evelo, Chris T., Gabriel, Davera, Graybeal, John, Gray, Alasdair, Gyori, Benjamin M., Haendel, Melissa, Harmse, Henriette, Harris, Nomi L., Harrow, Ian, Hegde, Harshad, Hoyt, Amelia L., Hoyt, Charles T., Jiao, Dazhi, Jiménez-Ruiz, Ernesto, Jupp, Simon, Kim, Hyeongsik, Koehler, Sebastian, Liener, Thomas, Long, Qinqin, Malone, James, McLaughlin, James A., McMurry, Julie A., Moxon, Sierra, Munoz-Torres, Monica C., Osumi-Sutherland, David, Overton, James A., Peters, Bjoern, Putman, Tim, Queralt-Rosinach, Núria, Shefchek, Kent, Solbrig, Harold, Thessen, Anne, Tudorache, Tania, Vasilevsky, Nicole, Wagner, Alex H., and Mungall, Christopher J.

Subjects
Computer Science - Databases
Abstract

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Are they associated in some other way? Such relationships between the mapped terms are often not documented, leading to incorrect assumptions and making them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Also, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. The Simple Standard for Sharing Ontological Mappings (SSSOM) addresses these problems by: 1. Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. 2. Defining an easy to use table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data standards. 3. Implementing open and community-driven collaborative workflows designed to evolve the standard continuously to address changing requirements and mapping practices. 4. Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases, and survey some existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable, and Reusable (FAIR). The SSSOM specification is at http://w3id.org/sssom/spec., Comment: Corresponding author: Christopher J. Mungall

Published
2021
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6. The GA4GH Phenopacket schema defines a computable representation of clinical data

Author

Jacobsen, Julius OB, Baudis, Michael, Baynam, Gareth S, Beckmann, Jacques S, Beltran, Sergi, Buske, Orion J, Callahan, Tiffany J, Chute, Christopher G, Courtot, Mélanie, Danis, Daniel, Elemento, Olivier, Essenwanger, Andrea, Freimuth, Robert R, Gargano, Michael A, Groza, Tudor, Hamosh, Ada, Harris, Nomi L, Kaliyaperumal, Rajaram, Lloyd, Kevin C Kent, Khalifa, Aly, Krawitz, Peter M, Köhler, Sebastian, Laraway, Brian J, Lehväslaiho, Heikki, Matalonga, Leslie, McMurry, Julie A, Metke-Jimenez, Alejandro, Mungall, Christopher J, Munoz-Torres, Monica C, Ogishima, Soichi, Papakonstantinou, Anastasios, Piscia, Davide, Pontikos, Nikolas, Queralt-Rosinach, Núria, Roos, Marco, Sass, Julian, Schofield, Paul N, Seelow, Dominik, Siapos, Anastasios, Smedley, Damian, Smith, Lindsay D, Steinhaus, Robin, Sundaramurthi, Jagadish Chandrabose, Swietlik, Emilia M, Thun, Sylvia, Vasilevsky, Nicole A, Wagner, Alex H, Warner, Jeremy L, Weiland, Claus, Haendel, Melissa A, and Robinson, Peter N

Subjects
GAGH Phenopacket Modeling Consortium
Published
2022

7. A Simple Standard for Sharing Ontological Mappings (SSSOM)

Author

Matentzoglu, Nicolas, Balhoff, James P, Bello, Susan M, Bizon, Chris, Brush, Matthew, Callahan, Tiffany J, Chute, Christopher G, Duncan, William D, Evelo, Chris T, Gabriel, Davera, Graybeal, John, Gray, Alasdair, Gyori, Benjamin M, Haendel, Melissa, Harmse, Henriette, Harris, Nomi L, Harrow, Ian, Hegde, Harshad B, Hoyt, Amelia L, Hoyt, Charles T, Jiao, Dazhi, Jiménez-Ruiz, Ernesto, Jupp, Simon, Kim, Hyeongsik, Koehler, Sebastian, Liener, Thomas, Long, Qinqin, Malone, James, McLaughlin, James A, McMurry, Julie A, Moxon, Sierra, Munoz-Torres, Monica C, Osumi-Sutherland, David, Overton, James A, Peters, Bjoern, Putman, Tim, Queralt-Rosinach, Núria, Shefchek, Kent, Solbrig, Harold, Thessen, Anne, Tudorache, Tania, Vasilevsky, Nicole, Wagner, Alex H, and Mungall, Christopher J

Subjects
Data Management and Data Science, Information and Computing Sciences, Networking and Information Technology R&D (NITRD), Data Science, Data Management, Databases, Factual, Metadata, Semantic Web, Workflow, Data Format, Library and Information Studies, Bioinformatics and computational biology, Data management and data science
Abstract

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec.

Published
2022

8. The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification

Author

Wagner, Alex H, Babb, Lawrence, Alterovitz, Gil, Baudis, Michael, Brush, Matthew, Cameron, Daniel L, Cline, Melissa, Griffith, Malachi, Griffith, Obi L, Hunt, Sarah E, Kreda, David, Lee, Jennifer M, Li, Stephanie, Lopez, Javier, Moyer, Eric, Nelson, Tristan, Patel, Ronak Y, Riehle, Kevin, Robinson, Peter N, Rynearson, Shawn, Schuilenburg, Helen, Tsukanov, Kirill, Walsh, Brian, Konopko, Melissa, Rehm, Heidi L, Yates, Andrew D, Freimuth, Robert R, and Hart, Reece K

Subjects
Biological Sciences, Genetics, Human Genome
Abstract

Maximizing the personal, public, research, and clinical value of genomic information will require the reliable exchange of genetic variation data. We report here the Variation Representation Specification (VRS, pronounced "verse"), an extensible framework for the computable representation of variation that complements contemporary human-readable and flat file standards for genomic variation representation. VRS provides semantically precise representations of variation and leverages this design to enable federated identification of biomolecular variation with globally consistent and unique computed identifiers. The VRS framework includes a terminology and information model, machine-readable schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. VRS was developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH).

Published
2021

9. Genomic architecture of FGFR2 fusions in cholangiocarcinoma and its implication for molecular testing

Author

Neumann, Olaf, Burn, Timothy C., Allgäuer, Michael, Ball, Markus, Kirchner, Martina, Albrecht, Thomas, Volckmar, Anna-Lena, Beck, Susanne, Endris, Volker, Goldschmid, Hannah, Lehmann, Ulrich, Seker-Cin, Huriye, Uhrig, Sebastian, Roessler, Stephanie, Budczies, Jan, Fröhling, Stefan, Longerich, Thomas, Wagner, Alex H., Vogel, Arndt, Schirmacher, Peter, Stenzinger, Albrecht, and Kazdal, Daniel

Published
2022
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10. A community approach to the cancer-variant-interpretation bottleneck

Author

Krysiak, Kilannin, Danos, Arpad M., Kiwala, Susanna, McMichael, Joshua F., Coffman, Adam C., Barnell, Erica K., Sheta, Lana, Saliba, Jason, Grisdale, Cameron J., Kujan, Lynzey, Pema, Shahil, Lever, Jake, Spies, Nicholas C., Chiorean, Andreea, Rieke, Damian T., Clark, Kaitlin A., Jani, Payal, Takahashi, Hideaki, Horak, Peter, Ritter, Deborah I., Zhou, Xin, Ainscough, Benjamin J., Delong, Sean, Lamping, Mario, Marr, Alex R., Li, Brian V., Lin, Wan-Hsin, Terraf, Panieh, Salama, Yasser, Campbell, Katie M., Farncombe, Kirsten M., Ji, Jianling, Zhao, Xiaonan, Xu, Xinjie, Kanagal-Shamanna, Rashmi, Cotto, Kelsy C., Skidmore, Zachary L., Walker, Jason R., Zhang, Jinghui, Milosavljevic, Aleksandar, Patel, Ronak Y., Giles, Rachel H., Kim, Raymond H., Schriml, Lynn M., Mardis, Elaine R., Jones, Steven J. M., Raca, Gordana, Rao, Shruti, Madhavan, Subha, Wagner, Alex H., Griffith, Obi L., and Griffith, Malachi

Published
2022
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11. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)

Author

Horak, Peter, Griffith, Malachi, Danos, Arpad M., Pitel, Beth A., Madhavan, Subha, Liu, Xuelu, Chow, Cynthia, Williams, Heather, Carmody, Leigh, Barrow-Laing, Lisa, Rieke, Damian, Kreutzfeldt, Simon, Stenzinger, Albrecht, Tamborero, David, Benary, Manuela, Rajagopal, Padma Sheila, Ida, Cristiane M., Lesmana, Harry, Satgunaseelan, Laveniya, Merker, Jason D., Tolstorukov, Michael Y., Campregher, Paulo Vidal, Warner, Jeremy L., Rao, Shruti, Natesan, Maya, Shen, Haolin, Venstrom, Jeffrey, Roy, Somak, Tao, Kayoko, Kanagal-Shamanna, Rashmi, Xu, Xinjie, Ritter, Deborah I., Pagel, Kym, Krysiak, Kilannin, Dubuc, Adrian, Akkari, Yassmine M., Li, Xuan Shirley, Lee, Jennifer, King, Ian, Raca, Gordana, Wagner, Alex H., Li, Marylin M., Plon, Sharon E., Kulkarni, Shashikant, Griffith, Obi L., Chakravarty, Debyani, and Sonkin, Dmitriy

Published
2022
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12. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Rehm, Heidi L., Page, Angela J.H., Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J.S., Beck, Tim, Beckmann, Jacques S., Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K., Boughtwood, Tiffany F., Bourque, Guillaume, Bowers, Sarion R., Brookes, Anthony J., Brudno, Michael, Brush, Matthew H., Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, L. Jonathan, Dyke, Stephanie O.M., Eddy, James A., Eilbeck, Karen, Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M., Ho, Calvin W.L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jené, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J.M., Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M., Kekesi-Lafrance, Kristina, Kelleher, Jerome, Kerry, Giselle, Khor, Seik-Soon, Knoppers, Bartha M., Konopko, Melissa A., Kosaki, Kenjiro, Kuba, Martin, Lawson, Jonathan, Leinonen, Rasko, Li, Stephanie, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Liyanage, Isuru Udara, Lopez, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Metke-Jimenez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Munoz-Torres, Monica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Ota Wang, Vivian, Paglione, Laura A.D., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Rodriguez, Laura Lyman, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos, Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Guimera, Roman Valls, Vamathevan, Jessica, Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, North, Kathryn, and Birney, Ewan

Published
2021
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13. DGIdb 5.0: rebuilding the drug–gene interaction database for precision medicine and drug discovery platforms

Author

Cannon, Matthew, primary, Stevenson, James, additional, Stahl, Kathryn, additional, Basu, Rohit, additional, Coffman, Adam, additional, Kiwala, Susanna, additional, McMichael, Joshua F, additional, Kuzma, Kori, additional, Morrissey, Dorian, additional, Cotto, Kelsy, additional, Mardis, Elaine R, additional, Griffith, Obi L, additional, Griffith, Malachi, additional, and Wagner, Alex H, additional

Published
2023
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14. 52. ClinGen Pediatric Cancer Taskforce initiatives to advance pediatric clinical interpretations through expert curation

Author

Saliba, Jason, primary, Corson, Laura B., additional, Lever, Jake, additional, Golem, Shivani, additional, Satgunaseelan, Laveniya, additional, Meredith, David M., additional, Grisdale, Cameron J., additional, Krysiak, Kilannin, additional, Evans, Mark G., additional, Luo, Minjie, additional, Sukhanova, Madina, additional, Mathew, Mariam T., additional, Seifi, Morteza, additional, Williams, Heather E., additional, Yap, Kai Lee, additional, Akesson, Lauren, additional, Kanagal-Shamanna, Rashmi, additional, Ji, Jianling, additional, Fakim, Yasmina Jaufeerally, additional, Danos, Arpad, additional, Akkari, Yassmine, additional, Parsons, D. Williams, additional, Schriml, Lynn, additional, Wagner, Alex H., additional, Griffith, Obi L., additional, Griffith, Malachi, additional, Roy, Angshumoy, additional, and Raca, Gordana, additional

Published
2023
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16. Discovery of clinically relevant fusions in pediatric cancer

Author

LaHaye, Stephanie, Fitch, James R., Voytovich, Kyle J., Herman, Adam C., Kelly, Benjamin J., Lammi, Grant E., Arbesfeld, Jeremy A., Wijeratne, Saranga, Franklin, Samuel J., Schieffer, Kathleen M., Bir, Natalie, McGrath, Sean D., Miller, Anthony R., Wetzel, Amy, Miller, Katherine E., Bedrosian, Tracy A., Leraas, Kristen, Varga, Elizabeth A., Lee, Kristy, Gupta, Ajay, Setty, Bhuvana, Boué, Daniel R., Leonard, Jeffrey R., Finlay, Jonathan L., Abdelbaki, Mohamed S., Osorio, Diana S., Koo, Selene C., Koboldt, Daniel C., Wagner, Alex H., Eisfeld, Ann-Kathrin, Mrózek, Krzysztof, Magrini, Vincent, Cottrell, Catherine E., Mardis, Elaine R., Wilson, Richard K., and White, Peter

Published
2021
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21. Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples

Author

Barnell, Erica K., Ronning, Peter, Campbell, Katie M., Krysiak, Kilannin, Ainscough, Benjamin J., Sheta, Lana M., Pema, Shahil P., Schmidt, Alina D., Richters, Megan, Cotto, Kelsy C., Danos, Arpad M., Ramirez, Cody, Skidmore, Zachary L., Spies, Nicholas C., Hundal, Jasreet, Sediqzad, Malik S., Kunisaki, Jason, Gomez, Felicia, Trani, Lee, Matlock, Matthew, Wagner, Alex H., Swamidass, S. Joshua, Griffith, Malachi, and Griffith, Obi L.

Published
2019
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23. Standard operating procedure for curation and clinical interpretation of variants in cancer

Author

Danos, Arpad M., Krysiak, Kilannin, Barnell, Erica K., Coffman, Adam C., McMichael, Joshua F., Kiwala, Susanna, Spies, Nicholas C., Sheta, Lana M., Pema, Shahil P., Kujan, Lynzey, Clark, Kaitlin A., Wollam, Amber Z., Rao, Shruti, Ritter, Deborah I., Sonkin, Dmitriy, Raca, Gordana, Lin, Wan-Hsin, Grisdale, Cameron J., Kim, Raymond H., Wagner, Alex H., Madhavan, Subha, Griffith, Malachi, and Griffith, Obi L.

Published
2019
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24. Tumor Heterogeneity

Author

Wagner, Alex H., primary, Krysiak, Kilannin, additional, Campbell, Katie M., additional, and Barnell, Erica K., additional

Published
2019
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25. CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

Author

Krysiak, Kilannin, primary, Danos, Arpad M, additional, Saliba, Jason, additional, McMichael, Joshua F, additional, Coffman, Adam C, additional, Kiwala, Susanna, additional, Barnell, Erica K, additional, Sheta, Lana, additional, Grisdale, Cameron J, additional, Kujan, Lynzey, additional, Pema, Shahil, additional, Lever, Jake, additional, Ridd, Sarah, additional, Spies, Nicholas C, additional, Andric, Veronica, additional, Chiorean, Andreea, additional, Rieke, Damian T, additional, Clark, Kaitlin A, additional, Reisle, Caralyn, additional, Venigalla, Ajay C, additional, Evans, Mark, additional, Jani, Payal, additional, Takahashi, Hideaki, additional, Suda, Avila, additional, Horak, Peter, additional, Ritter, Deborah I, additional, Zhou, Xin, additional, Ainscough, Benjamin J, additional, Delong, Sean, additional, Kesserwan, Chimene, additional, Lamping, Mario, additional, Shen, Haolin, additional, Marr, Alex R, additional, Hoang, My H, additional, Singhal, Kartik, additional, Khanfar, Mariam, additional, Li, Brian V, additional, Lin, Wan-Hsin, additional, Terraf, Panieh, additional, Corson, Laura B, additional, Salama, Yasser, additional, Campbell, Katie M, additional, Farncombe, Kirsten M, additional, Ji, Jianling, additional, Zhao, Xiaonan, additional, Xu, Xinjie, additional, Kanagal-Shamanna, Rashmi, additional, King, Ian, additional, Cotto, Kelsy C, additional, Skidmore, Zachary L, additional, Walker, Jason R, additional, Zhang, Jinghui, additional, Milosavljevic, Aleksandar, additional, Patel, Ronak Y, additional, Giles, Rachel H, additional, Kim, Raymond H, additional, Schriml, Lynn M, additional, Mardis, Elaine R, additional, Jones, Steven J M, additional, Raca, Gordana, additional, Rao, Shruti, additional, Madhavan, Subha, additional, Wagner, Alex H, additional, Griffith, Malachi, additional, and Griffith, Obi L, additional

Published
2022
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26. Development and application of a computable genotype model in the GA4GH Variation Representation Specification

Author

Goar, Wesley, primary, Babb, Lawrence, additional, Chamala, Srikar, additional, Cline, Melissa, additional, Freimuth, Robert R., additional, Hart, Reece K., additional, Kuzma, Kori, additional, Lee, Jennifer, additional, Nelson, Tristan, additional, Prlić, Andreas, additional, Riehle, Kevin, additional, Smith, Anastasia, additional, Stahl, Kathryn, additional, Yates, Andrew D., additional, Rehm, Heidi L., additional, and Wagner, Alex H., additional

Published
2022
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28. 11. The complex nature of variant interactions in cancer requires updates to variant interpretation resources

Author

Krysiak, Kilannin, primary, Kiwala, Susanna, additional, Coffman, Adam C., additional, McMichael, Joshua F., additional, Danos, Arpad M., additional, Saliba, Jason, additional, Grisdale, Cameron J., additional, Lever, Jake, additional, Sheta, Lana, additional, Rao, Shruti, additional, Wagner, Alex H., additional, Griffith, Malachi, additional, and Griffith, Obi L., additional

Published
2022
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30. Artificial intelligence and pathology: From principles to practice and future applications in histomorphology and molecular profiling

Author

Stenzinger, Albrecht, primary, Alber, Maximilian, additional, Allgäuer, Michael, additional, Jurmeister, Philipp, additional, Bockmayr, Michael, additional, Budczies, Jan, additional, Lennerz, Jochen, additional, Eschrich, Johannes, additional, Kazdal, Daniel, additional, Schirmacher, Peter, additional, Wagner, Alex H., additional, Tacke, Frank, additional, Capper, David, additional, Müller, Klaus-Robert, additional, and Klauschen, Frederick, additional

Published
2022
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31. GA4GH Phenopackets: A Practical Introduction

Author

Ladewig, Markus S., primary, Jacobsen, Julius O. B., additional, Wagner, Alex H., additional, Danis, Daniel, additional, El Kassaby, Baha, additional, Gargano, Michael, additional, Groza, Tudor, additional, Baudis, Michael, additional, Steinhaus, Robin, additional, Seelow, Dominik, additional, Bechrakis, Nikolaos E., additional, Mungall, Christopher J., additional, Schofield, Paul N., additional, Elemento, Olivier, additional, Smith, Lindsay, additional, McMurry, Julie A., additional, Munoz‐Torres, Monica, additional, Haendel, Melissa A., additional, and Robinson, Peter N., additional

Published
2022
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32. Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer

Author

Wagner, Alex H., Devarakonda, Siddhartha, Skidmore, Zachary L., Krysiak, Kilannin, Ramu, Avinash, Trani, Lee, Kunisaki, Jason, Masood, Ashiq, Waqar, Saiama N., Spies, Nicholas C., Morgensztern, Daniel, Waligorski, Jason, Ponce, Jennifer, Fulton, Robert S., Maggi, Jr., Leonard B., Weber, Jason D., Watson, Mark A., O’Conor, Christopher J., Ritter, Jon H., Olsen, Rachelle R., Cheng, Haixia, Mukhopadhyay, Anandaroop, Can, Ismail, Cessna, Melissa H., Oliver, Trudy G., Mardis, Elaine R., Wilson, Richard K., Griffith, Malachi, Griffith, Obi L., and Govindan, Ramaswamy

Published
2018
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33. Abstract 1194: Redesigning CIViC: Enhancing the structured curation of complex cancer variant data

Author

Krysiak, Kilannin C., primary, Coffman, Adam C., additional, Kiwala, Susanna, additional, McMichael, Joshua F., additional, Danos, Arpad M., additional, Saliba, Jason, additional, Grisdale, Cameron J., additional, Lever, Jake, additional, Sheta, Lana, additional, Rao, Shruti, additional, Wagner, Alex H., additional, Griffith, Malachi, additional, and Griffith, Obi L., additional

Published
2022
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34. Abstract 1177: Introduction of the GA4GH Variation Representation Specification (VRS) and supporting tools for discovery and exchange of clinical genomic and cytogenomic knowledge in cancers

Author

Cannon, Matthew, primary, Kuzma, Kori, additional, Stevenson, James, additional, Liu, Jiachen, additional, O'Sullivan, Colin, additional, Chaudhari, Bimal P., additional, Brush, Matthew, additional, Freimuth, Robert R., additional, Nelson, Tristan, additional, Baudis, Michael, additional, Griffith, Obi L., additional, Griffith, Malachi, additional, Babb, Lawrence, additional, Cline, Melissa S., additional, Liu, Xuelu, additional, Walsh, Brian, additional, and Wagner, Alex H., additional

Published
2022
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35. Mondo: Unifying diseases for the world, by the world

Author

Vasilevsky, Nicole A, primary, Matentzoglu, Nicolas A, additional, Toro, Sabrina, additional, Flack, Joseph E, additional, Hegde, Harshad, additional, Unni, Deepak R, additional, Alyea, Gioconda F, additional, Amberger, Joanna S, additional, Babb, Larry, additional, Balhoff, James P, additional, Bingaman, Taylor I, additional, Burns, Gully A, additional, Buske, Orion J, additional, Callahan, Tiffany J, additional, Carmody, Leigh C, additional, Cordo, Paula Carrio, additional, Chan, Lauren E, additional, Chang, George S, additional, Christiaens, Sean L, additional, Dumontier, Michel, additional, Failla, Laura E, additional, Flowers, May J, additional, Garrett, H. Alpha, additional, Goldstein, Jennifer L, additional, Gration, Dylan, additional, Groza, Tudor, additional, Hanauer, Marc, additional, Harris, Nomi L, additional, Hilton, Jason A, additional, Himmelstein, Daniel S, additional, Hoyt, Charles Tapley, additional, Kane, Megan S, additional, Köhler, Sebastian, additional, Lagorce, David, additional, Lai, Abbe, additional, Larralde, Martin, additional, Lock, Antonia, additional, López Santiago, Irene, additional, Maglott, Donna R, additional, Malheiro, Adriana J, additional, Meldal, Birgit H M, additional, Munoz-Torres, Monica C, additional, Nelson, Tristan H, additional, Nicholas, Frank W, additional, Ochoa, David, additional, Olson, Daniel P, additional, Oprea, Tudor I, additional, Osumi-Sutherland, David, additional, Parkinson, Helen, additional, Pendlington, Zoë May, additional, Rath, Ana, additional, Rehm, Heidi L, additional, Remennik, Lyubov, additional, Riggs, Erin R, additional, Roncaglia, Paola, additional, Ross, Justyne E, additional, Shadbolt, Marion F, additional, Shefchek, Kent A, additional, Similuk, Morgan N, additional, Sioutos, Nicholas, additional, Smedley, Damian, additional, Sparks, Rachel, additional, Stefancsik, Ray, additional, Stephan, Ralf, additional, Storm, Andrea L, additional, Stupp, Doron, additional, Stupp, Gregory S, additional, Sundaramurthi, Jagadish Chandrabose, additional, Tammen, Imke, additional, Tay, Darin, additional, Thaxton, Courtney L, additional, Valasek, Eloise, additional, Valls-Margarit, Jordi, additional, Wagner, Alex H, additional, Welter, Danielle, additional, Whetzel, Patricia L, additional, Whiteman, Lori L, additional, Wood, Valerie, additional, Xu, Colleen H, additional, Zankl, Andreas, additional, Zhang, Xingmin Aaron, additional, Chute, Christopher G, additional, Robinson, Peter N, additional, Mungall, Christopher J, additional, Hamosh, Ada, additional, and Haendel, Melissa A, additional

Published
2022
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37. 48. Crowdsourcing expert curation of somatic variants by the ClinGen Somatic Hematologic Cancer Taskforce

Author

Rao, Shruti, primary, Saliba, Jason, additional, Zhao, Xiaonan, additional, He, Rong, additional, Kesserwan, Chimene, additional, Danos, Arpad, additional, Sheta, Lana, additional, Terraf, Panieh, additional, Raca, Gordana, additional, Williams, Heather, additional, Blombery, Piers, additional, Viswanatha, David, additional, Eno, Celeste, additional, Mani, Coumarane, additional, Jiang, Nan, additional, Vavra, Kevin C., additional, Zhang, Liying, additional, Shi, Zonggao, additional, Li, Peng, additional, Li, Yuwen, additional, Ouseph, Madhu M., additional, Thompson, Ella, additional, Zhong, Yiming, additional, Krysiak, Kilannin, additional, Wagner, Alex H., additional, McCoy, Matthew, additional, Matthew, Mariam T., additional, Deeb, Kristin, additional, Zhang, Fengli, additional, Liu, Jie, additional, Shao, Xiangqiang, additional, Ferrer, Alejandro, additional, Kopp, Nathan, additional, Zhang, Wenying, additional, Pondugula, Santhi, additional, Fakim, Yasmina Jaufeerally, additional, Wu, David, additional, Pullarkat, Sheeja T., additional, Kulkarni, Shashikant, additional, Madhavan, Subha, additional, Xu, Xinjie, additional, and Kanagal-Shamana, Rashmi, additional

Published
2022
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38. A Simple Standard for Sharing Ontological Mappings (SSSOM)

Author

Matentzoglu, Nicolas, primary, Balhoff, James P, additional, Bello, Susan M, additional, Bizon, Chris, additional, Brush, Matthew, additional, Callahan, Tiffany J, additional, Chute, Christopher G, additional, Duncan, William D, additional, Evelo, Chris T, additional, Gabriel, Davera, additional, Graybeal, John, additional, Gray, Alasdair, additional, Gyori, Benjamin M, additional, Haendel, Melissa, additional, Harmse, Henriette, additional, Harris, Nomi L, additional, Harrow, Ian, additional, Hegde, Harshad B, additional, Hoyt, Amelia L, additional, Hoyt, Charles T, additional, Jiao, Dazhi, additional, Jiménez-Ruiz, Ernesto, additional, Jupp, Simon, additional, Kim, Hyeongsik, additional, Koehler, Sebastian, additional, Liener, Thomas, additional, Long, Qinqin, additional, Malone, James, additional, McLaughlin, James A, additional, McMurry, Julie A, additional, Moxon, Sierra, additional, Munoz-Torres, Monica C, additional, Osumi-Sutherland, David, additional, Overton, James A, additional, Peters, Bjoern, additional, Putman, Tim, additional, Queralt-Rosinach, Núria, additional, Shefchek, Kent, additional, Solbrig, Harold, additional, Thessen, Anne, additional, Tudorache, Tania, additional, Vasilevsky, Nicole, additional, Wagner, Alex H, additional, and Mungall, Christopher J, additional

Published
2022
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40. The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Author

Jacobsen, Julius O. B., primary, Baudis, Michael, additional, Baynam, Gareth S., additional, Beckmann, Jacques S., additional, Beltran, Sergi, additional, Callahan, Tiffany J., additional, Chute, Christopher G., additional, Courtot, Mélanie, additional, Danis, Daniel, additional, Elemento, Olivier, additional, Freimuth, Robert R., additional, Gargano, Michael A., additional, Groza, Tudor, additional, Hamosh, Ada, additional, Harris, Nomi L., additional, Kaliyaperumal, Rajaram, additional, Khalifa, Aly, additional, Krawitz, Peter M., additional, Köhler, Sebastian, additional, Laraway, Brian J., additional, Lehväslaiho, Heikki, additional, Lloyd, Kent C., additional, Matalonga, Leslie, additional, McMurry, Julie A., additional, Metke-Jimenez, Alejandro, additional, Mungall, Christopher J., additional, Munoz-Torres, Monica C., additional, Ogishima, Soichi, additional, Papakonstantinou, Anastasios, additional, Piscia, Davide, additional, Pontikos, Nikolas, additional, Queralt-Rosinach, Núria, additional, Roos, Marco, additional, Schofield, Paul N., additional, Siapos, Anastasios, additional, Smedley, Damian, additional, Smith, Lindsay D., additional, Steinhaus, Robin, additional, Sundaramurthi, Jagadish Chandrabose, additional, Swietlik, Emilia M., additional, Thun, Sylvia, additional, Vasilevsky, Nicole A., additional, Wagner, Alex H., additional, Warner, Jeremy L., additional, Weiland, Claus, additional, Haendel, Melissa A., additional, and Robinson, Peter N., additional

Published
2021
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41. Abstract 206: CIViC knowledgebase adapts to field experts and community input

Author

Sheta, Lana M., primary, Danos, Arpad M., additional, Saliba, Jason, additional, Krysiak, Kilannin, additional, Wagner, Alex H., additional, Barnell, Erica K., additional, Kiwala, Susanna, additional, McMichael, Joshua F., additional, Coffman, Adam, additional, Pema, Shahil, additional, Kujan, Lynzey, additional, Cotto, Kelsy C., additional, Ramirez, Cody, additional, Skidmore, Zachary L., additional, Grisdale, Cameron J., additional, Rao, Shruti, additional, Madhaven, Subha, additional, Griffith, Malachi, additional, and Griffith, Obi L., additional

Published
2021
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42. Abstract 449: A standard operating procedure for the curation of gene fusions

Author

Wagner, Alex H., primary, Vlachos, Ioannis S., additional, Sonkin, Dmitriy, additional, Terraf, Panieh, additional, Kesserwan, Chimene, additional, Sboner, Andrea, additional, Coard, Thomas, additional, Reich, Christian, additional, Ritter, Deborah I., additional, Horak, Peter, additional, Zou, Ying S., additional, Tanska, Anna, additional, Berlin, Aaron M., additional, Lu, Anna, additional, Cameron, Daniel, additional, Williams, Heather E., additional, Lin, Wan-Hsin, additional, Toruner, Gokce, additional, Danos, Arpad, additional, Saliba, Jason, additional, Xu, Huiling, additional, Xu, Xinjie, additional, Ryland, Georgina, additional, Ceccarelli, Michele, additional, Zhang, Liying, additional, Rapisardo, Sarah, additional, Rehder, Catherine, additional, Liu, Xuelu, additional, Pallavajjala, Aparna, additional, Park, Nicole, additional, Satgunaseelan, Laveniya, additional, Lee, Kristy, additional, Liu, Jie, additional, Griffith, Obi, additional, Freimuth, Robert R., additional, Stenzinger, Albrecht, additional, Baughn, Linda B., additional, Baudis, Michael, additional, Lee, Jennifer, additional, Li, Marilyn, additional, Roy, Angshumoy, additional, and Raca, Gordana, additional

Published
2021
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43. Additional file 1 of Discovery of clinically relevant fusions in pediatric cancer

Author

LaHaye, Stephanie, Fitch, James R., Voytovich, Kyle J., Herman, Adam C., Kelly, Benjamin J., Lammi, Grant E., Arbesfeld, Jeremy A., Wijeratne, Saranga, Franklin, Samuel J., Schieffer, Kathleen M., Bir, Natalie, McGrath, Sean D., Miller, Anthony R., Wetzel, Amy, Miller, Katherine E., Bedrosian, Tracy A., Leraas, Kristen, Varga, Elizabeth A., Lee, Kristy, Gupta, Ajay, Setty, Bhuvana, Bou��, Daniel R., Leonard, Jeffrey R., Finlay, Jonathan L., Abdelbaki, Mohamed S., Osorio, Diana S., Koo, Selene C., Koboldt, Daniel C., Wagner, Alex H., Eisfeld, Ann-Kathrin, Mr��zek, Krzysztof, Magrini, Vincent, Cottrell, Catherine E., Mardis, Elaine R., Wilson, Richard K., and White, Peter

Subjects
Data_FILES
Abstract

Additional file 1.

Published
2021
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46. Evolution of the open-access CIViC knowledgebase is driven by the needs of the cancer variant interpretation community

Author

Krysiak, Kilannin, primary, Danos, Arpad M, additional, Kiwala, Susanna, additional, McMichael, Joshua F, additional, Coffman, Adam C, additional, Barnell, Erica K, additional, Sheta, Lana, additional, Saliba, Jason, additional, Grisdale, Cameron J, additional, Kujan, Lynzey, additional, Pema, Shahil, additional, Lever, Jake, additional, Spies, Nicholas C, additional, Chiorean, Andreea, additional, Rieke, Damian T, additional, Clark, Kaitlin A, additional, Jani, Payal, additional, Takahashi, Hideaki, additional, Horak, Peter, additional, Ritter, Deborah I, additional, Zhou, Xin, additional, Ainscough, Benjamin J, additional, Delong, Sean, additional, Lamping, Mario, additional, Marr, Alex R, additional, Li, Brian V, additional, Lin, Wan-Hsin, additional, Terraf, Panieh, additional, Salama, Yasser, additional, Campbell, Katie, additional, Farncombe, Kirsten M, additional, Ji, Jianling, additional, Zhao, Xiaonan, additional, Xu, Xinjie, additional, Kanagal-Shamanna, Rashmi, additional, Cotto, Kelsy C, additional, Skidmore, Zachary L, additional, Walker, Jason R, additional, Zhang, Jinghui, additional, Milosavljevic, Aleksandar, additional, Patel, Ronak Y, additional, Giles, Rachel H, additional, Kim, Raymond H, additional, Schriml, Lynn M, additional, Mardis, Elaine R, additional, Jones, Steven JM, additional, Raca, Gordana, additional, Rao, Shruti, additional, Madhavan, Subha, additional, Wagner, Alex H, additional, Griffith, Obi L, additional, and Griffith, Malachi, additional

Published
2021
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47. The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

Author

Wagner, Alex H, primary, Babb, Lawrence, additional, Alterovitz, Gil, additional, Baudis, Michael, additional, Brush, Matthew, additional, Cameron, Daniel L, additional, Cline, Melissa, additional, Griffith, Malachi, additional, Griffith, Obi L, additional, Hunt, Sarah, additional, Kreda, David, additional, Lee, Jennifer, additional, Lopez, Javier, additional, Moyer, Eric, additional, Nelson, Tristan, additional, Patel, Ronak Y, additional, Riehle, Kevin, additional, Robinson, Peter N, additional, Rynearson, Shawn, additional, Schuilenburg, Helen, additional, Tsukanov, Kirill, additional, Walsh, Brian, additional, Konopko, Melissa, additional, Rehm, Heidi, additional, Yates, Andrew D, additional, Freimuth, Robert R, additional, and Hart, Reece K, additional

Published
2021
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