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182 results on '"Thorn, Caroline F."'

2. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.

Author

Dewey, Frederick E, Chen, Rong, Cordero, Sergio P, Ormond, Kelly E, Caleshu, Colleen, Karczewski, Konrad J, Whirl-Carrillo, Michelle, Wheeler, Matthew T, Dudley, Joel T, Byrnes, Jake K, Cornejo, Omar E, Knowles, Joshua W, Woon, Mark, Sangkuhl, Katrin, Gong, Li, Thorn, Caroline F, Hebert, Joan M, Capriotti, Emidio, David, Sean P, Pavlovic, Aleksandra, West, Anne, Thakuria, Joseph V, Ball, Madeleine P, Zaranek, Alexander W, Rehm, Heidi L, Church, George M, West, John S, Bustamante, Carlos D, Snyder, Michael, Altman, Russ B, Klein, Teri E, Butte, Atul J, and Ashley, Euan A

Subjects
Humans, Thrombophilia, Genetic Predisposition to Disease, Risk Assessment, Pedigree, Sequence Alignment, Sequence Analysis, DNA, DNA Mutational Analysis, Base Sequence, Genotype, Haplotypes, Alleles, Genes, Synthetic, Genome, Human, Reference Standards, Female, Male, Genetic Variation, Genome-Wide Association Study, Biotechnology, Genetics, Human Genome, 2.1 Biological and endogenous factors, Generic health relevance, Developmental Biology
Abstract

Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date (< 1,000 base pairs). We use family inheritance state analysis to control sequencing error and inform family-wide haplotype phasing, allowing quantification of genome-wide compound heterozygosity. We develop a sequence-based methodology for Human Leukocyte Antigen typing that contributes to disease risk prediction. Finally, we advance methods for analysis of disease and pharmacogenomic risk across the coding and non-coding genome that incorporate phased variant data. We show these methods are capable of identifying multigenic risk for inherited thrombophilia and informing the appropriate pharmacological therapy. These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.

Published
2011

4. Clinical assessment incorporating a personal genome

Author

Ashley, Euan A, Butte, Atul J, Wheeler, Matthew T, Chen, Rong, Klein, Teri E, Dewey, Frederick E, Dudley, Joel T, Ormond, Kelly E, Pavlovic, Aleksandra, Morgan, Alexander A, Pushkarev, Dmitry, Neff, Norma F, Hudgins, Louanne, Gong, Li, Hodges, Laura M, Berlin, Dorit S, Thorn, Caroline F, Sangkuhl, Katrin, Hebert, Joan M, Woon, Mark, Sagreiya, Hersh, Whaley, Ryan, Knowles, Joshua W, Chou, Michael F, Thakuria, Joseph V, Rosenbaum, Abraham M, Zaranek, Alexander Wait, Church, George M, Greely, Henry T, Quake, Stephen R, and Altman, Russ B

Published
2010
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12. Essential Characteristics of Pharmacogenomics Study Publications

Author

Thorn, Caroline F., primary, Whirl‐Carrillo, Michelle, additional, Hachad, Houda, additional, Johnson, Julie A., additional, McDonagh, Ellen M., additional, Ratain, Mark J., additional, Relling, Mary V., additional, Scott, Stuart A., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2018
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13. PharmGKB summary

Author

Thorn, Caroline F., primary, Müller, Daniel J., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2018
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14. PharmGKB summary

Author

Thorn, Caroline F., primary, Sharma, Manish R., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2017
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15. Essential Characteristics of Pharmacogenomics Study Publications.

Author

Thorn, Caroline F., Whirl‐Carrillo, Michelle, Hachad, Houda, Johnson, Julie A., McDonagh, Ellen M., Ratain, Mark J., Relling, Mary V., Scott, Stuart A., Altman, Russ B., and Klein, Teri E.

Subjects
PHARMACOGENOMICS, BIOMEDICAL engineering, CLINICAL trials, GENES, PHENOTYPES
Abstract

Pharmacogenomics (PGx) can be seen as a model for biomedical studies: it includes all disease areas of interest and spans in vitro studies to clinical trials, while focusing on the relationships between genes and drugs and the resulting phenotypes. This review will examine different characteristics of PGx study publications and provide examples of excellence in framing PGx questions and reporting their resulting data in a way that maximizes the knowledge that can be built on them. [ABSTRACT FROM AUTHOR]

Published
2019
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16. PharmGKB summary

Author

Klein, Daniel J., primary, Boukouvala, Sotiria, additional, McDonagh, Ellen M., additional, Shuldiner, Scott R., additional, Laurieri, Nicola, additional, Thorn, Caroline F., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2016
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17. PharmGKB summary

Author

Mazaleuskaya, Liudmila L., primary, Sangkuhl, Katrin, additional, Thorn, Caroline F., additional, FitzGerald, Garret A., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2015
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18. Incorporation of Pharmacogenomics into Routine Clinical Practice : the Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline Development Process

Author

Caudle, Kelly E, Klein, Teri E, Hoffman, James M, Muller, Daniel J, Whirl-Carrillo, Michelle, Gong, Li, McDonagh, Ellen M, Sangkuhl, Katrin, Thorn, Caroline F, Schwab, Matthias, Agundez, Jose A G, Freimuth, Robert R, Huser, Vojtech, Lee, Ming Ta Michael, Iwuchukwu, Otito F, Crews, Kristine R, Scott, Stuart A, Wadelius, Mia, Swen, Jesse J, Tyndale, Rachel F, Stein, C Michael, Roden, Dan, Relling, Mary V, Williams, Marc S, Johnson, Samuel G, Caudle, Kelly E, Klein, Teri E, Hoffman, James M, Muller, Daniel J, Whirl-Carrillo, Michelle, Gong, Li, McDonagh, Ellen M, Sangkuhl, Katrin, Thorn, Caroline F, Schwab, Matthias, Agundez, Jose A G, Freimuth, Robert R, Huser, Vojtech, Lee, Ming Ta Michael, Iwuchukwu, Otito F, Crews, Kristine R, Scott, Stuart A, Wadelius, Mia, Swen, Jesse J, Tyndale, Rachel F, Stein, C Michael, Roden, Dan, Relling, Mary V, Williams, Marc S, and Johnson, Samuel G

Abstract

The Clinical Pharmacogenetics Implementation Consortium (CPIC) publishes genotype-based drug guidelines to help clinicians understand how available genetic test results could be used to optimize drug therapy. CPIC has focused initially on well-known examples of pharmacogenomic associations that have been implemented in selected clinical settings, publishing nine to date. Each CPIC guideline adheres to a standardized format and includes a standard system for grading levels of evidence linking genotypes to phenotypes and assigning a level of strength to each prescribing recommendation. CPIC guidelines contain the necessary information to help clinicians translate patient-specific diplotypes for each gene into clinical phenotypes or drug dosing groups. This paper reviews the development process of the CPIC guidelines and compares this process to the Institute of Medicine's Standards for Developing Trustworthy Clinical Practice Guidelines.

Published
2014
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19. PharmGKB summary

Author

Alvarellos, Maria L., primary, Lamba, Jatinder, additional, Sangkuhl, Katrin, additional, Thorn, Caroline F., additional, Wang, Liewei, additional, Klein, Daniel J., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2014
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22. PharmGKB summary

Author

McDonagh, Ellen M., primary, Thorn, Caroline F., additional, Callaghan, John T., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2014
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23. PharmGKB summary

Author

Lowenberg, Daniella, primary, Thorn, Caroline F., additional, Desta, Zeruesenay, additional, Flockhart, David A., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2014
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24. PharmGKB summary

Author

Klein, Daniel J., primary, Thorn, Caroline F., additional, Desta, Zeruesenay, additional, Flockhart, David A., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2013
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25. Using ODIN for a PharmGKB re-validation experiment

Author

Rinaldi, Fabio; https://orcid.org/0000-0001-5718-5462, Clematide, Simon; https://orcid.org/0000-0003-1365-0662, Garten, Yael, Whirl-Carrillo, Michelle, Gong, Li, Hebert, Joan M, Sangkuhl, Katrin, Thorn, Caroline F, Klein, Teri E, Altman, Russ B, Rinaldi, Fabio; https://orcid.org/0000-0001-5718-5462, Clematide, Simon; https://orcid.org/0000-0003-1365-0662, Garten, Yael, Whirl-Carrillo, Michelle, Gong, Li, Hebert, Joan M, Sangkuhl, Katrin, Thorn, Caroline F, Klein, Teri E, and Altman, Russ B

Abstract

The need for efficient text-mining tools that support curation of the biomedical literature is ever increasing. In this article, we describe an experiment aimed at verifying whether a text-mining tool capable of extracting meaningful relationships among domain entities can be successfully integrated into the curation workflow of a major biological database. We evaluate in particular (i) the usability of the system's interface, as perceived by users, and (ii) the correlation of the ranking of interactions, as provided by the text-mining system, with the choices of the curators.

Published
2012

26. PharmGKB summary

Author

Thorn, Caroline F., primary, Ellison, David H., additional, Turner, Stephen T., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2013
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27. Valproic acid pathway

Author

Ghodke-Puranik, Yogita, primary, Thorn, Caroline F., additional, Lamba, Jatinder K., additional, Leeder, J. Steven, additional, Song, Wen, additional, Birnbaum, Angela K., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2013
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29. PharmGKB summary

Author

Thorn, Caroline F., primary, Ji, Yuan, additional, Weinshilboum, Richard M., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2012
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30. Celecoxib pathways

Author

Gong, Li, primary, Thorn, Caroline F., additional, Bertagnolli, Monica M., additional, Grosser, Tilo, additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2012
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31. PharmGKB summary

Author

McDonagh, Ellen M., primary, Thorn, Caroline F., additional, Bautista, José M., additional, Youngster, Ilan, additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2012
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32. PharmGKB summary

Author

Scott, Stuart A., primary, Sangkuhl, Katrin, additional, Shuldiner, Alan R., additional, Hulot, Jean-Sébastien, additional, Thorn, Caroline F., additional, Altman, Russ B., additional, and Klein, Teri E., additional

Published
2012
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33. PharmGKB summary

Author

Thorn, Caroline F., primary, Leckband, Susan G., additional, Kelsoe, John, additional, Steven Leeder, J., additional, Müller, Daniel J., additional, Klein, Teri E., additional, and Altman, Russ B., additional

Published
2011
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34. PharmGKB summary

Author

Mikkelsen, Torben S., primary, Thorn, Caroline F., additional, Yang, Jun J., additional, Ulrich, Cornelia M., additional, French, Deborah, additional, Zaza, Gianluigi, additional, Dunnenberger, Henry M., additional, Marsh, Sharon, additional, McLeod, Howard L., additional, Giacomini, Kathy, additional, Becker, Mara L., additional, Gaedigk, Roger, additional, Leeder, James Steven, additional, Kager, Leo, additional, Relling, Mary V., additional, Evans, William, additional, Klein, Teri E., additional, and Altman, Russ B., additional

Published
2011
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35. Doxorubicin pathways

Author

Thorn, Caroline F., primary, Oshiro, Connie, additional, Marsh, Sharon, additional, Hernandez-Boussard, Tina, additional, McLeod, Howard, additional, Klein, Teri E., additional, and Altman, Russ B., additional

Published
2011
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40. Cytotoxic Doses of Ketoconazole Affect Expression of a Subset of Hepatic Genes

Author

Casley, William L., primary, Ogrodowczyk, Carolina, additional, Larocque, Louise, additional, Jaentschke, Bozena, additional, LeBlanc-Westwood, Carole, additional, Menzies, J. Allan, additional, Whitehouse, Larry, additional, Hefford, Mary Alice, additional, Aubin, Rémy A., additional, Thorn, Caroline F., additional, Whitehead, Alexander S., additional, and Li, Xuguang, additional

Published
2007
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48. PharmGKB.

Author

Innocenti, Federico, Thorn, Caroline F., Klein, Teri E., and Altman, Russ B.

Abstract

The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB) is an interactive tool for researchers investigating how genetic variation effects drug response. The PharmGKB web site, http://www.pharmgkb.org, displays genotype, molecular, and clinical primary data integrated with literature, pathway representations, protocol information, and links to additional external resources. Users can search and browse the knowledge base by genes, drugs, diseases, and pathways. Registration is free to the entire research community but subject to an agreement to respect the rights and privacy of the individuals whose information is contained within the database. Registered users can access and download primary data to aid in the design of future pharmacogenetics and pharmacogenomics studies. [ABSTRACT FROM AUTHOR]

Published
2005
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