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  1. Article ; Online: Communicating new knowledge on previously reported genetic variants.

    Aronson, Samuel J / Clark, Eugene H / Varugheese, Matthew / Baxter, Samantha / Babb, Lawrence J / Rehm, Heidi L

    Genetics in medicine : official journal of the American College of Medical Genetics

    2012  Volume 14, Issue 8, Page(s) 713–719

    Abstract: Genetic tests often identify variants whose significance cannot be determined at the time they are reported. In many situations, it is critical that clinicians be informed when new information emerges on these variants. It is already extremely ... ...

    Abstract Genetic tests often identify variants whose significance cannot be determined at the time they are reported. In many situations, it is critical that clinicians be informed when new information emerges on these variants. It is already extremely challenging for laboratories to provide these updates. These challenges will grow rapidly as an increasing number of clinical genetic tests are ordered and as the amount of patient DNA assayed per test expands; the challenges will need to be addressed before whole-genome sequencing is used on a widespread basis.Information technology infrastructure can be useful in this context. We have deployed an infrastructure enabling clinicians to receive knowledge updates when a laboratory changes the classification of a variant. We have gathered statistics from this deployment regarding the frequency of both variant classification changes and the effects of these classification changes on patients. We report on the system's functionality as well as the statistics derived from its use.Genet Med advance online publication 5 April 2012.
    Language English
    Publishing date 2012-04-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1455352-1
    ISSN 1530-0366 ; 1098-3600
    ISSN (online) 1530-0366
    ISSN 1098-3600
    DOI 10.1038/gim.2012.19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genomic considerations for FHIR®; eMERGE implementation lessons.

    Murugan, Mullai / Babb, Lawrence J / Overby Taylor, Casey / Rasmussen, Luke V / Freimuth, Robert R / Venner, Eric / Yan, Fei / Yi, Victoria / Granite, Stephen J / Zouk, Hana / Aronson, Samuel J / Power, Kevin / Fedotov, Alex / Crosslin, David R / Fasel, David / Jarvik, Gail P / Hakonarson, Hakon / Bangash, Hana / Kullo, Iftikhar J /
    Connolly, John J / Nestor, Jordan G / Caraballo, Pedro J / Wei, WeiQi / Wiley, Ken / Rehm, Heidi L / Gibbs, Richard A

    Journal of biomedical informatics

    2021  Volume 118, Page(s) 103795

    Abstract: Structured representation of clinical genetic results is necessary for advancing precision medicine. The Electronic Medical Records and Genomics (eMERGE) Network's Phase III program initially used a commercially developed XML message format for ... ...

    Abstract Structured representation of clinical genetic results is necessary for advancing precision medicine. The Electronic Medical Records and Genomics (eMERGE) Network's Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7® FHIR®), to represent clinical genomics results. These new standards improve the utility of HL7® FHIR® as an international healthcare interoperability standard for management of genetic data from patients. This work advances the establishment of standards that are being designed for broad adoption in the current health information technology landscape.
    MeSH term(s) Electronic Health Records ; Genomics ; Health Level Seven ; Humans ; Medical Informatics ; Precision Medicine
    Language English
    Publishing date 2021-04-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2057141-0
    ISSN 1532-0480 ; 1532-0464
    ISSN (online) 1532-0480
    ISSN 1532-0464
    DOI 10.1016/j.jbi.2021.103795
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings.

    Lubin, Ira M / Aziz, Nazneen / Babb, Lawrence J / Ballinger, Dennis / Bisht, Himani / Church, Deanna M / Cordes, Shaun / Eilbeck, Karen / Hyland, Fiona / Kalman, Lisa / Landrum, Melissa / Lockhart, Edward R / Maglott, Donna / Marth, Gabor / Pfeifer, John D / Rehm, Heidi L / Roy, Somak / Tezak, Zivana / Truty, Rebecca /
    Ullman-Cullere, Mollie / Voelkerding, Karl V / Worthey, Elizabeth A / Zaranek, Alexander W / Zook, Justin M

    The Journal of molecular diagnostics : JMD

    2017  Volume 19, Issue 3, Page(s) 417–426

    Abstract: A national workgroup convened by the Centers for Disease Control and Prevention identified principles and made recommendations for standardizing the description of sequence data contained within the variant file generated during the course of clinical ... ...

    Abstract A national workgroup convened by the Centers for Disease Control and Prevention identified principles and made recommendations for standardizing the description of sequence data contained within the variant file generated during the course of clinical next-generation sequence analysis for diagnosing human heritable conditions. The specifications for variant files were initially developed to be flexible with regard to content representation to support a variety of research applications. This flexibility permits variation with regard to how sequence findings are described and this depends, in part, on the conventions used. For clinical laboratory testing, this poses a problem because these differences can compromise the capability to compare sequence findings among laboratories to confirm results and to query databases to identify clinically relevant variants. To provide for a more consistent representation of sequence findings described within variant files, the workgroup made several recommendations that considered alignment to a common reference sequence, variant caller settings, use of genomic coordinates, and gene and variant naming conventions. These recommendations were considered with regard to the existing variant file specifications presently used in the clinical setting. Adoption of these recommendations is anticipated to reduce the potential for ambiguity in describing sequence findings and facilitate the sharing of genomic data among clinical laboratories and other entities.
    MeSH term(s) Databases, Genetic ; Genetic Variation/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; Software
    Language English
    Publishing date 2017-03-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2000060-1
    ISSN 1943-7811 ; 1525-1578
    ISSN (online) 1943-7811
    ISSN 1525-1578
    DOI 10.1016/j.jmoldx.2016.12.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A novel clinician interface to improve clinician access to up-to-date genetic results.

    Wilcox, Allison R / Neri, Pamela M / Volk, Lynn A / Newmark, Lisa P / Clark, Eugene H / Babb, Lawrence J / Varugheese, Matthew / Aronson, Samuel J / Rehm, Heidi L / Bates, David W

    Journal of the American Medical Informatics Association : JAMIA

    2013  Volume 21, Issue e1, Page(s) e117–21

    Abstract: Objectives: To understand the impact of GeneInsight Clinic (GIC), a web-based tool designed to manage genetic information and facilitate communication of test results and variant updates from the laboratory to the clinics, we measured the use of GIC and ...

    Abstract Objectives: To understand the impact of GeneInsight Clinic (GIC), a web-based tool designed to manage genetic information and facilitate communication of test results and variant updates from the laboratory to the clinics, we measured the use of GIC and the time it took for new genetic knowledge to be available to clinicians.
    Methods: Usage data were collected across four study sites for the GIC launch and post-GIC implementation time periods. The primary outcome measures were the time (average number of days) between variant change approval and notification of clinic staff, and the time between notification and viewing the patient record.
    Results: Post-GIC, time between a variant change approval and provider notification was shorter than at launch (average days at launch 503.8, compared to 4.1 days post-GIC). After e-mail alerts were sent at launch, providers clicked into the patient record associated with 91% of these alerts. In the post period, clinic providers clicked into the patient record associated with 95% of the alerts, on average 12 days after the e-mail was sent.
    Discussion: We found that GIC greatly increased the likelihood that a provider would receive updated variant information as well as reduced the time associated with distributing that variant information, thus providing a more efficient process for incorporating new genetic knowledge into clinical care.
    Conclusions: Our study results demonstrate that health information technology systems have the potential effectively to assist providers in utilizing genetic information in patient care.
    MeSH term(s) Communication ; Electronic Mail ; Genetic Testing ; Humans ; Internet ; Time Factors
    Language English
    Publishing date 2013-09-07
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1205156-1
    ISSN 1527-974X ; 1067-5027
    ISSN (online) 1527-974X
    ISSN 1067-5027
    DOI 10.1136/amiajnl-2013-001965
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The GeneInsight Suite: a platform to support laboratory and provider use of DNA-based genetic testing.

    Aronson, Samuel J / Clark, Eugene H / Babb, Lawrence J / Baxter, Samantha / Farwell, Lisa M / Funke, Birgit H / Hernandez, Amy Lovelette / Joshi, Victoria A / Lyon, Elaine / Parthum, Andrew R / Russell, Franklin J / Varugheese, Matthew / Venman, Thomas C / Rehm, Heidi L

    Human mutation

    2011  Volume 32, Issue 5, Page(s) 532–536

    Abstract: The future of personalized medicine will hinge on effective management of patient genetic profiles. Molecular diagnostic testing laboratories need to track knowledge surrounding an increasingly large number of genetic variants, incorporate this knowledge ...

    Abstract The future of personalized medicine will hinge on effective management of patient genetic profiles. Molecular diagnostic testing laboratories need to track knowledge surrounding an increasingly large number of genetic variants, incorporate this knowledge into interpretative reports, and keep ordering clinicians up to date as this knowledge evolves. Treating clinicians need to track which variants have been identified in each of their patients along with the significance of these variants. The GeneInsight(SM) Suite assists in these areas. The suite also provides a basis for interconnecting laboratories and clinicians in a manner that increases the scalability of personalized medicine processes.
    MeSH term(s) Expert Systems ; Genetic Testing/methods ; Genetic Variation ; Humans ; Knowledge Bases ; Molecular Diagnostic Techniques/methods ; Precision Medicine/methods ; Software
    Language English
    Publishing date 2011-03-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1126646-6
    ISSN 1098-1004 ; 1059-7794
    ISSN (online) 1098-1004
    ISSN 1059-7794
    DOI 10.1002/humu.21470
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  6. Article ; Online: GA4GH: International policies and standards for data sharing across genomic research and healthcare.

    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 / Auvil, Jaime M Guidry / 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 / Udara Liyanage, Isuru / 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 / Wang, Vivian Ota / 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 / Birney, Ewan

    Cell genomics

    2022  Volume 1, Issue 2

    Abstract: The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic ... ...

    Abstract The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
    Language English
    Publishing date 2022-02-24
    Publishing country United States
    Document type Journal Article
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2021.100029
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