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Artikel ; Online: Implementing Evidence-Based Assertions of Clinical Actionability in the Context of Secondary Findings: Updates from the ClinGen Actionability Working Group.

Pak, Christine M / Gilmore, Marian J / Bulkley, Joanna E / Chakraborty, Pranesh / Dagan-Rosenfeld, Orit / Foreman, Ann Katherine M / Gollob, Michael H / Jenkins, Charisma L / Katz, Alexander E / Lee, Kristy / Meeks, Naomi / O'Daniel, Julianne M / Posey, Jennifer E / Rego, Shannon M / Shah, Neethu / Steiner, Robert D / Stergachis, Andrew B / Subramanian, Sai Lakshmi / Trotter, Tracy /

Wallace, Kathleen / Williams, Marc S / Goddard, Katrina A B / Buchanan, Adam H / Manickam, Kandamurugu / Powell, Bradford / Ezzell Hunter, Jessica

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

2024 , Seite(n) 101164

Abstract: Purpose: The ClinGen Actionability Working Group (AWG) developed an evidence-based framework to generate actionability reports and scores of gene-condition pairs in the context of secondary findings from genome sequencing. Here we describe the expansion ...

Abstract	Purpose: The ClinGen Actionability Working Group (AWG) developed an evidence-based framework to generate actionability reports and scores of gene-condition pairs in the context of secondary findings from genome sequencing. Here we describe the expansion of the framework to include actionability assertions. Methods: Initial development of the actionability rubric was based on previously scored adult gene-condition pairs and individual expert evaluation. Rubric refinement was iterative and based on evaluation, feedback, and discussion. The final rubric was pragmatically evaluated via integration into actionability assessments for 27 gene-condition pairs. Results: The resulting rubric has a four-point scale (limited, moderate, strong, definitive) and uses the highest-scoring outcome-intervention pair of each gene-condition pair to generate a preliminary assertion. During AWG discussions, pre-defined criteria and factors guide discussion to produce a consensus assertion for a gene-condition pair, which may differ from the preliminary assertion. The AWG has retrospectively generated assertions for all previously scored gene-condition pairs and are prospectively asserting on gene-condition pairs under assessment, having completed over 170 adult and 188 pediatric gene-condition pairs. Conclusion: The AWG expanded its framework to provide actionability assertions to enhance the clinical value of their resources and increase their utility as decision aids regarding return of secondary findings.
Sprache	Englisch
Erscheinungsdatum	2024-05-14
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	1455352-1
ISSN	1530-0366 ; 1098-3600
ISSN (online)	1530-0366
ISSN	1098-3600
DOI	10.1016/j.gim.2024.101164
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: ClinGen's Pediatric Actionability Working Group: Clinical actionability of secondary findings from genome-scale sequencing in children and adolescents.

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

2022 Band 24, Heft 6, Seite(n) 1328–1335

Abstract: Purpose: Synthesis and curation of evidence regarding the clinical actionability of secondary findings (SFs) from genome-scale sequencing are needed to support decision-making on reporting of these findings. To assess actionability of SFs in children ... ...

Abstract	Purpose: Synthesis and curation of evidence regarding the clinical actionability of secondary findings (SFs) from genome-scale sequencing are needed to support decision-making on reporting of these findings. To assess actionability of SFs in children and adolescents, the Clinical Genome Resource established the Pediatric Actionability Working Group (AWG). Methods: The Pediatric AWG modified the framework of the existing Adult AWG, which included production of summary reports of actionability for genes and associated conditions and consensus actionability scores for specific outcome-intervention pairs. Modification of the adult framework for the pediatric setting included accounting for special considerations for reporting presymptomatic or predictive genetic findings in the pediatric context, such as maintaining future autonomy by not disclosing conditions not actionable until adulthood. The Pediatric AWG then applied this new framework to genes and associated conditions with putative actionability. Results: As of September 2021, the Pediatric AWG applied the new framework to 70 actionability topics representing 143 genes. Reports and scores are publicly available at www.clinicalgenome.org. Conclusion: The Pediatric AWG continues to curate gene-condition topics and build an evidence-based resource, supporting clinical communities and decision-makers with policy development on the return of SFs in pediatric populations.
Mesh-Begriff(e)	Adolescent ; Adult ; Child ; Chromosome Mapping ; Genetic Testing ; Humans ; Research Report
Sprache	Englisch
Erscheinungsdatum	2022-03-25
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1455352-1
ISSN	1530-0366 ; 1098-3600
ISSN (online)	1530-0366
ISSN	1098-3600
DOI	10.1016/j.gim.2022.02.019
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Infective endocarditis due to Granulicatella adiacens: a case report and review.

Padmaja, Kanne / Lakshmi, Vemu / Subramanian, Sreevdya / Neeraja, Mamidi / Krishna, Siva Rama / Satish, O Sai

Journal of infection in developing countries

2014 Band 8, Heft 4, Seite(n) 548–550

Abstract: Infective endocarditis (IE) caused by nutritionally variant Streptococci (NVS) is associated with high bacteriologic and treatment failure and mortality rates compared to endocarditis caused by other Streptococci. With automated blood culture systems, ... ...

Abstract	Infective endocarditis (IE) caused by nutritionally variant Streptococci (NVS) is associated with high bacteriologic and treatment failure and mortality rates compared to endocarditis caused by other Streptococci. With automated blood culture systems, the rates of NVS-associated IE accounts for 5%-6% cases. We report a case of IE caused by NVS in an elderly female patient with no risk factors. The patient was successfully treated with combination antimicrobial therapy.
Mesh-Begriff(e)	Carnobacteriaceae/isolation & purification ; Endocarditis, Bacterial/drug therapy ; Endocarditis, Bacterial/microbiology ; Female ; Gram-Positive Bacterial Infections/drug therapy ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Middle Aged
Sprache	Englisch
Erscheinungsdatum	2014-04-15
Erscheinungsland	Italy
Dokumenttyp	Case Reports ; Journal Article ; Review
ZDB-ID	2394024-4
ISSN	1972-2680 ; 2036-6590
ISSN (online)	1972-2680
ISSN	2036-6590
DOI	10.3855/jidc.3689
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines.

Preston, Christine G / Wright, Matt W / Madhavrao, Rao / Harrison, Steven M / Goldstein, Jennifer L / Luo, Xi / Wand, Hannah / Wulf, Bryan / Cheung, Gloria / Mandell, Mark E / Tong, Howard / Cheng, Shaung / Iacocca, Michael A / Pineda, Arturo Lopez / Popejoy, Alice B / Dalton, Karen / Zhen, Jimmy / Dwight, Selina S / Babb, Lawrence /

DiStefano, Marina / O'Daniel, Julianne M / Lee, Kristy / Riggs, Erin R / Zastrow, Diane B / Mester, Jessica L / Ritter, Deborah I / Patel, Ronak Y / Subramanian, Sai Lakshmi / Milosavljevic, Aleksander / Berg, Jonathan S / Rehm, Heidi L / Plon, Sharon E / Cherry, J Michael / Bustamante, Carlos D / Costa, Helio A

Genome medicine

2022 Band 14, Heft 1, Seite(n) 6

Abstract: Background: Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive ... ...

Abstract	Background: Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking. Results: Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications. Conclusions: The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, facilitates widespread adoption of standards for clinical curation, and is available at https://curation.clinicalgenome.org.
Mesh-Begriff(e)	Humans ; Genetic Testing ; Genetic Variation ; Genome, Human ; Genomics
Sprache	Englisch
Erscheinungsdatum	2022-01-18
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-021-01004-8
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery.

Koc, Soner / Lloyd, Michael W / Grover, Jeffrey W / Xiao, Nan / Seepo, Sara / Subramanian, Sai Lakshmi / Ray, Manisha / Frech, Christian / DiGiovanna, John / Webster, Phillip / Neuhauser, Steven / Srivastava, Anuj / Woo, Xing Yi / Sanderson, Brian J / White, Brian / Lott, Paul / Dobrolecki, Lacey E / Dowst, Heidi / Evrard, Yvonne A /

NAR cancer

2022 Band 4, Heft 2, Seite(n) zcac014

Abstract: We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources, to facilitate collaboration among researchers and to make these data easily available ... ...

Abstract	We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources, to facilitate collaboration among researchers and to make these data easily available for research. The portal includes sections for resources, analysis results, metrics for PDXNet activities, data processing protocols and training materials for processing PDX data. Currently, the portal contains PDXNet model information and data resources from 334 new models across 33 cancer types. Tissue samples of these models were deposited in the NCI's Patient-Derived Model Repository (PDMR) for public access. These models have 2134 associated sequencing files from 873 samples across 308 patients, which are hosted on the Cancer Genomics Cloud powered by Seven Bridges and the NCI Cancer Data Service for long-term storage and access with dbGaP permissions. The portal includes results from freely available, robust, validated and standardized analysis workflows on PDXNet sequencing files and PDMR data (3857 samples from 629 patients across 85 disease types). The PDXNet portal is continuously updated with new data and is of significant utility to the cancer research community as it provides a centralized location for PDXNet resources, which support multi-agent treatment studies, determination of sensitivity and resistance mechanisms, and preclinical trials.
Sprache	Englisch
Erscheinungsdatum	2022-04-22
Erscheinungsland	England
Dokumenttyp	Journal Article
ISSN	2632-8674
ISSN (online)	2632-8674
DOI	10.1093/narcan/zcac014
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Amino-functionalised mesoporous silica microspheres for immobilisation of

Saikia, Kongkona / Senthil Kumar, Ponnusamy / Karanam Rathankumar, Abiram / SaiLavanyaa, Sundar / Srinivasan, Lakshmi / Subramanian, Sivanesan / Cabana, Hubert / Gosselin, Mathilde / Vinoth Kumar, Vaidyanathan

IET nanobiotechnology

2022 Band 14, Heft 8, Seite(n) 732–738

Abstract: In the present study, amino-functionalised mesoporous silica microspheres were utilised as support for the covalent immobilisation ... ...

Abstract	In the present study, amino-functionalised mesoporous silica microspheres were utilised as support for the covalent immobilisation of
Mesh-Begriff(e)	Amino Acids/chemistry ; Biocatalysis ; Dicarboxylic Acids/chemistry ; Dicarboxylic Acids/metabolism ; Enzymes, Immobilized/chemistry ; Enzymes, Immobilized/metabolism ; Fungal Proteins/chemistry ; Fungal Proteins/metabolism ; Furans/chemistry ; Furans/metabolism ; Green Chemistry Technology ; Lipase/chemistry ; Lipase/metabolism ; Microspheres ; Silicon Dioxide/chemistry
Chemische Substanzen	Amino Acids ; Dicarboxylic Acids ; Enzymes, Immobilized ; Fungal Proteins ; Furans ; 2,5-furandicarboxylic acid (73C4JJ695C) ; Silicon Dioxide (7631-86-9) ; Lipase (EC 3.1.1.3) ; lipase B, Candida antarctica (EC 3.1.1.3)
Sprache	Englisch
Erscheinungsdatum	2022-02-03
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	2264529-9
ISSN	1751-875X ; 1751-8741
ISSN (online)	1751-875X
ISSN	1751-8741
DOI	10.1049/iet-nbt.2020.0021
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: ClinGen Variant Curation Interface

Christine G. Preston / Matt W. Wright / Rao Madhavrao / Steven M. Harrison / Jennifer L. Goldstein / Xi Luo / Hannah Wand / Bryan Wulf / Gloria Cheung / Mark E. Mandell / Howard Tong / Shaung Cheng / Michael A. Iacocca / Arturo Lopez Pineda / Alice B. Popejoy / Karen Dalton / Jimmy Zhen / Selina S. Dwight / Lawrence Babb /

Marina DiStefano / Julianne M. O’Daniel / Kristy Lee / Erin R. Riggs / Diane B. Zastrow / Jessica L. Mester / Deborah I. Ritter / Ronak Y. Patel / Sai Lakshmi Subramanian / Aleksander Milosavljevic / Jonathan S. Berg / Heidi L. Rehm / Sharon E. Plon / J. Michael Cherry / Carlos D. Bustamante / Helio A. Costa / on behalf of the Clinical Genome Resource (ClinGen)

Genome Medicine, Vol 14, Iss 1, Pp 1-

a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines

2022 Band 12

Abstract: Abstract Background Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible ... ...

Abstract	Abstract Background Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking. Results Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications. Conclusions The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, facilitates widespread adoption of standards for clinical curation, and is available at https://curation.clinicalgenome.org
Schlagwörter	Variant curation ; Precision medicine ; Clinical genetics ; Clinical Genome Resource Consortium ; Medicine ; R ; Genetics ; QH426-470
Thema/Rubrik (Code)	020
Sprache	Englisch
Erscheinungsdatum	2022-01-01T00:00:00Z
Verlag	BMC
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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Artikel ; Online: Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.

Amin, Viren / Harris, R Alan / Onuchic, Vitor / Jackson, Andrew R / Charnecki, Tim / Paithankar, Sameer / Lakshmi Subramanian, Sai / Riehle, Kevin / Coarfa, Cristian / Milosavljevic, Aleksandar

Nature communications

2015 Band 6, Seite(n) 6370

Abstract: Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics ... ...

Abstract	Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters. A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3. The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation. Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation. The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes.
Mesh-Begriff(e)	Cell Differentiation ; Embryonic Stem Cells/physiology ; Epigenesis, Genetic ; Epigenomics ; Humans ; Organ Specificity ; Phenotype ; Polycomb-Group Proteins/physiology ; RNA, Long Noncoding/metabolism ; Regulatory Elements, Transcriptional
Chemische Substanzen	Polycomb-Group Proteins ; RNA, Long Noncoding
Sprache	Englisch
Erscheinungsdatum	2015-02-18
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2041-1723
ISSN (online)	2041-1723
DOI	10.1038/ncomms7370
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.

Subramanian, Sai Lakshmi / Kitchen, Robert R / Alexander, Roger / Carter, Bob S / Cheung, Kei-Hoi / Laurent, Louise C / Pico, Alexander / Roberts, Lewis R / Roth, Matthew E / Rozowsky, Joel S / Su, Andrew I / Gerstein, Mark B / Milosavljevic, Aleksandar

Journal of extracellular vesicles

2015 Band 4, Seite(n) 27497

Abstract: The large diversity and volume of extracellular RNA (exRNA) data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is ... ...

Abstract	The large diversity and volume of extracellular RNA (exRNA) data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNA profiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a) selection of samples from a virtual biorepository for exRNA profiling and for inclusion in the exRNA Atlas; (b) retrieval of a data slice from the exRNA Atlas for integrative analysis and (c) interpretation of exRNA analysis results in the context of pathways and networks. As exRNA profiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data.
Sprache	Englisch
Erscheinungsdatum	2015-08-28
Erscheinungsland	Sweden
Dokumenttyp	Journal Article
ZDB-ID	2683797-3
ISSN	2001-3078
ISSN	2001-3078
DOI	10.3402/jev.v4.27497
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

Sai Lakshmi Subramanian / Robert R. Kitchen / Roger Alexander / Bob S. Carter / Kei-Hoi Cheung / Louise C. Laurent / Alexander Pico / Lewis R. Roberts / Matthew E. Roth / Joel S. Rozowsky / Andrew I. Su / Mark B. Gerstein / Aleksandar Milosavljevic

Journal of Extracellular Vesicles, Vol 4, Iss 0, Pp 1-

2015 Band 6

Abstract	The large diversity and volume of extracellular RNA (exRNA) data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNA profiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a) selection of samples from a virtual biorepository for exRNA profiling and for inclusion in the exRNA Atlas; (b) retrieval of a data slice from the exRNA Atlas for integrative analysis and (c) interpretation of exRNA analysis results in the context of pathways and networks. As exRNA profiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data.
Schlagwörter	ERC Consortium ; DMRR ; exRNA ; exRNA Atlas ; exRNA Portal ; Biology (General) ; QH301-705.5 ; Science ; Q
Thema/Rubrik (Code)	004
Sprache	Englisch
Erscheinungsdatum	2015-08-01T00:00:00Z
Verlag	Co-Action Publishing
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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