Literature DB >> 29790234

ClinVar Miner: Demonstrating utility of a Web-based tool for viewing and filtering ClinVar data.

Alex Henrie1, Sarah E Hemphill2, Nicole Ruiz-Schultz1, Brandon Cushman2, Marina T DiStefano2, Danielle Azzariti2, Steven M Harrison2, Heidi L Rehm2,3, Karen Eilbeck1.   

Abstract

ClinVar Miner is a Web-based suite that utilizes the data held in the National Center for Biotechnology Information's ClinVar archive. The goal is to render the data more accessible to processes pertaining to conflict resolution of variant interpretation as well as tracking details of data submission and data management for detailed variant curation. Here, we establish the use of these tools to address three separate use cases and to perform analyses across submissions. We demonstrate that the ClinVar Miner tools are an effective means to browse and consolidate data for variant submitters, curation groups, and general oversight. These tools are also relevant to the variant interpretation community in general.
© 2018 Wiley Periodicals, Inc.

Entities:  

Keywords:  ClinVar; clinical domain working group; expert panel; variant archive; variant curation; variant interpretation

Mesh:

Year:  2018        PMID: 29790234      PMCID: PMC6043391          DOI: 10.1002/humu.23555

Source DB:  PubMed          Journal:  Hum Mutat        ISSN: 1059-7794            Impact factor:   4.878


  14 in total

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3.  Reassessment of Genomic Sequence Variation to Harmonize Interpretation for Personalized Medicine.

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4.  Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource.

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Journal:  Am J Hum Genet       Date:  2017-05-25       Impact factor: 11.025

5.  A new era in the interpretation of human genomic variation.

Authors:  Heidi L Rehm
Journal:  Genet Med       Date:  2017-07-13       Impact factor: 8.822

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Authors:  Sarah S Kalia; Kathy Adelman; Sherri J Bale; Wendy K Chung; Christine Eng; James P Evans; Gail E Herman; Sophia B Hufnagel; Teri E Klein; Bruce R Korf; Kent D McKelvey; Kelly E Ormond; C Sue Richards; Christopher N Vlangos; Michael Watson; Christa L Martin; David T Miller
Journal:  Genet Med       Date:  2016-11-17       Impact factor: 8.822

7.  Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Authors:  Sue Richards; Nazneen Aziz; Sherri Bale; David Bick; Soma Das; Julie Gastier-Foster; Wayne W Grody; Madhuri Hegde; Elaine Lyon; Elaine Spector; Karl Voelkerding; Heidi L Rehm
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Review 8.  The Human Phenotype Ontology in 2017.

Authors:  Sebastian Köhler; Nicole A Vasilevsky; Mark Engelstad; Erin Foster; Julie McMurry; Ségolène Aymé; Gareth Baynam; Susan M Bello; Cornelius F Boerkoel; Kym M Boycott; Michael Brudno; Orion J Buske; Patrick F Chinnery; Valentina Cipriani; Laureen E Connell; Hugh J S Dawkins; Laura E DeMare; Andrew D Devereau; Bert B A de Vries; Helen V Firth; Kathleen Freson; Daniel Greene; Ada Hamosh; Ingo Helbig; Courtney Hum; Johanna A Jähn; Roger James; Roland Krause; Stanley J F Laulederkind; Hanns Lochmüller; Gholson J Lyon; Soichi Ogishima; Annie Olry; Willem H Ouwehand; Nikolas Pontikos; Ana Rath; Franz Schaefer; Richard H Scott; Michael Segal; Panagiotis I Sergouniotis; Richard Sever; Cynthia L Smith; Volker Straub; Rachel Thompson; Catherine Turner; Ernest Turro; Marijcke W M Veltman; Tom Vulliamy; Jing Yu; Julie von Ziegenweidt; Andreas Zankl; Stephan Züchner; Tomasz Zemojtel; Julius O B Jacobsen; Tudor Groza; Damian Smedley; Christopher J Mungall; Melissa Haendel; Peter N Robinson
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

9.  ClinVar: public archive of interpretations of clinically relevant variants.

Authors:  Melissa J Landrum; Jennifer M Lee; Mark Benson; Garth Brown; Chen Chao; Shanmuga Chitipiralla; Baoshan Gu; Jennifer Hart; Douglas Hoffman; Jeffrey Hoover; Wonhee Jang; Kenneth Katz; Michael Ovetsky; George Riley; Amanjeev Sethi; Ray Tully; Ricardo Villamarin-Salomon; Wendy Rubinstein; Donna R Maglott
Journal:  Nucleic Acids Res       Date:  2015-11-17       Impact factor: 16.971

10.  Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar.

Authors:  Steven M Harrison; Jill S Dolinsky; Amy E Knight Johnson; Tina Pesaran; Danielle R Azzariti; Sherri Bale; Elizabeth C Chao; Soma Das; Lisa Vincent; Heidi L Rehm
Journal:  Genet Med       Date:  2017-03-16       Impact factor: 8.822

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  20 in total

1.  The clinical imperative for inclusivity: Race, ethnicity, and ancestry (REA) in genomics.

Authors:  Alice B Popejoy; Deborah I Ritter; Kristy Crooks; Erin Currey; Stephanie M Fullerton; Lucia A Hindorff; Barbara Koenig; Erin M Ramos; Elena P Sorokin; Hannah Wand; Mathew W Wright; James Zou; Christopher R Gignoux; Vence L Bonham; Sharon E Plon; Carlos D Bustamante
Journal:  Hum Mutat       Date:  2018-11       Impact factor: 4.878

2.  Scaling resolution of variant classification differences in ClinVar between 41 clinical laboratories through an outlier approach.

Authors:  Steven M Harrison; Jill S Dolinksy; Wenjie Chen; Christin D Collins; Soma Das; Joshua L Deignan; Kathryn B Garber; John Garcia; Olga Jarinova; Amy E Knight Johnson; Juha W Koskenvuo; Hane Lee; Rong Mao; Rebecca Mar-Heyming; Andrew S McFaddin; Krista Moyer; Narasimhan Nagan; Stefan Rentas; Avni B Santani; Eija H Seppälä; Brian H Shirts; Timothy Tidwell; Scott Topper; Lisa M Vincent; Kathy Vinette; Heidi L Rehm
Journal:  Hum Mutat       Date:  2018-11       Impact factor: 4.878

3.  Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): The ClinGen IEM Working Group and the Phenylalanine Hydroxylase Gene.

Authors:  Diane B Zastrow; Heather Baudet; Wei Shen; Amanda Thomas; Yue Si; Meredith A Weaver; Angela M Lager; Jixia Liu; Rachel Mangels; Selina S Dwight; Matt W Wright; Steven F Dobrowolski; Karen Eilbeck; Gregory M Enns; Annette Feigenbaum; Uta Lichter-Konecki; Elaine Lyon; Marzia Pasquali; Michael Watson; Nenad Blau; Robert D Steiner; William J Craigen; Rong Mao
Journal:  Hum Mutat       Date:  2018-11       Impact factor: 4.878

4.  A calibrated functional patch-clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome.

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5.  Extending the Phenotypic Spectrum Associated with STUB1 Mutations: A Case of Dystonia.

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6.  Prenatal Ultrasound Suspicion of Cystic Fibrosis in a Multiethnic Population: Is Extensive CFTR Genotyping Needed?

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7.  A Validated Functional Analysis of Partner and Localizer of BRCA2 Missense Variants for Use in Clinical Variant Interpretation.

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8.  Harmonizing variant classification for return of results in the All of Us Research Program.

Authors:  Steven M Harrison; Christina A Austin-Tse; Serra Kim; Matthew Lebo; Annette Leon; David Murdock; Aparna Radhakrishnan; Brian H Shirts; Marcie Steeves; Eric Venner; Richard A Gibbs; Gail P Jarvik; Heidi L Rehm
Journal:  Hum Mutat       Date:  2021-12-28       Impact factor: 4.700

9.  Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts.

Authors:  Robert R Butler Iii; Pablo V Gejman
Journal:  F1000Res       Date:  2018-04-13

10.  Rapid communication of efforts to resolve differences or update variant interpretations in ClinVar through case-level data sharing.

Authors:  Heidi Rehm
Journal:  Cold Spring Harb Mol Case Stud       Date:  2018-10-01
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