Literature DB >> 27037489

Using ClinVar as a Resource to Support Variant Interpretation.

Steven M Harrison1,2, Erin R Riggs3, Donna R Maglott4, Jennifer M Lee4, Danielle R Azzariti1, Annie Niehaus5, Erin M Ramos5, Christa L Martin3, Melissa J Landrum4,6, Heidi L Rehm1,2,6.   

Abstract

ClinVar is a freely accessible, public archive of reports of the relationships among genomic variants and phenotypes. To facilitate evaluation of the clinical significance of each variant, ClinVar aggregates submissions of the same variant, displays supporting data from each submission, and determines if the submitted clinical interpretations are conflicting or concordant. The unit describes how to (1) identify sequence and structural variants of interest in ClinVar by multiple searching approaches, including Variation Viewer and (2) understand the display of submissions to ClinVar and the evidence supporting each interpretation. By following this protocol, ClinVar users will be able to learn how to incorporate the wealth of resources and knowledge in ClinVar into variant curation and interpretation.
Copyright © 2016 John Wiley & Sons, Inc.

Entities:  

Keywords:  ClinVar; clinical genetics; data sharing; databases; variant interpretation

Mesh:

Year:  2016        PMID: 27037489      PMCID: PMC4832236          DOI: 10.1002/0471142905.hg0816s89

Source DB:  PubMed          Journal:  Curr Protoc Hum Genet        ISSN: 1934-8258


  7 in total

1.  Nomenclature for the description of human sequence variations.

Authors:  J T den Dunnen; S E Antonarakis
Journal:  Hum Genet       Date:  2001-07       Impact factor: 4.132

Review 2.  Towards an evidence-based process for the clinical interpretation of copy number variation.

Authors:  E R Riggs; D M Church; K Hanson; V L Horner; E B Kaminsky; R M Kuhn; K E Wain; E S Williams; S Aradhya; H M Kearney; D H Ledbetter; S T South; E C Thorland; C L Martin
Journal:  Clin Genet       Date:  2011-12-13       Impact factor: 4.438

3.  American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants.

Authors:  Hutton M Kearney; Erik C Thorland; Kerry K Brown; Fabiola Quintero-Rivera; Sarah T South
Journal:  Genet Med       Date:  2011-07       Impact factor: 8.822

4.  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
Journal:  Genet Med       Date:  2015-03-05       Impact factor: 8.822

5.  RefSeq: an update on mammalian reference sequences.

Authors:  Kim D Pruitt; Garth R Brown; Susan M Hiatt; Françoise Thibaud-Nissen; Alexander Astashyn; Olga Ermolaeva; Catherine M Farrell; Jennifer Hart; Melissa J Landrum; Kelly M McGarvey; Michael R Murphy; Nuala A O'Leary; Shashikant Pujar; Bhanu Rajput; Sanjida H Rangwala; Lillian D Riddick; Andrei Shkeda; Hanzhen Sun; Pamela Tamez; Raymond E Tully; Craig Wallin; David Webb; Janet Weber; Wendy Wu; Michael DiCuccio; Paul Kitts; Donna R Maglott; Terence D Murphy; James M Ostell
Journal:  Nucleic Acids Res       Date:  2013-11-19       Impact factor: 16.971

6.  ClinVar: public archive of relationships among sequence variation and human phenotype.

Authors:  Melissa J Landrum; Jennifer M Lee; George R Riley; Wonhee Jang; Wendy S Rubinstein; Deanna M Church; Donna R Maglott
Journal:  Nucleic Acids Res       Date:  2013-11-14       Impact factor: 16.971

7.  Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants.

Authors:  Jacqueline A L MacArthur; Joannella Morales; Ray E Tully; Alex Astashyn; Laurent Gil; Elspeth A Bruford; Pontus Larsson; Paul Flicek; Raymond Dalgleish; Donna R Maglott; Fiona Cunningham
Journal:  Nucleic Acids Res       Date:  2013-11-26       Impact factor: 16.971

  7 in total
  48 in total

1.  Tissue-specific FAH deficiency alters sleep-wake patterns and results in chronic tyrosinemia in mice.

Authors:  Shuzhang Yang; Sandra M Siepka; Kimberly H Cox; Vivek Kumar; Marleen de Groot; Yogarany Chelliah; Jun Chen; Benjamin Tu; Joseph S Takahashi
Journal:  Proc Natl Acad Sci U S A       Date:  2019-10-14       Impact factor: 11.205

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

Authors:  Alex Henrie; Sarah E Hemphill; Nicole Ruiz-Schultz; Brandon Cushman; Marina T DiStefano; Danielle Azzariti; Steven M Harrison; Heidi L Rehm; Karen Eilbeck
Journal:  Hum Mutat       Date:  2018-06-21       Impact factor: 4.878

Review 3.  First Responder to Genomic Information: A Guide for Primary Care Providers.

Authors:  Susanne B Haga
Journal:  Mol Diagn Ther       Date:  2019-08       Impact factor: 4.074

Review 4.  Settling the score: variant prioritization and Mendelian disease.

Authors:  Karen Eilbeck; Aaron Quinlan; Mark Yandell
Journal:  Nat Rev Genet       Date:  2017-08-14       Impact factor: 53.242

5.  ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants.

Authors:  Najmeh Alirezaie; Kristin D Kernohan; Taila Hartley; Jacek Majewski; Toby Dylan Hocking
Journal:  Am J Hum Genet       Date:  2018-09-13       Impact factor: 11.025

6.  Detection of Pathogenic Germline Variants Among Patients With Advanced Colorectal Cancer Undergoing Tumor Genomic Profiling for Precision Medicine.

Authors:  Y Nancy You; Ester Borras; Kyle Chang; Brandee A Price; Maureen Mork; George J Chang; Miguel A Rodriguez-Bigas; Brian K Bednarski; Funda Meric-Bernstam; Eduardo Vilar
Journal:  Dis Colon Rectum       Date:  2019-04       Impact factor: 4.585

7.  "Matching" consent to purpose: The example of the Matchmaker Exchange.

Authors:  Stephanie O M Dyke; Bartha M Knoppers; Ada Hamosh; Helen V Firth; Matthew Hurles; Michael Brudno; Kym M Boycott; Anthony A Philippakis; Heidi L Rehm
Journal:  Hum Mutat       Date:  2017-07-12       Impact factor: 4.878

8.  The value of genomic variant ClinVar submissions from clinical providers: Beyond the addition of novel variants.

Authors:  Karen E Wain; Emily Palen; Juliann M Savatt; Devin Shuman; Brenda Finucane; Andrea Seeley; Thomas D Challman; Scott M Myers; Christa Lese Martin
Journal:  Hum Mutat       Date:  2018-11       Impact factor: 4.878

9.  ClinVar database of global familial hypercholesterolemia-associated DNA variants.

Authors:  Michael A Iacocca; Joana R Chora; Alain Carrié; Tomáš Freiberger; Sarah E Leigh; Joep C Defesche; C Lisa Kurtz; Marina T DiStefano; Raul D Santos; Steve E Humphries; Pedro Mata; Cinthia E Jannes; Amanda J Hooper; Katherine A Wilemon; Pascale Benlian; Robert O'Connor; John Garcia; Hannah Wand; Lukáš Tichy; Eric J Sijbrands; Robert A Hegele; Mafalda Bourbon; Joshua W Knowles
Journal:  Hum Mutat       Date:  2018-11       Impact factor: 4.878

10.  Recurrent arginine substitutions in the ACTG2 gene are the primary driver of disease burden and severity in visceral myopathy.

Authors:  Nurit Assia Batzir; Pranjali Kishor Bhagwat; Austin Larson; Zeynep Coban Akdemir; Maciej Bagłaj; Leon Bofferding; Katherine B Bosanko; Skander Bouassida; Bert Callewaert; Ashley Cannon; Yazmin Enchautegui Colon; Adolfo D Garnica; Margaret H Harr; Sandra Heck; Anna C E Hurst; Shalini N Jhangiani; Bertrand Isidor; Rebecca O Littlejohn; Pengfei Liu; Pilar Magoulas; Helen Mar Fan; Ronit Marom; Scott McLean; Marjan M Nezarati; Kimberly M Nugent; Michael B Petersen; Maria L Rocha; Elizabeth Roeder; Robert Smigiel; Ian Tully; James Weisfeld-Adams; Katerina O Wells; Jennifer E Posey; James R Lupski; Arthur L Beaudet; Michael F Wangler
Journal:  Hum Mutat       Date:  2019-12-19       Impact factor: 4.878

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