Literature DB >> 28630944

ClinVar data parsing.

Xiaolei Zhang1,2, Eric V Minikel3,4, Anne H O'Donnell-Luria3,4,5, Daniel G MacArthur3,4, James S Ware1,2,6, Ben Weisburd3,4.   

Abstract

This software repository provides a pipeline for converting raw ClinVar data files into analysis-friendly tab-delimited tables, and also provides these tables for the most recent ClinVar release. Separate tables are generated for genome builds GRCh37 and GRCh38 as well as for mono-allelic variants and complex multi-allelic variants. Additionally, the tables are augmented with allele frequencies from the ExAC and gnomAD datasets as these are often consulted when analyzing ClinVar variants. Overall, this work provides ClinVar data in a format that is easier to work with and can be directly loaded into a variety of popular analysis tools such as R, python pandas, and SQL databases.

Entities:  

Keywords:  ClinVar; Mendelian disease; XML parsing; pathogenic variants; variant interpretation

Year:  2017        PMID： 28630944      PMCID： PMC5473414          DOI： 10.12688/wellcomeopenres.11640.1

Source DB:  PubMed          Journal:  Wellcome Open Res        ISSN： 2398-502X


  5 in total

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Journal:  Bioinformatics       Date:  2011-01-05       Impact factor: 6.937

2.  Unified representation of genetic variants.

Authors:  Adrian Tan; Gonçalo R Abecasis; Hyun Min Kang
Journal:  Bioinformatics       Date:  2015-02-19       Impact factor: 6.937

3.  Analysis of protein-coding genetic variation in 60,706 humans.

Authors:  Monkol Lek; Konrad J Karczewski; Eric V Minikel; Kaitlin E Samocha; Eric Banks; Timothy Fennell; Anne H O'Donnell-Luria; James S Ware; Andrew J Hill; Beryl B Cummings; Taru Tukiainen; Daniel P Birnbaum; Jack A Kosmicki; Laramie E Duncan; Karol Estrada; Fengmei Zhao; James Zou; Emma Pierce-Hoffman; Joanne Berghout; David N Cooper; Nicole Deflaux; Mark DePristo; Ron Do; Jason Flannick; Menachem Fromer; Laura Gauthier; Jackie Goldstein; Namrata Gupta; Daniel Howrigan; Adam Kiezun; Mitja I Kurki; Ami Levy Moonshine; Pradeep Natarajan; Lorena Orozco; Gina M Peloso; Ryan Poplin; Manuel A Rivas; Valentin Ruano-Rubio; Samuel A Rose; Douglas M Ruderfer; Khalid Shakir; Peter D Stenson; Christine Stevens; Brett P Thomas; Grace Tiao; Maria T Tusie-Luna; Ben Weisburd; Hong-Hee Won; Dongmei Yu; David M Altshuler; Diego Ardissino; Michael Boehnke; John Danesh; Stacey Donnelly; Roberto Elosua; Jose C Florez; Stacey B Gabriel; Gad Getz; Stephen J Glatt; Christina M Hultman; Sekar Kathiresan; Markku Laakso; Steven McCarroll; Mark I McCarthy; Dermot McGovern; Ruth McPherson; Benjamin M Neale; Aarno Palotie; Shaun M Purcell; Danish Saleheen; Jeremiah M Scharf; Pamela Sklar; Patrick F Sullivan; Jaakko Tuomilehto; Ming T Tsuang; Hugh C Watkins; James G Wilson; Mark J Daly; Daniel G MacArthur
Journal:  Nature       Date:  2016-08-18       Impact factor: 49.962

4.  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

5.  Using high-resolution variant frequencies to empower clinical genome interpretation.

Authors:  Nicola Whiffin; Eric Minikel; Roddy Walsh; Anne H O'Donnell-Luria; Konrad Karczewski; Alexander Y Ing; Paul J R Barton; Birgit Funke; Stuart A Cook; Daniel MacArthur; James S Ware
Journal:  Genet Med       Date:  2017-05-18       Impact factor: 8.822
  5 in total
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Journal:  Proc Natl Acad Sci U S A       Date:  2020-02-18       Impact factor: 11.205

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

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

4.  Heterozygosity mapping for human dominant trait variants.

Authors:  Atsuko Imai-Okazaki; Yi Li; Sukanya Horpaopan; Yasser Riazalhosseini; Masoud Garshasbi; Yael P Mosse; Di Zhang; Isabelle Schrauwen; Aarushi Sharma; Cathy S J Fann; Suzanne M Leal; Mark Lathrop; Jurg Ott
Journal:  Hum Mutat       Date:  2019-04-24       Impact factor: 4.878

5.  Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database.

Authors:  Eduardo Pérez-Palma; Marie Gramm; Peter Nürnberg; Patrick May; Dennis Lal
Journal:  Nucleic Acids Res       Date:  2019-07-02       Impact factor: 16.971

6.  Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance.

Authors:  Robert P Adelson; Alan E Renton; Wentian Li; Nir Barzilai; Gil Atzmon; Alison M Goate; Peter Davies; Yun Freudenberg-Hua
Journal:  Sci Rep       Date:  2019-11-06       Impact factor: 4.379

Review 7.  The Role of Impaired Mitochondrial Dynamics in MFN2-Mediated Pathology.

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Journal:  Front Cell Dev Biol       Date:  2022-03-24

8.  MFN2 mutations in Charcot-Marie-Tooth disease alter mitochondria-associated ER membrane function but do not impair bioenergetics.

Authors:  Delfina Larrea; Marta Pera; Adriano Gonnelli; Rubén Quintana-Cabrera; H Orhan Akman; Cristina Guardia-Laguarta; Kevin R Velasco; Estela Area-Gomez; Federica Dal Bello; Diego De Stefani; Rita Horvath; Michael E Shy; Eric A Schon; Marta Giacomello
Journal:  Hum Mol Genet       Date:  2019-06-01       Impact factor: 6.150

9.  Under-ascertainment of breast cancer susceptibility gene carriers in a cohort of New Zealand female breast cancer patients.

Authors:  Vanessa Lattimore; Michael T Parsons; Amanda B Spurdle; John Pearson; Klaus Lehnert; Jan Sullivan; Caroline Lintott; Suzannah Bawden; Helen Morrin; Bridget Robinson; Logan Walker
Journal:  Breast Cancer Res Treat       Date:  2020-10-28       Impact factor: 4.872
  9 in total

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