Literature DB >> 31524990

Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity.

Julia Wang1, Dongxue Mao2, Fatima Fazal3, Seon-Young Kim3,4, Shinya Yamamoto5,6,7, Hugo Bellen3,4, Zhandong Liu8,9,10.   

Abstract

One of the greatest challenges in the bioinformatic analysis of human sequencing data is identifying which variants are pathogenic. Numerous databases and tools have been generated to address this difficulty. However, these many useful data and tools are broadly dispersed, requiring users to search for their variants of interest through human genetic databases, variant function prediction tools, and model organism databases. To solve this problem, we collected data and observed workflows of human geneticists, clinicians, and model organism researchers to carefully select and display valuable information that facilitates the evaluation of whether a variant is likely to be pathogenic. This program, Model organism Aggregated Resources for Rare Variant ExpLoration (MARRVEL) v1.2, allows users to collect relevant data from 27 public sources for further efficient bioinformatic analysis of the pathogenicity of human variants.
© 2019 by John Wiley & Sons, Inc. © 2019 John Wiley & Sons, Inc.

Entities:  

Keywords:  genes of unknown significance; genetics; genomics databases; model organisms; variants of unknown significance

Mesh:

Year:  2019        PMID: 31524990      PMCID: PMC6750039          DOI: 10.1002/cpbi.85

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN: 1934-3396


  41 in total

1.  Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research.

Authors:  Teri A Manolio; Douglas M Fowler; Lea M Starita; Melissa A Haendel; Daniel G MacArthur; Leslie G Biesecker; Elizabeth Worthey; Rex L Chisholm; Eric D Green; Howard J Jacob; Howard L McLeod; Dan Roden; Laura Lyman Rodriguez; Marc S Williams; Gregory M Cooper; Nancy J Cox; Gail E Herman; Stephen Kingsmore; Cecilia Lo; Cathleen Lutz; Calum A MacRae; Robert L Nussbaum; Jose M Ordovas; Erin M Ramos; Peter N Robinson; Wendy S Rubinstein; Christine Seidman; Barbara E Stranger; Haoyi Wang; Monte Westerfield; Carol Bult
Journal:  Cell       Date:  2017-03-23       Impact factor: 41.582

2.  Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.

Authors:  Christian Grove; Scott Cain; Wen J Chen; Paul Davis; Todd Harris; Kevin L Howe; Ranjana Kishore; Raymond Lee; Michael Paulini; Daniela Raciti; Mary Ann Tuli; Kimberly Van Auken; Gary Williams
Journal:  Methods Mol Biol       Date:  2018

3.  Bi-allelic Loss-of-Function Variants in DNMBP Cause Infantile Cataracts.

Authors:  Muhammad Ansar; Hyung-Lok Chung; Rachel L Taylor; Aamir Nazir; Samina Imtiaz; Muhammad T Sarwar; Alkistis Manousopoulou; Periklis Makrythanasis; Sondas Saeed; Emilie Falconnet; Michel Guipponi; Constantin J Pournaras; Maqsood A Ansari; Emmanuelle Ranza; Federico A Santoni; Jawad Ahmed; Inayat Shah; Khitab Gul; Graeme Cm Black; Hugo J Bellen; Stylianos E Antonarakis
Journal:  Am J Hum Genet       Date:  2018-10-04       Impact factor: 11.025

4.  Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease.

Authors:  Kimberly Splinter; David R Adams; Carlos A Bacino; Hugo J Bellen; Jonathan A Bernstein; Alys M Cheatle-Jarvela; Christine M Eng; Cecilia Esteves; William A Gahl; Rizwan Hamid; Howard J Jacob; Bijal Kikani; David M Koeller; Isaac S Kohane; Brendan H Lee; Joseph Loscalzo; Xi Luo; Alexa T McCray; Thomas O Metz; John J Mulvihill; Stanley F Nelson; Christina G S Palmer; John A Phillips; Leslie Pick; John H Postlethwait; Chloe Reuter; Vandana Shashi; David A Sweetser; Cynthia J Tifft; Nicole M Walley; Michael F Wangler; Monte Westerfield; Matthew T Wheeler; Anastasia L Wise; Elizabeth A Worthey; Shinya Yamamoto; Euan A Ashley
Journal:  N Engl J Med       Date:  2018-10-10       Impact factor: 91.245

5.  Identifying a high fraction of the human genome to be under selective constraint using GERP++.

Authors:  Eugene V Davydov; David L Goode; Marina Sirota; Gregory M Cooper; Arend Sidow; Serafim Batzoglou
Journal:  PLoS Comput Biol       Date:  2010-12-02       Impact factor: 4.475

6.  An integrative approach to ortholog prediction for disease-focused and other functional studies.

Authors:  Yanhui Hu; Ian Flockhart; Arunachalam Vinayagam; Clemens Bergwitz; Bonnie Berger; Norbert Perrimon; Stephanie E Mohr
Journal:  BMC Bioinformatics       Date:  2011-08-31       Impact factor: 3.169

7.  dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions.

Authors:  Xiaoming Liu; Xueqiu Jian; Eric Boerwinkle
Journal:  Hum Mutat       Date:  2011-08       Impact factor: 4.878

Review 8.  Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research.

Authors:  Michael F Wangler; Shinya Yamamoto; Hsiao-Tuan Chao; Jennifer E Posey; Monte Westerfield; John Postlethwait; Philip Hieter; Kym M Boycott; Philippe M Campeau; Hugo J Bellen
Journal:  Genetics       Date:  2017-09       Impact factor: 4.562

9.  Parallelization of MAFFT for large-scale multiple sequence alignments.

Authors:  Tsukasa Nakamura; Kazunori D Yamada; Kentaro Tomii; Kazutaka Katoh
Journal:  Bioinformatics       Date:  2018-07-15       Impact factor: 6.937

Review 10.  PomBase: The Scientific Resource for Fission Yeast.

Authors:  Antonia Lock; Kim Rutherford; Midori A Harris; Valerie Wood
Journal:  Methods Mol Biol       Date:  2018
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  7 in total

Review 1.  Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure-function studies in Drosophila.

Authors:  Shinya Yamamoto
Journal:  Dev Growth Differ       Date:  2020-01-13       Impact factor: 2.053

2.  Bi-allelic Variants in IQSEC1 Cause Intellectual Disability, Developmental Delay, and Short Stature.

Authors:  Muhammad Ansar; Hyung-Lok Chung; Ali Al-Otaibi; Mohammad Nael Elagabani; Thomas A Ravenscroft; Sohail A Paracha; Ralf Scholz; Tayseer Abdel Magid; Muhammad T Sarwar; Sayyed Fahim Shah; Azhar Ali Qaisar; Periklis Makrythanasis; Paul C Marcogliese; Erik-Jan Kamsteeg; Emilie Falconnet; Emmanuelle Ranza; Federico A Santoni; Hesham Aldhalaan; Ali Al-Asmari; Eissa Ali Faqeih; Jawad Ahmed; Hans-Christian Kornau; Hugo J Bellen; Stylianos E Antonarakis
Journal:  Am J Hum Genet       Date:  2019-10-10       Impact factor: 11.025

3.  BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms.

Authors:  Scott Barish; Tahsin Stefan Barakat; Brittany C Michel; Nazar Mashtalir; Jennifer B Phillips; Alfredo M Valencia; Berrak Ugur; Jeremy Wegner; Tiana M Scott; Brett Bostwick; David R Murdock; Hongzheng Dai; Elena Perenthaler; Anita Nikoncuk; Marjon van Slegtenhorst; Alice S Brooks; Boris Keren; Caroline Nava; Cyril Mignot; Jessica Douglas; Lance Rodan; Catherine Nowak; Sian Ellard; Karen Stals; Sally Ann Lynch; Marie Faoucher; Gaetan Lesca; Patrick Edery; Kendra L Engleman; Dihong Zhou; Isabelle Thiffault; John Herriges; Jennifer Gass; Raymond J Louie; Elliot Stolerman; Camerun Washington; Francesco Vetrini; Aiko Otsubo; Victoria M Pratt; Erin Conboy; Kayla Treat; Nora Shannon; Jose Camacho; Emma Wakeling; Bo Yuan; Chun-An Chen; Jill A Rosenfeld; Monte Westerfield; Michael Wangler; Shinya Yamamoto; Cigall Kadoch; Daryl A Scott; Hugo J Bellen
Journal:  Am J Hum Genet       Date:  2020-11-23       Impact factor: 11.025

4.  Functional Studies of Genetic Variants Associated with Human Diseases in Notch Signaling-Related Genes Using Drosophila.

Authors:  Sheng-An Yang; Jose L Salazar; David Li-Kroeger; Shinya Yamamoto
Journal:  Methods Mol Biol       Date:  2022

5.  The microRNA processor DROSHA is a candidate gene for a severe progressive neurological disorder.

Authors:  Scott Barish; Mumine Senturk; Kelly Schoch; Amanda L Minogue; Diego Lopergolo; Chiara Fallerini; Jake Harland; Jacob H Seemann; Nicholas Stong; Peter G Kranz; Sujay Kansagra; Mohamad A Mikati; Joan Jasien; Mays El-Dairi; Paolo Galluzzi; Francesca Ariani; Alessandra Renieri; Francesca Mari; Michael F Wangler; Swathi Arur; Yong-Hui Jiang; Shinya Yamamoto; Vandana Shashi; Hugo J Bellen
Journal:  Hum Mol Genet       Date:  2022-08-25       Impact factor: 5.121

6.  Model organisms contribute to diagnosis and discovery in the undiagnosed diseases network: current state and a future vision.

Authors:  Dustin Baldridge; Michael F Wangler; Angela N Bowman; Shinya Yamamoto; Tim Schedl; Stephen C Pak; John H Postlethwait; Jimann Shin; Lilianna Solnica-Krezel; Hugo J Bellen; Monte Westerfield
Journal:  Orphanet J Rare Dis       Date:  2021-05-07       Impact factor: 4.123

Review 7.  Invertebrate Model Organisms as a Platform to Investigate Rare Human Neurological Diseases.

Authors:  Ji-Hye Lee
Journal:  Exp Neurobiol       Date:  2022-02-28       Impact factor: 3.261

  7 in total

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