Literature DB >> 24763993

Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data.

Brett Kennedy1, Zev Kronenberg, Hao Hu, Barry Moore, Steven Flygare, Martin G Reese, Lynn B Jorde, Mark Yandell, Chad Huff.   

Abstract

The VAAST pipeline is specifically designed to identify disease-associated alleles in next-generation sequencing data. In the protocols presented in this paper, we outline the best practices for variant prioritization using VAAST. Examples and test data are provided for case-control, small pedigree, and large pedigree analyses. These protocols will teach users the fundamentals of VAAST, VAAST 2.0, and pVAAST analyses.
Copyright © 2014 John Wiley & Sons, Inc.

Entities:  

Keywords:  VAAST; bioinformatics; computational genomics; disease-gene identification; genome-wide association studies; genomics; human disease; next-generation sequencing; rare-variant association test; variant classification

Mesh：

Year:  2014        PMID： 24763993      PMCID： PMC4137768          DOI： 10.1002/0471142905.hg0614s81

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


  29 in total

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2.  Sturge-Weber syndrome and port-wine stains caused by somatic mutation in GNAQ.

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Journal:  N Engl J Med       Date:  2013-05-08       Impact factor: 91.245

3.  A space-time process model for the evolution of DNA sequences.

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Review 4.  Genotype and SNP calling from next-generation sequencing data.

Authors:  Rasmus Nielsen; Joshua S Paul; Anders Albrechtsen; Yun S Song
Journal:  Nat Rev Genet       Date:  2011-06       Impact factor: 53.242

5.  Maternal coding variants in complement receptor 1 and spontaneous idiopathic preterm birth.

Authors:  Jude J McElroy; Courtney E Gutman; Christian M Shaffer; Tamara D Busch; Hilkka Puttonen; Kari Teramo; Jeffrey C Murray; Mikko Hallman; Louis J Muglia
Journal:  Hum Genet       Date:  2013-04-17       Impact factor: 4.132

6.  Clinical analysis of genome next-generation sequencing data using the Omicia platform.

Authors:  Emily M Coonrod; Rebecca L Margraf; Archie Russell; Karl V Voelkerding; Martin G Reese
Journal:  Expert Rev Mol Diagn       Date:  2013-07       Impact factor: 5.225

7.  A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

Authors:  Hao Hu; Jared C Roach; Hilary Coon; Stephen L Guthery; Karl V Voelkerding; Rebecca L Margraf; Jacob D Durtschi; Sean V Tavtigian; Wilfred Wu; Paul Scheet; Shuoguo Wang; Jinchuan Xing; Gustavo Glusman; Robert Hubley; Hong Li; Vidu Garg; Barry Moore; Leroy Hood; David J Galas; Deepak Srivastava; Martin G Reese; Lynn B Jorde; Mark Yandell; Chad D Huff
Journal:  Nat Biotechnol       Date:  2014-05-18       Impact factor: 54.908

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9.  VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix.

Authors:  Hao Hu; Chad D Huff; Barry Moore; Steven Flygare; Martin G Reese; Mark Yandell
Journal:  Genet Epidemiol       Date:  2013-07-08       Impact factor: 2.135

10.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962
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  10 in total

Review 1.  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

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Journal:  J Clin Endocrinol Metab       Date:  2022-02-17       Impact factor: 5.958

3.  Exome Sequencing Identifies Genetic Variants Associated with Extreme Manifestations of the Cardiovascular Phenotype in Marfan Syndrome.

Authors:  Yanireth Jimenez; Cesar Paulsen; Eduardo Turner; Sebastian Iturra; Oscar Cuevas; Guillermo Lay-Son; Gabriela M Repetto; Marcelo Rojas; Juan F Calderon
Journal:  Genes (Basel)       Date:  2022-06-08       Impact factor: 4.141

4.  Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus.

Authors:  Neil E Bowles; Chuanchau J Jou; Cammon B Arrington; Brett J Kennedy; Aubree Earl; Norisada Matsunami; Lindsay L Meyers; Susan P Etheridge; Elizabeth V Saarel; Steven B Bleyl; H Joseph Yost; Mark Yandell; Mark F Leppert; Martin Tristani-Firouzi; Peter J Gruber
Journal:  Am J Med Genet A       Date:  2015-08-18       Impact factor: 2.802

5.  Primary Ovarian Insufficiency and Azoospermia in Carriers of a Homozygous PSMC3IP Stop Gain Mutation.

Authors:  Abdulmoein Eid Al-Agha; Ihab Abdulhamed Ahmed; Esther Nuebel; Mika Moriwaki; Barry Moore; Katherine A Peacock; Tim Mosbruger; Deborah W Neklason; Lynn B Jorde; Mark Yandell; Corrine K Welt
Journal:  J Clin Endocrinol Metab       Date:  2018-02-01       Impact factor: 5.958

6.  KBG syndrome involving a single-nucleotide duplication in ANKRD11.

Authors:  Robert Kleyner; Janet Malcolmson; David Tegay; Kenneth Ward; Annette Maughan; Glenn Maughan; Lesa Nelson; Kai Wang; Reid Robison; Gholson J Lyon
Journal:  Cold Spring Harb Mol Case Stud       Date:  2016-11

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Authors:  Wesley C Warren; Raquel García-Pérez; Sen Xu; Kathrin P Lampert; Domitille Chalopin; Matthias Stöck; Laurence Loewe; Yuan Lu; Lukas Kuderna; Patrick Minx; Michael J Montague; Chad Tomlinson; LaDeana W Hillier; Daniel N Murphy; John Wang; Zhongwei Wang; Constantino Macias Garcia; Gregg C W Thomas; Jean-Nicolas Volff; Fabiana Farias; Bronwen Aken; Ronald B Walter; Kim D Pruitt; Tomas Marques-Bonet; Matthew W Hahn; Susanne Kneitz; Michael Lynch; Manfred Schartl
Journal:  Nat Ecol Evol       Date:  2018-02-12       Impact factor: 15.460

8.  The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool.

Authors:  Steven Flygare; Edgar Javier Hernandez; Lon Phan; Barry Moore; Man Li; Anthony Fejes; Hao Hu; Karen Eilbeck; Chad Huff; Lynn Jorde; Martin G Reese; Mark Yandell
Journal:  BMC Bioinformatics       Date:  2018-02-20       Impact factor: 3.169

9.  The history and geographic distribution of a KCNQ1 atrial fibrillation risk allele.

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Journal:  Nat Commun       Date:  2021-11-08       Impact factor: 14.919

Review 10.  Prioritization of Variants Detected by Next Generation Sequencing According to the Mutation Tolerance and Mutational Architecture of the Corresponding Genes.

Authors:  Iria Roca; Ana Fernández-Marmiesse; Sofía Gouveia; Marta Segovia; María L Couce
Journal:  Int J Mol Sci       Date:  2018-05-27       Impact factor: 5.923
  10 in total

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