Literature DB >> 26192085

Phenolyzer: phenotype-based prioritization of candidate genes for human diseases.

Hui Yang1,2, Peter N Robinson3,4,5,6, Kai Wang1,7,8.   

Abstract

Prior biological knowledge and phenotype information may help to identify disease genes from human whole-genome and whole-exome sequencing studies. We developed Phenolyzer (http://phenolyzer.usc.edu), a tool that uses prior information to implicate genes involved in diseases. Phenolyzer exhibits superior performance over competing methods for prioritizing Mendelian and complex disease genes, based on disease or phenotype terms entered as free text.

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Year:  2015        PMID： 26192085      PMCID： PMC4718403          DOI： 10.1038/nmeth.3484

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  36 in total

1.  Jannovar: a java library for exome annotation.

Authors:  Marten Jäger; Kai Wang; Sebastian Bauer; Damian Smedley; Peter Krawitz; Peter N Robinson
Journal:  Hum Mutat       Date:  2014-04-09       Impact factor: 4.878

2.  Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units.

Authors:  Carol Jean Saunders; Neil Andrew Miller; Sarah Elizabeth Soden; Darrell Lee Dinwiddie; Aaron Noll; Noor Abu Alnadi; Nevene Andraws; Melanie LeAnn Patterson; Lisa Ann Krivohlavek; Joel Fellis; Sean Humphray; Peter Saffrey; Zoya Kingsbury; Jacqueline Claire Weir; Jason Betley; Russell James Grocock; Elliott Harrison Margulies; Emily Gwendolyn Farrow; Michael Artman; Nicole Pauline Safina; Joshua Erin Petrikin; Kevin Peter Hall; Stephen Francis Kingsmore
Journal:  Sci Transl Med       Date:  2012-10-03       Impact factor: 17.956

3.  Phen-Gen: combining phenotype and genotype to analyze rare disorders.

Authors:  Asif Javed; Saloni Agrawal; Pauline C Ng
Journal:  Nat Methods       Date:  2014-08-03       Impact factor: 28.547

Review 4.  Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress.

Authors:  Gholson J Lyon; Kai Wang
Journal:  Genome Med       Date:  2012-07-26       Impact factor: 11.117

5.  Disease Ontology: a backbone for disease semantic integration.

Authors:  Lynn Marie Schriml; Cesar Arze; Suvarna Nadendla; Yu-Wei Wayne Chang; Mark Mazaitis; Victor Felix; Gang Feng; Warren Alden Kibbe
Journal:  Nucleic Acids Res       Date:  2011-11-12       Impact factor: 16.971

6.  MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database.

Authors:  Allan Peter Davis; Thomas C Wiegers; Michael C Rosenstein; Carolyn J Mattingly
Journal:  Database (Oxford)       Date:  2012-03-20       Impact factor: 3.451

7.  The NCBI BioSystems database.

Authors:  Lewis Y Geer; Aron Marchler-Bauer; Renata C Geer; Lianyi Han; Jane He; Siqian He; Chunlei Liu; Wenyao Shi; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2009-10-23       Impact factor: 16.971

8.  HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

Authors:  Luiz A Bovolenta; Marcio L Acencio; Ney Lemke
Journal:  BMC Genomics       Date:  2012-08-17       Impact factor: 3.969

9.  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

10.  RADB: a database of rheumatoid arthritis-related polymorphisms.

Authors:  Ruijie Zhang; Meiwei Luan; Zhenwei Shang; Lian Duan; Guoping Tang; Miao Shi; Wenhua Lv; Hongjie Zhu; Jin Li; Hongchao Lv; Mingming Zhang; Guiyou Liu; He Chen; Yongshuai Jiang
Journal:  Database (Oxford)       Date:  2014-09-15       Impact factor: 3.451
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  145 in total

1.  Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR.

Authors:  Hui Yang; Kai Wang
Journal:  Nat Protoc       Date:  2015-09-17       Impact factor: 13.491

2.  Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

Authors:  Roxana Daneshjou; Yanran Wang; Yana Bromberg; Samuele Bovo; Pier L Martelli; Giulia Babbi; Pietro Di Lena; Rita Casadio; Matthew Edwards; David Gifford; David T Jones; Laksshman Sundaram; Rajendra Rana Bhat; Xiaolin Li; Lipika R Pal; Kunal Kundu; Yizhou Yin; John Moult; Yuxiang Jiang; Vikas Pejaver; Kymberleigh A Pagel; Biao Li; Sean D Mooney; Predrag Radivojac; Sohela Shah; Marco Carraro; Alessandra Gasparini; Emanuela Leonardi; Manuel Giollo; Carlo Ferrari; Silvio C E Tosatto; Eran Bachar; Johnathan R Azaria; Yanay Ofran; Ron Unger; Abhishek Niroula; Mauno Vihinen; Billy Chang; Maggie H Wang; Andre Franke; Britt-Sabina Petersen; Mehdi Pirooznia; Peter Zandi; Richard McCombie; James B Potash; Russ B Altman; Teri E Klein; Roger A Hoskins; Susanna Repo; Steven E Brenner; Alexander A Morgan
Journal:  Hum Mutat       Date:  2017-07-07       Impact factor: 4.878

3.  A genetic-phenotypic classification for syndromic micrognathia.

Authors:  Qiming Chen; Yan Zhao; Yifeng Qian; Chenpei Lu; Guofang Shen; Jiewen Dai
Journal:  J Hum Genet       Date:  2019-07-04       Impact factor: 3.172

4.  A Case of UDP-Galactose 4'-Epimerase Deficiency Associated with Dyshematopoiesis and Atrioventricular Valve Malformations: An Exceptional Clinical Phenotype Explained by Altered N-Glycosylation with Relative Preservation of the Leloir Pathway.

Authors:  Christopher A Febres-Aldana; Liset Pelaez; Meredith S Wright; Ossama M Maher; Anthony J Febres-Aldana; Jun Sasaki; Parul Jayakar; Anuj Jayakar; Magaly Diaz-Barbosa; Michelin Janvier; Bala Totapally; Daria Salyakina; Jorge R Galvez-Silva
Journal:  Mol Syndromol       Date:  2020-10-29

Review 5.  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

6.  Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits.

Authors:  Malika Kumar Freund; Kathryn S Burch; Huwenbo Shi; Nicholas Mancuso; Gleb Kichaev; Kristina M Garske; David Z Pan; Zong Miao; Karen L Mohlke; Markku Laakso; Päivi Pajukanta; Bogdan Pasaniuc; Valerie A Arboleda
Journal:  Am J Hum Genet       Date:  2018-10-04       Impact factor: 11.025

7.  Rapid and accurate interpretation of clinical exomes using Phenoxome: a computational phenotype-driven approach.

Authors:  Chao Wu; Batsal Devkota; Perry Evans; Xiaonan Zhao; Samuel W Baker; Rojeen Niazi; Kajia Cao; Michael A Gonzalez; Pushkala Jayaraman; Laura K Conlin; Bryan L Krock; Matthew A Deardorff; Nancy B Spinner; Ian D Krantz; Avni B Santani; Ahmad N Abou Tayoun; Mahdi Sarmady
Journal:  Eur J Hum Genet       Date:  2019-01-09       Impact factor: 4.246

8.  PubCaseFinder: A Case-Report-Based, Phenotype-Driven Differential-Diagnosis System for Rare Diseases.

Authors:  Toyofumi Fujiwara; Yasunori Yamamoto; Jin-Dong Kim; Orion Buske; Toshihisa Takagi
Journal:  Am J Hum Genet       Date:  2018-08-30       Impact factor: 11.025

9.  CAGI4 SickKids clinical genomes challenge: A pipeline for identifying pathogenic variants.

Authors:  Lipika R Pal; Kunal Kundu; Yizhou Yin; John Moult
Journal:  Hum Mutat       Date:  2017-06-27       Impact factor: 4.878

10.  A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

Authors:  Damian Smedley; Max Schubach; Julius O B Jacobsen; Sebastian Köhler; Tomasz Zemojtel; Malte Spielmann; Marten Jäger; Harry Hochheiser; Nicole L Washington; Julie A McMurry; Melissa A Haendel; Christopher J Mungall; Suzanna E Lewis; Tudor Groza; Giorgio Valentini; Peter N Robinson
Journal:  Am J Hum Genet       Date:  2016-08-25       Impact factor: 11.025
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