Literature DB >> 27999115

The performance of deleteriousness prediction scores for rare non-protein-changing single nucleotide variants in human genes.

Xiaoming Liu1, Chang Li1, Eric Boerwinkle1,2.   

Abstract

Entities:  

Keywords:  Clinical genetics; Genetic screening/counselling; Genetics; Genome-wide

Mesh：

Year:  2016        PMID： 27999115      PMCID： PMC5736365          DOI： 10.1136/jmedgenet-2016-104369

Source DB:  PubMed          Journal:  J Med Genet        ISSN： 0022-2593            Impact factor:   6.318


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  10 in total

1.  WGSA: an annotation pipeline for human genome sequencing studies.

Authors:  Xiaoming Liu; Simon White; Bo Peng; Andrew D Johnson; Jennifer A Brody; Alexander H Li; Zhuoyi Huang; Andrew Carroll; Peng Wei; Richard Gibbs; Robert J Klein; Eric Boerwinkle
Journal:  J Med Genet       Date:  2015-09-22       Impact factor: 6.318

2.  Predicting effects of noncoding variants with deep learning-based sequence model.

Authors:  Jian Zhou; Olga G Troyanskaya
Journal:  Nat Methods       Date:  2015-08-24       Impact factor: 28.547

3.  An integrative approach to predicting the functional effects of non-coding and coding sequence variation.

Authors:  Hashem A Shihab; Mark F Rogers; Julian Gough; Matthew Mort; David N Cooper; Ian N M Day; Tom R Gaunt; Colin Campbell
Journal:  Bioinformatics       Date:  2015-01-11       Impact factor: 6.937

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.  A method to predict the impact of regulatory variants from DNA sequence.

Authors:  Dongwon Lee; David U Gorkin; Maggie Baker; Benjamin J Strober; Alessandro L Asoni; Andrew S McCallion; Michael A Beer
Journal:  Nat Genet       Date:  2015-06-15       Impact factor: 38.330

6.  A general framework for estimating the relative pathogenicity of human genetic variants.

Authors:  Martin Kircher; Daniela M Witten; Preti Jain; Brian J O'Roak; Gregory M Cooper; Jay Shendure
Journal:  Nat Genet       Date:  2014-02-02       Impact factor: 38.330

Review 7.  The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine.

Authors:  Peter D Stenson; Matthew Mort; Edward V Ball; Katy Shaw; Andrew Phillips; David N Cooper
Journal:  Hum Genet       Date:  2014-01       Impact factor: 4.132

8.  A method for calculating probabilities of fitness consequences for point mutations across the human genome.

Authors:  Brad Gulko; Melissa J Hubisz; Ilan Gronau; Adam Siepel
Journal:  Nat Genet       Date:  2015-01-19       Impact factor: 38.330

9.  A spectral approach integrating functional genomic annotations for coding and noncoding variants.

Authors:  Iuliana Ionita-Laza; Kenneth McCallum; Bin Xu; Joseph D Buxbaum
Journal:  Nat Genet       Date:  2016-01-04       Impact factor: 38.330

10.  The UK10K project identifies rare variants in health and disease.

Authors:  Klaudia Walter; Josine L Min; Jie Huang; Lucy Crooks; Yasin Memari; Shane McCarthy; John R B Perry; ChangJiang Xu; Marta Futema; Daniel Lawson; Valentina Iotchkova; Stephan Schiffels; Audrey E Hendricks; Petr Danecek; Rui Li; James Floyd; Louise V Wain; Inês Barroso; Steve E Humphries; Matthew E Hurles; Eleftheria Zeggini; Jeffrey C Barrett; Vincent Plagnol; J Brent Richards; Celia M T Greenwood; Nicholas J Timpson; Richard Durbin; Nicole Soranzo
Journal:  Nature       Date:  2015-09-14       Impact factor: 49.962
  10 in total
  7 in total

1.  FunSPU: A versatile and adaptive multiple functional annotation-based association test of whole-genome sequencing data.

Authors:  Yiding Ma; Peng Wei
Journal:  PLoS Genet       Date:  2019-04-29       Impact factor: 5.917

2.  dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs.

Authors:  Xiaoming Liu; Chang Li; Chengcheng Mou; Yibo Dong; Yicheng Tu
Journal:  Genome Med       Date:  2020-12-02       Impact factor: 11.117

3.  Classification of non-coding variants with high pathogenic impact.

Authors:  Lambert Moyon; Camille Berthelot; Alexandra Louis; Nga Thi Thuy Nguyen; Hugues Roest Crollius
Journal:  PLoS Genet       Date:  2022-04-29       Impact factor: 5.917

4.  CScape: a tool for predicting oncogenic single-point mutations in the cancer genome.

Authors:  Mark F Rogers; Hashem A Shihab; Tom R Gaunt; Colin Campbell
Journal:  Sci Rep       Date:  2017-09-14       Impact factor: 4.379

5.  FATHMM-XF: accurate prediction of pathogenic point mutations via extended features.

Authors:  Mark F Rogers; Hashem A Shihab; Matthew Mort; David N Cooper; Tom R Gaunt; Colin Campbell
Journal:  Bioinformatics       Date:  2018-02-01       Impact factor: 6.937

6.  CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome.

Authors:  Mark F Rogers; Tom R Gaunt; Colin Campbell
Journal:  Bioinformatics       Date:  2020-06-01       Impact factor: 6.937

Review 7.  Prediction of driver variants in the cancer genome via machine learning methodologies.

Authors:  Mark F Rogers; Tom R Gaunt; Colin Campbell
Journal:  Brief Bioinform       Date:  2021-07-20       Impact factor: 11.622
  7 in total

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