Literature DB >> 22640420

Consensus: a framework for evaluation of uncertain gene variants in laboratory test reporting.

David K Crockett1, Perry G Ridge, Andrew R Wilson, Elaine Lyon, Marc S Williams, Scott P Narus, Julio C Facelli, Joyce A Mitchell.   

Abstract

Accurate interpretation of gene testing is a key component in customizing patient therapy. Where confirming evidence for a gene variant is lacking, computational prediction may be employed. A standardized framework, however, does not yet exist for quantitative evaluation of disease association for uncertain or novel gene variants in an objective manner. Here, complementary predictors for missense gene variants were incorporated into a weighted Consensus framework that includes calculated reference intervals from known disease outcomes. Data visualization for clinical reporting is also discussed.

Entities:  

Year:  2012        PMID: 22640420      PMCID: PMC3506914          DOI: 10.1186/gm347

Source DB:  PubMed          Journal:  Genome Med        ISSN: 1756-994X            Impact factor:   11.117


  47 in total

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Authors:  Pauline C Ng; Steven Henikoff
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

2.  The case for locus-specific databases.

Authors:  Mark E Samuels; Guy A Rouleau
Journal:  Nat Rev Genet       Date:  2011-05-04       Impact factor: 53.242

3.  Variants of uncertain clinical significance as a result of BRCA1/2 testing: impact of an ambiguous breast cancer risk message.

Authors:  Sandra van Dijk; Christi J van Asperen; Catharina E Jacobi; Geraldine R Vink; Aad Tibben; Martijn H Breuning; Wilma Otten
Journal:  Genet Test       Date:  2004

4.  Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants.

Authors:  David K Crockett; Elaine Lyon; Marc S Williams; Scott P Narus; Julio C Facelli; Joyce A Mitchell
Journal:  J Am Med Inform Assoc       Date:  2011-10-28       Impact factor: 4.497

5.  In silico prediction of the deleterious effect of a mutation: proceed with caution in clinical genetics.

Authors:  Dimitri Tchernitchko; Michel Goossens; Henri Wajcman
Journal:  Clin Chem       Date:  2004-11       Impact factor: 8.327

Review 6.  The hereditary nonpolyposis colorectal cancer syndrome: genetics and clinical implications.

Authors:  Daniel C Chung; Anil K Rustgi
Journal:  Ann Intern Med       Date:  2003-04-01       Impact factor: 25.391

7.  Clinical characteristics of individuals with germline mutations in BRCA1 and BRCA2: analysis of 10,000 individuals.

Authors:  Thomas S Frank; Amie M Deffenbaugh; Julia E Reid; Mark Hulick; Brian E Ward; Beth Lingenfelter; Kathi L Gumpper; Thomas Scholl; Sean V Tavtigian; Dmitry R Pruss; Gregory C Critchfield
Journal:  J Clin Oncol       Date:  2002-03-15       Impact factor: 44.544

8.  Data mining in bioinformatics using Weka.

Authors:  Eibe Frank; Mark Hall; Len Trigg; Geoffrey Holmes; Ian H Witten
Journal:  Bioinformatics       Date:  2004-04-08       Impact factor: 6.937

9.  Human non-synonymous SNPs: server and survey.

Authors:  Vasily Ramensky; Peer Bork; Shamil Sunyaev
Journal:  Nucleic Acids Res       Date:  2002-09-01       Impact factor: 16.971

10.  Likelihood ratios to assess genetic evidence for clinical significance of uncertain variants: hereditary hemorrhagic telangiectasia as a model.

Authors:  Pinar Bayrak-Toydemir; Jamie McDonald; Rong Mao; Amit Phansalkar; Friederike Gedge; Jorge Robles; David Goldgar; Elaine Lyon
Journal:  Exp Mol Pathol       Date:  2008-04-08       Impact factor: 3.362

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  5 in total

1.  REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.

Authors:  Nilah M Ioannidis; Joseph H Rothstein; Vikas Pejaver; Sumit Middha; Shannon K McDonnell; Saurabh Baheti; Anthony Musolf; Qing Li; Emily Holzinger; Danielle Karyadi; Lisa A Cannon-Albright; Craig C Teerlink; Janet L Stanford; William B Isaacs; Jianfeng Xu; Kathleen A Cooney; Ethan M Lange; Johanna Schleutker; John D Carpten; Isaac J Powell; Olivier Cussenot; Geraldine Cancel-Tassin; Graham G Giles; Robert J MacInnis; Christiane Maier; Chih-Lin Hsieh; Fredrik Wiklund; William J Catalona; William D Foulkes; Diptasri Mandal; Rosalind A Eeles; Zsofia Kote-Jarai; Carlos D Bustamante; Daniel J Schaid; Trevor Hastie; Elaine A Ostrander; Joan E Bailey-Wilson; Predrag Radivojac; Stephen N Thibodeau; Alice S Whittemore; Weiva Sieh
Journal:  Am J Hum Genet       Date:  2016-09-22       Impact factor: 11.025

2.  Usability evaluation of pharmacogenomics clinical decision support aids and clinical knowledge resources in a computerized provider order entry system: a mixed methods approach.

Authors:  Emily Beth Devine; Chia-Ju Lee; Casey L Overby; Neil Abernethy; Jeannine McCune; Joe W Smith; Peter Tarczy-Hornoch
Journal:  Int J Med Inform       Date:  2014-05-09       Impact factor: 4.046

3.  A classification system for clinical relevance of somatic variants identified in molecular profiling of cancer.

Authors:  Mahadeo A Sukhai; Kenneth J Craddock; Mariam Thomas; Aaron R Hansen; Tong Zhang; Lillian Siu; Philippe Bedard; Tracy L Stockley; Suzanne Kamel-Reid
Journal:  Genet Med       Date:  2015-04-16       Impact factor: 8.822

4.  Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP.

Authors:  Morten Bo Johansen; Jose M G Izarzugaza; Søren Brunak; Thomas Nordahl Petersen; Ramneek Gupta
Journal:  PLoS One       Date:  2013-07-25       Impact factor: 3.240

5.  VarRanker: rapid prioritization of sequence variations associated with human disease.

Authors:  Brendan D O'Fallon; Whitney Wooderchak-Donahue; Pinar Bayrak-Toydemir; David Crockett
Journal:  BMC Bioinformatics       Date:  2013-10-01       Impact factor: 3.169

  5 in total

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