Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

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作者
Adam Frankish
Barbara Uszczynska
Graham RS Ritchie
Jose M Gonzalez
Dmitri Pervouchine
Robert Petryszak
Jonathan M Mudge
Nuno Fonseca
Alvis Brazma
Roderic Guigo
Jennifer Harrow
机构
[1] Wellcome Trust Genome Campus,Wellcome Trust Sanger Institute
[2] Centre for Genomic Regulation,European Molecular Biology Laboratory
[3] European Bioinformatics Institute,Faculty of Bioengineering and Bioinformatics, 119992 Moscow GSP
[4] Wellcome Trust Genome Campus,2, Leninskie Gory
[5] Moscow State University 1-73,undefined
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BMC Genomics | / 16卷
关键词
Variant Annotation; Nonsense Mediate Decay; Exome Sequencing Project; Transcript Annotation; Variant Effect Predictor;
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  • [1] Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
    Frankish, Adam
    Uszczynska, Barbara
    Ritchie, Graham R. S.
    Gonzalez, Jose M.
    Pervouchine, Dmitri
    Petryszak, Robert
    Mudge, Jonathan M.
    Fonseca, Nuno
    Brazma, Alvis
    Guigo, Roderic
    Harrow, Jennifer
    [J]. BMC GENOMICS, 2015, 16
  • [2] Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow
    Wright, James C.
    Mudge, Jonathan
    Weisser, Hendrik
    Barzine, Mitra P.
    Gonzalez, Jose M.
    Brazma, Alvis
    Choudhary, Jyoti S.
    Harrow, Jennifer
    [J]. NATURE COMMUNICATIONS, 2016, 7
  • [3] Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow
    James C. Wright
    Jonathan Mudge
    Hendrik Weisser
    Mitra P. Barzine
    Jose M. Gonzalez
    Alvis Brazma
    Jyoti S. Choudhary
    Jennifer Harrow
    [J]. Nature Communications, 7
  • [4] Enhanced molecular consequence prediction and variant annotation with the Ensembl Variant Effect Predictor
    Lemos, Diana
    Saraiva-Agostinho, Nuno
    Orimoloye, Ola Austine
    Azov, Andrey
    Marques-Coelho, Diego
    Hossain, S. Nakib
    Schuilenburg, Helen
    Allen, Jamie
    Trevanion, Stephen
    Hunt, Sarah
    Flicek, Paul
    Cunningham, Fiona
    [J]. EUROPEAN JOURNAL OF HUMAN GENETICS, 2023, 31 : 607 - 608
  • [5] 'Deep dive' disease gene re-annotation in GENCODE: identifying and reporting new variant interpretations of likely clinical relevance.
    Mudge, J. M.
    Hunt, T.
    Gonzalez, J. M.
    Frankish, A.
    [J]. EUROPEAN JOURNAL OF HUMAN GENETICS, 2020, 28 (SUPPL 1) : 668 - 669
  • [6] Large-scale prokaryotic gene prediction and comparison to genome annotation
    Nielsen, P
    Krogh, A
    [J]. BIOINFORMATICS, 2005, 21 (24) : 4322 - 4329
  • [7] SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation
    Salz, Renee
    Saraiva-Agostinho, Nuno
    Vorsteveld, Emil
    van der Made, Caspar I.
    Kersten, Simone
    Stemerdink, Merel
    Allen, Jamie
    Volders, Pieter-Jan
    Hunt, Sarah E.
    Hoischen, Alexander
    't Hoen, Peter A. C.
    [J]. BMC GENOMICS, 2023, 24 (01)
  • [8] SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation
    Renee Salz
    Nuno Saraiva-Agostinho
    Emil Vorsteveld
    Caspar I. van der Made
    Simone Kersten
    Merel Stemerdink
    Jamie Allen
    Pieter-Jan Volders
    Sarah E. Hunt
    Alexander Hoischen
    Peter A.C. ’t Hoen
    [J]. BMC Genomics, 24
  • [9] Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies
    Florea, Liliana
    Souvorov, Alexander
    Kalbfleisch, Theodore S.
    Salzberg, Steven L.
    [J]. PLOS ONE, 2011, 6 (06):
  • [10] Genetic Analysis Workshop 18 single-nucleotide variant prioritization based on protein impact, sequence conservation, and gene annotation
    Thomas Nalpathamkalam
    Andriy Derkach
    Andrew D Paterson
    Daniele Merico
    [J]. BMC Proceedings, 8 (Suppl 1)