title: Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
abstract: Complete annotation of the human genome is indispensable for medical research. The GENCODE consortium strives to provide this, augmenting computational and experimental evidence with manual annotation. The rapidly developing field of proteogenomics provides evidence for the translation of genes into proteins and can be used to discover and refine gene models. However, for both the proteomics and annotation groups, there is a lack of guidelines for integrating this data. Here we report a stringent workflow for the interpretation of proteogenomic data that could be used by the annotation community to interpret novel proteogenomic evidence. Based on reprocessing of three large-scale publicly available human data sets, we show that a conservative approach, using stringent filtering is required to generate valid identifications. Evidence has been found supporting 16 novel protein-coding genes being added to GENCODE. Despite this many peptide identifications in pseudogenes cannot be annotated due to the absence of orthogonal supporting evidence.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: James C
authors.identifier: http://orcid.org/0000-0001-6950-4328
authors.initials: JC
authors.lastname: Wright
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Mudge
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Hendrik
authors.initials: H
authors.lastname: Weisser
authors.affiliation: European Bioinformatics Institute, EMBL, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Mitra P
authors.identifier: http://orcid.org/0000-0002-0860-9510
authors.initials: MP
authors.lastname: Barzine
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Jose M
authors.initials: JM
authors.lastname: Gonzalez
authors.affiliation: European Bioinformatics Institute, EMBL, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Alvis
authors.initials: A
authors.lastname: Brazma
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Jyoti S
authors.initials: JS
authors.lastname: Choudhary
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Harrow
mesh_terms: D000595:Amino Acid Sequence; D005786:Gene Expression Regulation; D063990:Gene Ontology; D015894:Genome, Human; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods* / Q000706:statistics & numerical data; D016366:Open Reading Frames; D011506:Proteins / Q000235:genetics* / Q000378:metabolism; D000071696:Proteogenomics / Q000379:methods*; D011544:Pseudogenes
chemical_list: D011506:Proteins