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Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants

SUMMARY: Reading frame altering genomic variants can impact gene expression levels and the structure of protein products, thus potentially inducing disease phenotypes. Current annotation approaches report the impact of such variants in the context of altered DNA sequence only; attributes of the resu...

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Detalles Bibliográficos
Autores principales: Butkiewicz, Mariusz, Haines, Jonathan L, Bush, William S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423451/
https://www.ncbi.nlm.nih.gov/pubmed/28122779
http://dx.doi.org/10.1093/bioinformatics/btw820
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author Butkiewicz, Mariusz
Haines, Jonathan L
Bush, William S
author_facet Butkiewicz, Mariusz
Haines, Jonathan L
Bush, William S
author_sort Butkiewicz, Mariusz
collection PubMed
description SUMMARY: Reading frame altering genomic variants can impact gene expression levels and the structure of protein products, thus potentially inducing disease phenotypes. Current annotation approaches report the impact of such variants in the context of altered DNA sequence only; attributes of the resulting transcript, reading frame and translated protein product are not reported. To remedy this shortcoming, we present a new genetic annotation approach termed Codon Consequence Scanner (COCOS). Implemented as an Ensembl variant effect predictor (VEP) plugin, COCOS captures amino acid sequence alterations stemming from variants that produce an altered reading frame, such as stop-lost variants and small insertions and deletions (InDels). To highlight its significance, COCOS was applied to data from the 1000 Genomes Project. Transcripts affected by stop-lost variants introduce a median of 15 amino acids, while InDels have a more extensive impact with a median of 66 amino acids being incorporated. Captured sequence alterations are written out in FASTA format and can be further analyzed for impact on the underlying protein structure. AVAILABILITY AND IMPLEMENTATION: COCOS is available to all users on github: https://github.com/butkiem/COCOS
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spelling pubmed-54234512017-05-11 Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants Butkiewicz, Mariusz Haines, Jonathan L Bush, William S Bioinformatics Applications Notes SUMMARY: Reading frame altering genomic variants can impact gene expression levels and the structure of protein products, thus potentially inducing disease phenotypes. Current annotation approaches report the impact of such variants in the context of altered DNA sequence only; attributes of the resulting transcript, reading frame and translated protein product are not reported. To remedy this shortcoming, we present a new genetic annotation approach termed Codon Consequence Scanner (COCOS). Implemented as an Ensembl variant effect predictor (VEP) plugin, COCOS captures amino acid sequence alterations stemming from variants that produce an altered reading frame, such as stop-lost variants and small insertions and deletions (InDels). To highlight its significance, COCOS was applied to data from the 1000 Genomes Project. Transcripts affected by stop-lost variants introduce a median of 15 amino acids, while InDels have a more extensive impact with a median of 66 amino acids being incorporated. Captured sequence alterations are written out in FASTA format and can be further analyzed for impact on the underlying protein structure. AVAILABILITY AND IMPLEMENTATION: COCOS is available to all users on github: https://github.com/butkiem/COCOS Oxford University Press 2017-05-15 2017-01-18 /pmc/articles/PMC5423451/ /pubmed/28122779 http://dx.doi.org/10.1093/bioinformatics/btw820 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Butkiewicz, Mariusz
Haines, Jonathan L
Bush, William S
Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
title Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
title_full Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
title_fullStr Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
title_full_unstemmed Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
title_short Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
title_sort introducing cocos: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423451/
https://www.ncbi.nlm.nih.gov/pubmed/28122779
http://dx.doi.org/10.1093/bioinformatics/btw820
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