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Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model
Large-scale sequencing efforts have captured a rapidly growing catalogue of genetic variations. However, the accurate establishment of gene variant pathogenicity remains a central challenge in translating personal genomics information to clinical decisions. Interferon Regulatory Factor 6 (IRF6) gene...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5628943/ https://www.ncbi.nlm.nih.gov/pubmed/28945736 http://dx.doi.org/10.1371/journal.pgen.1007009 |
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author | Li, Edward B. Truong, Dawn Hallett, Shawn A. Mukherjee, Kusumika Schutte, Brian C. Liao, Eric C. |
author_facet | Li, Edward B. Truong, Dawn Hallett, Shawn A. Mukherjee, Kusumika Schutte, Brian C. Liao, Eric C. |
author_sort | Li, Edward B. |
collection | PubMed |
description | Large-scale sequencing efforts have captured a rapidly growing catalogue of genetic variations. However, the accurate establishment of gene variant pathogenicity remains a central challenge in translating personal genomics information to clinical decisions. Interferon Regulatory Factor 6 (IRF6) gene variants are significant genetic contributors to orofacial clefts. Although approximately three hundred IRF6 gene variants have been documented, their effects on protein functions remain difficult to interpret. Here, we demonstrate the protein functions of human IRF6 missense gene variants could be rapidly assessed in detail by their abilities to rescue the irf6 (-/-) phenotype in zebrafish through variant mRNA microinjections at the one-cell stage. The results revealed many missense variants previously predicted by traditional statistical and computational tools to be loss-of-function and pathogenic retained partial or full protein function and rescued the zebrafish irf6 (-/-) periderm rupture phenotype. Through mRNA dosage titration and analysis of the Exome Aggregation Consortium (ExAC) database, IRF6 missense variants were grouped by their abilities to rescue at various dosages into three functional categories: wild type function, reduced function, and complete loss-of-function. This sensitive and specific biological assay was able to address the nuanced functional significances of IRF6 missense gene variants and overcome many limitations faced by current statistical and computational tools in assigning variant protein function and pathogenicity. Furthermore, it unlocked the possibility for characterizing yet undiscovered human IRF6 missense gene variants from orofacial cleft patients, and illustrated a generalizable functional genomics paradigm in personalized medicine. |
format | Online Article Text |
id | pubmed-5628943 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-56289432017-10-20 Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model Li, Edward B. Truong, Dawn Hallett, Shawn A. Mukherjee, Kusumika Schutte, Brian C. Liao, Eric C. PLoS Genet Research Article Large-scale sequencing efforts have captured a rapidly growing catalogue of genetic variations. However, the accurate establishment of gene variant pathogenicity remains a central challenge in translating personal genomics information to clinical decisions. Interferon Regulatory Factor 6 (IRF6) gene variants are significant genetic contributors to orofacial clefts. Although approximately three hundred IRF6 gene variants have been documented, their effects on protein functions remain difficult to interpret. Here, we demonstrate the protein functions of human IRF6 missense gene variants could be rapidly assessed in detail by their abilities to rescue the irf6 (-/-) phenotype in zebrafish through variant mRNA microinjections at the one-cell stage. The results revealed many missense variants previously predicted by traditional statistical and computational tools to be loss-of-function and pathogenic retained partial or full protein function and rescued the zebrafish irf6 (-/-) periderm rupture phenotype. Through mRNA dosage titration and analysis of the Exome Aggregation Consortium (ExAC) database, IRF6 missense variants were grouped by their abilities to rescue at various dosages into three functional categories: wild type function, reduced function, and complete loss-of-function. This sensitive and specific biological assay was able to address the nuanced functional significances of IRF6 missense gene variants and overcome many limitations faced by current statistical and computational tools in assigning variant protein function and pathogenicity. Furthermore, it unlocked the possibility for characterizing yet undiscovered human IRF6 missense gene variants from orofacial cleft patients, and illustrated a generalizable functional genomics paradigm in personalized medicine. Public Library of Science 2017-09-25 /pmc/articles/PMC5628943/ /pubmed/28945736 http://dx.doi.org/10.1371/journal.pgen.1007009 Text en © 2017 Li et al 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 use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Li, Edward B. Truong, Dawn Hallett, Shawn A. Mukherjee, Kusumika Schutte, Brian C. Liao, Eric C. Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model |
title | Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model |
title_full | Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model |
title_fullStr | Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model |
title_full_unstemmed | Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model |
title_short | Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model |
title_sort | rapid functional analysis of computationally complex rare human irf6 gene variants using a novel zebrafish model |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5628943/ https://www.ncbi.nlm.nih.gov/pubmed/28945736 http://dx.doi.org/10.1371/journal.pgen.1007009 |
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