Leveraging splice-affecting variant predictors and a minigene validation system to identify Mendelian disease-causing variants among exon-captured variants of uncertain significance

Leveraging splice-affecting variant predictors and a minigene validation system to identify Mendelian disease-causing variants among exon-captured variants of uncertain significance

Author Soens, Zachry T. Google Scholar
Branch, Justin Google Scholar
Wu, Shijing Google Scholar
Yuan, Zhisheng Google Scholar
Li, Yumei Google Scholar
Li, Hui Google Scholar
Wang, Keqing Google Scholar
Xu, Mingchu Google Scholar
Rajan, Lavan Google Scholar
Motta, Fabiana L. Autor UNIFESP Google Scholar
Simoes, Renata T. Google Scholar
Lopez-Solache, Irma Google Scholar
Ajlan, Radwan Google Scholar
Birch, David G. Google Scholar
Zhao, Peiquan Google Scholar
Porto, Fernanda B. Google Scholar
Sallum, Juliana Autor UNIFESP Google Scholar
Koenekoop, Robert K. Google Scholar
Sui, Ruifang Google Scholar
Chen, Rui Google Scholar
Abstract The genetic heterogeneity of Mendelian disorders results in a significant proportion of patients that are unable to be assigned a confident molecular diagnosis after conventional exon sequencing and variant interpretation. Here, we evaluated how many patients with an inherited retinal disease (IRD) have variants of uncertain significance (VUS) that are disrupting splicing in a known IRD gene by means other than affecting the canonical dinucleotide splice site. Three in silico splice-affecting variant predictors were leveraged to annotate and prioritize variants for splicing functional validation. An in vitro minigene system was used to assay each variant's effect on splicing. Starting with 745 IRD patients lacking a confident molecular diagnosis, we validated 23 VUS as splicing variants that likely explain disease in 26 patients. Using our results, we optimized in silico score cutoffs to guide future variant interpretation. Variants that alter base pairs other than the canonical GT-AG dinucleotide are often not considered for their potential effect on RNA splicing but in silico tools and a minigene system can be utilized for the prioritization and validation of such splice-disrupting variants. These variants can be overlooked causes of human disease but can be identified using conventional exon sequencing with proper interpretation guidelines.
Keywords inherited retinal degenerations
minigene
Mendelian disease
molecular diagnosis
noncanonical splicing variants
variants of uncertain significance (VUS)
xmlui.dri2xhtml.METS-1.0.item-coverage Hoboken
Language English
Sponsor National Eye Institute
NIH
Foundation Fighting Blindness
Retinal Research Foundation
National Natural Science Foundation of China
Beijing Natural Science Foundation
CAMS Innovation Fund for Medical Sciences
Canadian Institutes of Health Research
NEI
Fonds de recherche Sante Quebec et Reseau Vision
Grant number National Eye Institute: R01EY022356
National Eye Institute: R01EY018571
National Eye Institute: EY002520
National Eye Institute: R01EY09076
NIH: 1S10RR026550
Foundation Fighting Blindness: BR-GE-0613-0618-BCM
Foundation Fighting Blindness: CD-CL-0214-0631-PUMCH
National Natural Science Foundation of China: 81470669
Beijing Natural Science Foundation: 7152116
CAMS Innovation Fund for Medical Sciences: CIFMS 2016-12M-1-002
NEI: 5T32EY007001-40
Date 2017
Published in Human Mutation. Hoboken, v. 38, n. 11, p. 1521-1533, 2017.
ISSN 1059-7794 (Sherpa/Romeo, impact factor)
Publisher Wiley
Extent 1521-1533
Origin http://dx.doi.org/10.1002/humu.23294
Access rights Closed access
Type Article
Web of Science ID WOS:000412835700010
URI https://repositorio.unifesp.br/handle/11600/58293

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