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

Autor: Mingchu Xu, Hui Li, Yumei Li, Peiquan Zhao, Irma Lopez-Solache, Radwan Ajlan, Fabiana Louise Motta, Robert K. Koenekoop, Juliana Maria Ferraz Sallum, Lavan Rajan, Keqing Wang, Shijing Wu, Rui Chen, David G. Birch, Justin Branch, Renata T Simões, Ruifang Sui, Zachry T. Soens, Fernanda Belga Ottoni Porto, Zhisheng Yuan
Rok vydání: 2017
Předmět:
Zdroj: Human Mutation. 38:1521-1533
ISSN: 1098-1004
1059-7794
DOI: 10.1002/humu.23294
Popis: 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's) 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's 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.
Databáze: OpenAIRE
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