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

TitleLeveraging splice-affecting variant predictors and a minigene validation system to identify Mendelian disease-causing variants among exon-captured variants of uncertain significance.
Publication TypeJournal Article
Year of Publication2017
AuthorsSoens, ZT, Branch, J, Wu, S, Yuan, Z, Li, Y, Li, H, Wang, K, Xu, M, Rajan, L, Motta, FL, Simões, RT, Lopez-Solache, I, Ajlan, R, Birch, DG, Zhao, P, Porto, FB, Sallum, J, Koenekoop, RK, Sui, R, Chen, R
JournalHum Mutat
Volume38
Issue11
Pagination1521-1533
Date Published2017 Nov
ISSN1098-1004
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.

DOI10.1002/humu.23294
Alternate JournalHum. Mutat.
PubMed ID28714225
PubMed Central IDPMC5638688
Grant ListR01 EY009076 / EY / NEI NIH HHS / United States
T32 EY007001 / EY / NEI NIH HHS / United States
S10 RR026550 / RR / NCRR NIH HHS / United States
R01 EY022356 / EY / NEI NIH HHS / United States
P30 EY002520 / EY / NEI NIH HHS / United States
R01 EY018571 / EY / NEI NIH HHS / United States