Whole-Exome Sequencing Identifies Damaging de novo Variants in Anencephalic Cases.

Linlin Wang,Yunping Lei,Xuanye Cao,Yan Shen,Lei Jin,Peng Zhang,Bo Zhang,Richard H Finnell,Tian Tian,Nan Li,Aiguo Ren,Zhiwen Li

doi:10.3389/fnins.2019.01285

Abstract

BackgroundAnencephaly is a lethal neural tube defect (NTD). Although variants in several genes have been implicated in the development of anencephaly, a more complete picture of variants in the genome, especially de novo variants (DNVs), remains unresolved. We aim to identify DNVs that play an important role in the development of anencephaly by performing whole-exome DNA sequencing (WES) of proband–parent trios.ResultsA total of 13 DNVs were identified in 8 anencephaly trios by WES, including two loss of function (LoF) variants detected in pLI > 0.9 genes (SPHKAP, c.2629_2633del, and NCOR1, p.Y1907X). Damaging DNVs were identified in 61.5% (8/13) of the anencephalic cases. Independent validation was conducted in an additional 502 NTD cases. Gene inactivation using targeted morpholino antisense oligomers and rescue assays were conducted in zebrafish, and transfection expression in HEK293T cells. Four DNVs in four cases were identified and predicted to alter protein function, including p.R328Q in WD repeat domain phosphoinositide-interacting 1 (WIPI1). Three variants, p.G313R, p.T418M, and p.L406P, in the WIPI1 gene were identified from the independent replication cohort consisting of 502 cases. Functional analysis suggested that the wipi1 p.L406P and p.R328Q variants most likely displayed loss-of-function effects during embryonic development.ConclusionDe novo damaging variants are the main culprit for majority of anencephalic cases. Missense variants in WIPI1 may play a role in the genetic etiology of anencephaly, and LoF variants in SPHKAP and NCOR1 may also contribute to anencephaly. These findings add to our existing understanding of the genetic mechanisms of NTD formation.

Highlights

Neural tube defects (NTDs) are severe congenital malformations of the central nervous system that are caused by a partial or incomplete closure of the neural tube during embryogenesis (Wallingford et al, 2013)
We focus on the detection of de novo variants (DNVs) from cases with the most severe subtype of NTDs, anencephaly
Two loss of function (LoF) variants were identified in SPHKAP (c.2629_2633del) and NCOR1 (p.Y1907X) gene, respectively

Summary

Introduction

Neural tube defects (NTDs) are severe congenital malformations of the central nervous system (including anencephaly, spina bifida, and encephalocele) that are caused by a partial or incomplete closure of the neural tube during embryogenesis (Wallingford et al, 2013). While over ∼300 causative genes have been linked to mouse NTDs (Harris and Juriloff, 2007, 2010; Juriloff and Harris, 2012; Wilde et al, 2014), identification of NTD genes in humans is difficult, and the predisposing genetic factors for human NTDs are still unclear To characterize these genetic underpinnings, efforts have been made toward identifying common, rare, or de novo DNA variants that contribute to the occurrence of NTDs. Very few common DNA variations, such as variations in folate-related genes including methylenetetrahydrofolate reductase (MTHFR), have been identified using genetic association studies; and these common variations might at most confer a modest risk and account for only a very small portion of disease heritability. We aim to identify DNVs that play an important role in the development of anencephaly by performing whole-exome DNA sequencing (WES) of proband–parent trios

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