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Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex.

ABSTRACT: Specific language impairment (SLI) is a common neurodevelopmental disorder (NDD) that displays high heritability estimates. Genetic studies have identified several loci, but the molecular basis of SLI remains unclear. With the aim to better understand the genetic architecture of SLI, we performed whole-exome sequencing (WES) in a single family (ID: 489; n = 11). We identified co-segregating rare variants in three new genes: BUD13, APLP2, and NDRG2. To determine the significance of these genes in SLI, we Sanger sequenced all coding regions of each gene in unrelated individuals with SLI (n = 175). We observed 13 additional rare variants in 18 unrelated individuals. Variants in BUD13 reached genome-wide significance (p-value < 0.01) upon comparison with similar variants in the 1000 Genomes Project, providing gene level evidence that BUD13 is involved in SLI. Additionally, five BUD13 variants showed cohesive variant level evidence of likely pathogenicity. Bud13 is a component of the retention and splicing (RES) complex. Additional supportive evidence from studies of an animal model (loss-of-function mutations in BUD13 caused a profound neural phenotype) and individuals with an NDD phenotype (carrying a CNV spanning BUD13), indicates BUD13 could be a target for investigation of the neural basis of language.

SUBMITTER: Andres EM

PROVIDER: S-EPMC8773923 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundDevelopmental language disorder (DLD, also called specific language impairment, SLI) is a common developmental disorder comprising the largest disability group in pre-school-aged children. Approximately 7% of the population is expected to have developmental language difficulties. However, the specific etiological factors leading to DLD are not yet known and even the typical linguistic features appear to vary by language. We present here a project that investigates DLD at multiple levels of analysis and aims to make the reliable prediction and early identification of the difficulties possible. Following the multiple deficit model of developmental disorders, we investigate the DLD phenomenon at the etiological, neural, cognitive, behavioral, and psychosocial levels, in a longitudinal study of preschool children.MethodsIn January 2013, we launched the Helsinki Longitudinal SLI study (HelSLI) at the Helsinki University Hospital ( http://tiny.cc/HelSLI ). We will study 227 children aged 3-6 years with suspected DLD and their 160 typically developing peers. Five subprojects will determine how the child's psychological characteristics and environment correlate with DLD and how the child's well-being relates to DLD, the characteristics of DLD in monolingual versus bilingual children, nonlinguistic cognitive correlates of DLD, electrophysiological underpinnings of DLD, and the role of genetic risk factors. Methods include saliva samples, EEG, computerized cognitive tasks, neuropsychological and speech and language assessments, video-observations, and questionnaires.DiscussionThe project aims to increase our understanding of the multiple interactive risk and protective factors that affect the developing heterogeneous cognitive and behavioral profile of DLD, including factors affecting literacy development. This accumulated knowledge will form a heuristic basis for the development of new interventions targeting linguistic and non-linguistic aspects of DLD.

Dataset Information

Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex.

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