Genetic aetiologies for childhood speech disorder: novel pathways co-expressed during brain development

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Kaspi, Antony
Hildebrand, Michael S
Jackson, Victoria E
Braden, Ruth
van Reyk, Olivia
Howell, Tegan
Debono, Simone
Lauretta, Mariana
Morison, Lottie
Coleman, Matthew J
Webster, Richard
Coman, David
Goel, Himanshu
Wallis, Mathew
Ziegenfusz, Shaun
et al.
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2022
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Abstract

Childhood apraxia of speech (CAS), the prototypic severe childhood speech disorder, is characterized by motor programming and planning deficits. Genetic factors make substantive contributions to CAS aetiology, with a monogenic pathogenic variant identified in a third of cases, implicating around 20 single genes to date. Here we aimed to identify molecular causation in 70 unrelated probands ascertained with CAS. We performed trio genome sequencing. Our bioinformatic analysis examined single nucleotide, indel, copy number, structural and short tandem repeat variants. We prioritised appropriate variants arising de novo or inherited that were expected to be damaging based on in silico predictions. We identified high confidence variants in 18/70 (26%) probands, almost doubling the current number of candidate genes for CAS. Three of the 18 variants affected SETBP1, SETD1A and DDX3X, thus confirming their roles in CAS, while the remaining 15 occurred in genes not previously associated with this disorder. Fifteen variants arose de novo and three were inherited. We provide further novel insights into the biology of child speech disorder, highlighting the roles of chromatin organization and gene regulation in CAS, and confirm that genes involved in CAS are co-expressed during brain development. Our findings confirm a diagnostic yield comparable to, or even higher, than other neurodevelopmental disorders with substantial de novo variant burden. Data also support the increasingly recognised overlaps between genes conferring risk for a range of neurodevelopmental disorders. Understanding the aetiological basis of CAS is critical to end the diagnostic odyssey and ensure affected individuals are poised for precision medicine trials.

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Molecular Psychiatry

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© The Author(s) 2022, corrected publication 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

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Genetics

Clinical sciences

Biological psychology

Clinical and health psychology

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Life Sciences & Biomedicine

Biochemistry & Molecular Biology

Neurosciences

Psychiatry

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Kaspi, A; Hildebrand, MS; Jackson, VE; Braden, R; van Reyk, O; Howell, T; Debono, S; Lauretta, M; Morison, L; Coleman, MJ; Webster, R; Coman, D; Goel, H; Wallis, M; Dabscheck, G; Downie, L; Baker, EK; Parry-Fielder, B; Ballard, K; Harrold, E; Ziegenfusz, S; Bennett, MF; Robertson, E; Wang, L; Boys, A; Fisher, SE; Amor, DJ; Scheffer, IE; Bahlo, M; Morgan, AT, Genetic aetiologies for childhood speech disorder: novel pathways co-expressed during brain development, Molecular Psychiatry, 2022

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