Objective: Determining the genetic basis of speech disorders provides insight into the neurobiology of human communication. Despite intensive investigation over the past two decades, the etiology of most children with speech disorder remains unexplained. Here we searched for a genetic etiology in children with severe speech disorder, specifically childhood apraxia of speech (CAS).

Methods: Precise phenotyping together with research genome or exome analysis were performed on children referred with a primary diagnosis of CAS, as well as other medical or neurodevelopmental co-morbidities. Gene co-expression and gene set enrichment analyses analyses were conducted on high confidence gene candidates.

Results: 34 probands ascertained for CAS were studied. In 11/34 (32%) probands, we identified highly plausible pathogenic single nucleotide (n=10, CDK13, EBF3, GNAO1, GNB1, DDX3X, MEIS2, POGZ, SETBP1, UPF2, ZNF142) or copy number (n = 1, 5q14.3q21.1 locus) variants in novel genes or loci for CAS. Testing of parental DNA was available for nine probands and confirmed that the variants had arisen de novo. Eight genes encode proteins critical for regulation of gene transcription, and analyses of transcriptomic data found CAS-implicated genes were highly co-expressed in the developing human brain.

Conclusion: We identify the likely genetic aetiology in 11 patients with CAS and implicate 9 genes for the first time. We find that CAS is often a sporadic monogenic disorder, and highly genetically heterogeneous. Highly penetrant variants implicate shared pathways in broad transcriptional regulation, highlighting the key role of transcriptional regulation in normal speech development. CAS is a distinctive, socially debilitating clinical disorder, and understanding its molecular basis is the first step towards identifying precision medicine approaches.

Supplementary Material for Severe childhood speech disorder: gene discovery highlights transcriptional dysregulation.

1. Contents of "Supplemental_Material_Neurology_2019_010520.pdf":

SUPPLEMENTARY MATERIALS AND METHODS

Replication of Gene co-expression analysis

SUPPLEMENTARY FIGURES

Figure e-1 Evidence of co-expression of ten high confidence genes

Figure e-2: Network resulting from Brain co-expression analysis for the combined set of the ten newly identified candidate CAS genes and eight genes previously shown to carry pathogenic variants in an independent speech apraxia cohort (Eising et al.)

Figure e-3 Evidence of co-expression of ten high confidence genes, and eight Eising candidates

Figure e-4: GO Pathways for which there is significant over-representation of our candidate genes

Figure e-5: Replication results for the brain co-expression analysis

SUPPLEMENTARY TABLES

Table e-1a - Proband language, literacy & cognitive assessments

Table e-1b - Assessment battery used with adult family members to determine affected status

Table e-2 – List of known pathogenic loci, examined in the STR Analysis

Table e-3 – Summary of samples from the BrainSpan dataset, included in the discovery gene co-expression analyses

Table e-4 - Summary of samples from the Colantuoni and Miller datasets, included in the replication gene co-expression analyses

Table e-5 – Damaging variants in probands without an identified pathogenic (deemed causal) variant

Table e-6: Gene set Enrichment analysis

SUPPLEMENTARY REFERENCES

2. "Table_e-5_Neurology_2019_010520.csv"

This is a comma separated text file, containing the results shown in e-5 of "Supplemental_Material_Neurology_2019_010520.pdf": Damaging variants in probands without an identified pathogenic (deemed causal) variant.