Using machine-learning methods to identify early-life predictors of 11-year language outcome

BACKGROUND

Language is foundational for neurodevelopment and quality of life, but an estimated 10% of children have a language disorder at age 5. Many children shift between classifications of typical and low language if assessed at multiple times in the early years, making it difficult to identify which children will have persisting difficulties and benefit most from support. This study aims to identify a parsimonious set of preschool indicators that predict language outcomes in late childhood, using data from the population-based Early Language in Victoria Study (n = 839).

METHODS

Parents completed surveys about their children at ages 8, 12, 24, and 36 months. At 11 years, children were assessed using the Clinical Evaluation of Language Fundamentals 4th Edition (CELF-4). We used random forests to identify which of the 1990 parent-reported questions best predict children's 11-year language outcome (CELF-4 score ≤81 representing low language) and used SuperLearner to estimate the accuracy of the constrained sets of questions.

RESULTS

At 24 months, seven predictors relating to vocabulary, symbolic play, pragmatics and behavior yielded 73% sensitivity (95% CI: 57, 85) and 77% specificity (95% CI: 74, 80) for predicting low language at 11 years. [Corrections made on 5 May 2023, after first online publication: In the preceding sentence 'motor skills' has been corrected to 'behavior' in this version.] At 36 months, 7 predictors relating to morphosyntax, vocabulary, parent-child interactions, and parental stress yielded 75% sensitivity (95% CI: 58, 88) and 85% specificity (95% CI: 81, 87). Measures at 8 and 12 months yielded unsatisfactory accuracy.

CONCLUSIONS

We identified two short sets of questions that predict language outcomes at age 11 with fair accuracy. Future research should seek to replicate results in a separate cohort.

Incidence of traumatic brain injuries in head-injured children with seizures

OBJECTIVE

Incidence and short-term outcomes of clinically important traumatic brain injury (ciTBI) in head-injured children presenting to ED with post-traumatic seizure (PTS) is not described in current literature.

METHODS

Planned secondary analysis of a prospective observational study undertaken in 10 Australasian Paediatric Research in Emergency Departments International Collaborative (PREDICT) network EDs between 2011 and 2014 of head-injured children <18 years with and without PTS. Clinical predictors and outcomes were analysed by attributable risk (AR), risk ratios (RR) and 95% confidence interval (CI), including the association with Glasgow Coma Scale (GCS) scores.

RESULTS

Of 20 137 head injuries, 336 (1.7%) had PTS with median age of 4.8 years. Initial GCS was 15 in 268/336 (79.8%, AR -16.1 [95% CI -20.4 to -11.8]), 14 in 24/336 (7.1%, AR 4.4 [95% CI 1.6-7.2]) and ≤13 in 44/336 (13.1%, AR 11.7 [95% CI 8.1-15.3]) in comparison with those without PTS, respectively. The ciTBI rate was 34 (10.1%) with PTS versus 219 (1.1%) without PTS (AR 9.0 [95% CI 5.8-12.2]) with 5/268 (1.9%), 6/24 (25.0%) and 23/44 (52.3%) with GCS 15, 14 and ≤13, respectively. In PTS, rates of admission ≥2 nights (34 [10.1%] AR 9.0 [95% CI 5.8-12.3]), intubation >24 h (9 [2.7%] AR 2.5 [95% CI 0.8-4.2]) and neurosurgery (8 [2.4%] AR 2.0 [95% CI 0.4-3.7]), were higher than those without PTS. Children with PTS and GCS 15 or 14 had no neurosurgery, intubations or death, with two deaths in children with PTS and GCS ≤13.

CONCLUSIONS

PTS was uncommon in head-injured children presenting to the ED but associated with an increased risk of ciTBI in those with reduced GCS on arrival.

Tissue mosaicism, FMR1 expression and intellectual functioning in males with fragile X syndrome

Fragile X syndrome (FXS) is caused by hypermethylation of the FMR1 promoter due to the full mutation expansion (full mutation [FM]: CGG ≥ 200 repeats) and silencing of FMR1. Assessment of mosaicism for active-unmethylated alleles has prognostic utility. This study examined relationships between FMR1 methylation in different tissues with FMR1 messenger ribonucleic acid (mRNA) and intellectual functioning in 87 males with FXS (1.89-43.17 years of age). Methylation sensitive Southern blot (mSB) and Methylation Specific-Quantitative Melt Aanalysis (MS-QMA) were used to examine FMR1 methylation. FMR1 mRNA levels in blood showed strong relationships with FMR1 methylation assessed using MS-QMA in blood (n = 68; R2  = 0.597; p = 1.4 × 10-10 ) and buccal epithelial cells (BEC) (n = 62; R2  = 0.24; p = 0.003), with these measures also showing relationships with intellectual functioning scores (p < 0.01). However, these relationships were not as strong for mSB, with ~40% of males with only FM alleles that were 100% methylated and non-mosaic by mSB, showing methylation mosaicism by MS-QMA. This was confirmed through presence of detectable levels of FMR1 mRNA in blood. In summary, FMR1 methylation levels in blood and BEC examined by MS-QMA were significantly associated with FMR1 mRNA levels and intellectual functioning in males with FXS. These relationships were not as strong for mSB, which underestimated prevalence of mosaicism.

Exome sequencing for patients with developmental and epileptic encephalopathies in clinical practice

AIM

To assess the clinical utility of exome sequencing for patients with developmental and epileptic encephalopathies (DEEs).

METHOD

Over 2 years, patients with DEEs were recruited for singleton exome sequencing. Parental segregation was performed where indicated.

RESULTS

Of the 103 patients recruited (54 males, 49 females; aged 2 weeks-17 years), the genetic aetiology was identified in 36 out of 103 (35%) with management implications in 13 out of 36. Exome sequencing revealed pathogenic or likely pathogenic variants in 30 out of 103 (29%) patients, variants of unknown significance in 39 out of 103 (38%), and 34 out of 103 (33%) were negative on exome analysis. After the description of new genetic diseases, a molecular diagnosis was subsequently made for six patients or through newly available high-density chromosomal microarray testing.

INTERPRETATION

We demonstrate the utility of exome sequencing in routine clinical care of children with DEEs. We highlight that molecular diagnosis often leads to changes in management and informs accurate prognostic and reproductive counselling. Our findings reinforce the need for ongoing analysis of genomic data to identify the aetiology in patients in whom the cause is unknown. The implementation of genomic testing in the care of children with DEEs should become routine in clinical practice.

WHAT THIS PAPER ADDS

The cause was identified in 35% of patients with developmental and epileptic encephalopathies. KCNQ2, CDKL5, SCN1A, and STXBP1 were the most frequently identified genes. Reanalysis of genomic data found the cause in an additional six patients. Genetic aetiology was identified in 41% of children with seizure onset under 2 years, compared to 18% with older onset. Finding the molecular cause led to management changes in 36% of patients with DEEs.

Clinical and biochemical distinctions for a metabolite repair disorder caused by NAXD or NAXE deficiency

The central cofactors NAD(P)H are prone to damage by hydration, resulting in formation of redox-inactive derivatives designated NAD(P)HX. The highly conserved enzymes NAD(P)HX dehydratase (NAXD) and NAD(P)HX epimerase (NAXE) function to repair intracellular NAD(P)HX. Recently, pathogenic variants in both the NAXD and NAXE genes were associated with rapid deterioration and death after an otherwise trivial fever, infection, or illness in young patients. As more patients are identified, distinct clinical features are emerging depending on the location of the pathogenic variant. In this review, we carefully catalogued the clinical features of all published NAXD deficiency patients and found distinct patterns in clinical presentations depending on which subcellular compartment is affected by the enzymatic deficiency. Exon 1 of NAXD contains a mitochondrial propeptide, and a unique cytosolic isoform is initiated from an alternative start codon in exon 2. NAXD deficiency patients with variants that affect both the cytosolic and mitochondrial isoforms present with neurological defects, seizures and skin lesions. Interestingly, patients with NAXD variants exclusively affecting the mitochondrial isoform present with myopathy, moderate neuropathy and a cardiac presentation, without the characteristic skin lesions, seizures or neurological degeneration. This suggests that cytosolic NAD(P)HX repair may protect from neurological damage, whereas muscle fibres may be more sensitive to mitochondrial NAD(P)HX damage. A deeper understanding of the clinical phenotype may facilitate rapid identification of new cases and allow earlier therapeutic intervention. Niacin-based therapies are promising, but advances in disease modelling for both NAXD and NAXE deficiency may identify more specific compounds as targeted treatments. In this review, we found distinct patterns in the clinical presentations of NAXD deficiency patients based on the location of the pathogenic variant, which determines the subcellular compartment that is affected by the enzymatic deficiency.

Accessing hearing-health services for deaf and hard-of-hearing children during the COVID-19 pandemic: Parent and child perspectives

To describe hearing-health service use, especially use of telehealth, during the early stages of the COVID-19 pandemic in deaf/hard-of-hearing children. In 2020, the Victorian Childhood Hearing Longitudinal Databank surveyed 497 (61.6%) families of deaf/hard-of-hearing children aged 0.4-19.6 years, with 449 (90.3%) providing quantitative data and 336 (67.6%) providing free-text comments about COVID-19's impact on service use and access. We summarised quantitative data using descriptive statistics and analysed free-text responses using inductive and deductive reasoning. Of the 1152 services families used during the pandemic, 711 (62%) were accessed via telehealth. Parents reported several challenges and facilitators of service access during the pandemic, particularly regarding telehealth. Parents reported that their child found telehealth appointments more difficult (347/665, 52.1%) and of worse quality (363/649, 55.9%) compared to in-person. These difficulties were more evident in pre-school than school-age children. Consideration of these factors when implementing telehealth practice beyond the pandemic would improve family experiences, ensuring quality of care.