Trio Exome Sequencing Reveals Genetic Clues to Autism in Rwandan Children

In a landmark step for genomic medicine in East Africa, researchers have carried out one of the first trio-based whole-exome sequencing studies of autism spectrum disorder in Rwanda, uncovering rare genetic variants in nearly a third of the children studied. The work, conducted at Ndera Neuropsychiatric Teaching Hospital in Kigali in collaboration with the accredited clinical genetics laboratory of the University Teaching Hospital of Liège in Belgium, offers a rare window into the genetic architecture of autism in a population that has long been absent from global genomic databases. For families who often endure years of uncertainty about the biological roots of their child’s condition, the findings demonstrate that cutting-edge sequencing can deliver clinically meaningful answers even in resource-limited settings.

Autism spectrum disorder is a heterogeneous neurodevelopmental condition defined by differences in social communication and by restricted, repetitive patterns of behavior or interests. It affects roughly one in 100 children worldwide, yet its prevalence in African populations remains inconsistently documented. Decades of genomic research have established that autism is strongly genetic, with heritability estimates between 60 and 90 percent, driven by a combination of common polygenic risk and rare, high-impact variants. Despite this, African populations, which harbor the greatest genetic diversity on Earth, remain markedly underrepresented in sequencing studies and reference databases, leaving variant interpretation in these communities imprecise and diagnosis incomplete.

The Rwandan team recruited 34 children with a clinical diagnosis of autism, established through DSM-5-TR criteria and the Autism Diagnostic Interview-Revised, along with both biological parents for each child. After first-tier Fragile X syndrome screening identified three positive cases, the remaining 31 trios underwent whole-exome sequencing on an Illumina NovaSeq6000 platform. The sequencing achieved a median coverage depth of approximately 200-fold, with more than 97 percent of targeted regions covered at greater than 30-fold depth, ensuring high confidence in variant detection. Analyses were performed under ISO 15189-accredited protocols using clinically validated bioinformatic pipelines, with copy-number variants detected by an in-house tool and all variants classified according to ACMG and ClinGen standards.

The children in the cohort presented with a striking burden of additional neurodevelopmental features. Intellectual disability was present in nearly 97 percent of participants, delayed speech and language development in more than 80 percent, and global developmental delay in over half. Seizures affected roughly a quarter of the children, and dysmorphic features appeared in nearly a quarter. Most cases were classified as severe autism. This clinical complexity reflects the syndromic end of the autism spectrum, where autism occurs alongside intellectual disability, epilepsy, congenital anomalies, or other neurological signs, and it is precisely in such cases that exome sequencing tends to be most diagnostically productive.

The sequencing effort identified 11 rare genomic findings of potential clinical significance in nine patients. Four of these were classified as likely pathogenic, yielding a diagnostic rate of 12.9 percent, a figure that rises to 29 percent when variants of uncertain significance with strong phenotypic concordance are included. That range sits comfortably within the 10 to 30 percent diagnostic yields reported in large trio-based sequencing studies of autism in Europe and North America, suggesting that the genetic underpinnings of autism in Rwandan children are broadly comparable to those described elsewhere, even as the specific variants differ.

Among the likely pathogenic findings were two de novo single-nucleotide variants in well-established autism genes. One child carried a de novo missense variant in GABRB3, a gene encoding a GABA receptor subunit critical for inhibitory neurotransmission; the child’s early-onset seizures, intellectual disability, and language delay align with developmental and epileptic encephalopathy linked to this gene. Another child harbored a de novo splice-region variant in SYNGAP1, a key regulator of synaptic plasticity, in a presentation consistent with the global developmental delay and intellectual disability characteristic of SYNGAP1-related disorders. Both discoveries reinforce the central role of synaptic dysfunction in autism pathogenesis.

The study also uncovered two likely pathogenic copy-number variants. One patient carried a large de novo deletion on chromosome 1p35.3-p35.2 spanning dozens of genes, including dosage-sensitive contributors to neurodevelopment such as PUM1, SDC3, and MECR, associated with autism, hypotonia, seizures, and developmental delay. A second patient carried a deletion within the GNAS locus on chromosome 20q13.32, inherited from an unaffected parent, a finding that highlights the interpretive complexity of inherited variants and the roles of variable penetrance and expressivity in autism genetics.

Beyond the likely pathogenic results, the team identified seven variants of uncertain significance in genes including SHANK3, SYNJ1, KIF15, HUWE1, and EPG5. Several showed notable phenotypic overlap with known disorders: a de novo SHANK3 variant in a child with autism, developmental delay, and craniofacial anomalies echoes the spectrum of Phelan-McDermid syndrome, while compound heterozygous SYNJ1 variants in a child with epilepsy and intellectual disability fit with the gene’s established role in synaptic vesicle recycling. These variants cannot yet be deemed causative, but their concordance with published phenotypes makes them strong candidates for future functional studies and reclassification as evidence accumulates.

The researchers emphasize that the study’s single-site design and modest sample size limit statistical power, and that exome sequencing cannot capture non-coding regulatory variants or all structural variation. More fundamentally, the reliance on reference databases such as gnomAD and ClinVar, which incompletely represent African populations, likely inflated the proportion of variants of uncertain significance observed. Expanding African genomic reference datasets, the authors argue, is essential to improve variant classification, sharpen diagnostic accuracy, and ensure that the benefits of genomic medicine are distributed equitably rather than concentrated in well-studied populations.

Even with these caveats, the study marks a meaningful advance. It demonstrates that trio-based exome sequencing is feasible and clinically useful in Rwanda, capable of shortening the diagnostic odyssey for families, informing medical management, and clarifying recurrence risks for future pregnancies. The path forward, the authors conclude, lies in continued inclusion of ancestrally diverse populations, functional validation through RNA sequencing, splicing assays, and patient-derived neuronal models, and longitudinal phenotyping to translate genetic discovery into better care for children with autism worldwide.

Subject of Research: Trio-based whole-exome sequencing to identify rare genetic variants in Rwandan children with autism spectrum disorder

Article Title: Clinical Utility of Trio Exome Sequencing in Rwandan Children With Autism Spectrum Disorder

Article References: Hakizimana, O., Hitayezu, J., Uyisenga, J. P., Dukuze, N., Akimana, M. V., Mizero, L., Bampire, C., Mudenge, C., Butoto, X. K., Helou, L., Charloteaux, B., Caberg, J.-H., Dideberg, V., Palmeira, L., Alagbonsi, A. I., Bours, V., & Uwineza, A. (2026). Clinical Utility of Trio Exome Sequencing in Rwandan Children With Autism Spectrum Disorder. Molecular Genetics & Genomic Medicine, 14(9), Article e70294. https://doi.org/10.1002/mgg3.70294

Image Credits: AI Generated

DOI: 10.1002/mgg3.70294

Keywords: autism spectrum disorder, whole-exome sequencing, Rwanda, trio sequencing, genetic variants, copy-number variants, de novo mutations, GABRB3, SYNGAP1, SHANK3, genomic medicine, African genomics