Whole-Exome Sequencing Finds Genetic Answers in a Third of Complex Autism Cases

For decades, autism spectrum disorder has been diagnosed by behavior alone, but a new study from Türkiye adds to the growing evidence that, for a substantial share of children, the condition has a traceable molecular cause. In a retrospective cohort of 320 individuals with autism who underwent whole-exome sequencing between 2020 and 2025, researchers identified established molecular diagnoses in 104 patients, or 32.5 percent of the cohort. The finding, published in BMC Psychiatry, underscores a point that clinical geneticists have been making with increasing urgency: autism is not a single entity, and the probability of finding a genetic explanation depends heavily on what else is going on in the patient.

The study, led by Mehmet Burak Mutlu of the Detagen Genetic Diseases Evaluation Center in Kayseri together with collaborators from hospitals and universities across Türkiye, divided participants into two clinically meaningful groups. Those with isolated autism had no co-occurring neurodevelopmental, neurological, dysmorphic, congenital, or systemic findings. Those with complex autism presented with at least one such additional feature, such as developmental delay or intellectual disability, epilepsy, characteristic facial features, congenital anomalies, or abnormalities on brain imaging. This distinction turned out to be the single most important predictor of whether sequencing would yield an answer.

The numbers were striking. Among the 22 patients with isolated autism, only two received an established molecular diagnosis, a yield of 9.1 percent with a wide 95 percent confidence interval of 1.1 to 29.2 percent that reflects the small size of that subgroup. Among the 298 patients with complex presentations, by contrast, 102 received established diagnoses, a yield of 34.2 percent. The difference was statistically significant, with a p-value of 0.017. In practical terms, a child with autism plus epilepsy or intellectual disability was several times more likely to receive a genetic explanation from exome sequencing than a child whose autism appeared in isolation.

Whole-exome sequencing works by reading the protein-coding portions of the genome, the roughly one to two percent of DNA that contains most known disease-causing variants. In this study, sequencing data were processed through a standard bioinformatics pipeline, with reads aligned using the Burrows-Wheeler Aligner and variants called and refined with the Genome Analysis Toolkit, the tools that form the backbone of most clinical sequencing laboratories worldwide. Single-nucleotide variants and small insertions and deletions were then classified according to the criteria jointly published by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology, the framework that governs whether a variant is called pathogenic, likely pathogenic, or uncertain.

The researchers were deliberately strict about what counted as an established diagnosis. A finding qualified only if the patient carried pathogenic or likely pathogenic variants linked to disorders defined in the Online Mendelian Inheritance in Man catalog, or if the variants occurred in genes carrying definitive, strong, or moderate evidence from ClinGen, the Clinical Genome Resource that curates gene-disease relationships. This conservatism matters because the literature on autism genetics is littered with premature claims, and the field has moved toward frameworks that separate well-established diagnoses from speculative ones. By holding themselves to this standard, the authors produced a yield figure that can be compared meaningfully with international cohorts.

Beyond the established diagnoses, the study also surfaced a further layer of findings that the authors treated with appropriate caution. Twelve additional patients carried pathogenic or likely pathogenic variants in candidate or emerging genes, genes suspected of involvement in neurodevelopmental disorders but not yet backed by definitive evidence. Including these, the overall rate of pathogenic or likely pathogenic findings rose to 116 of 320 patients, or 36.3 percent. The authors argue that such candidate-gene results should always be reported separately and interpreted as hypothesis-generating rather than diagnostic, a distinction that has real consequences for families who may otherwise be told they have a definitive answer when they do not.

The remaining results illustrate the messy middle ground of clinical genomics. Variants of uncertain significance, genetic changes that cannot currently be classified as benign or disease-causing, were identified in 147 patients, nearly half the cohort. In 57 patients, no variant related to autism or neurodevelopmental disorders was found at all. These categories are not dead ends. Uncertain variants can be reclassified as evidence accumulates, and negative results can be revisited as new genes are discovered, which is why many centers recommend periodic reanalysis of sequencing data. But they highlight the gap between the promise of genomic medicine and its current limits, particularly for patients whose presentations do not fit known syndromes.

Why does a molecular diagnosis matter so much? For families, an etiological answer can end years of diagnostic odyssey, provide a realistic prognosis, clarify recurrence risk for future pregnancies, and connect families to condition-specific support communities. For clinicians, a precise diagnosis can change management directly. Many of the genes implicated in autism-related neurodevelopmental disorders carry risks for treatable complications, including epilepsy, cardiac anomalies, or metabolic problems, and some monogenic conditions have targeted therapies or surveillance protocols. A genetic result transforms autism from a behavioral description into a medical diagnosis with a concrete care pathway.

The Turkish cohort itself fills an important gap. Most large exome-sequencing studies of autism have been conducted in North American and European populations, and data on yield and variant spectra in Turkish patients have been limited. Population-specific cohorts matter because variant frequencies, founder effects, and rates of consanguinity can all influence which genetic causes appear and how they are inherited. The study’s supplementary material catalogs the pathogenic and likely pathogenic variants, uncertain variants, and compound heterozygous cases in detail, along with segregation analyses where family members were available for testing, providing a resource for clinicians in the region and for the broader research community.

The study was approved by the Harran University Clinical Research Ethics Committee and conducted under the Declaration of Helsinki, with written informed consent obtained from all participants or their legal guardians. The authors received no specific funding for the work and declare no competing interests. Published open access under a Creative Commons license, the paper arrived with the caveats of an early-release version subject to final edits, but its core message is already clear and consistent with the international literature: whole-exome sequencing earns its place in the autism diagnostic workup, especially when autism travels with other clinical findings. As the authors conclude, sequencing supports etiological clarification in clinically complex autism, while candidate-gene findings should be handled as leads, not verdicts. For the growing number of families navigating an autism diagnosis, that nuance may be the most valuable result of all.

Subject of Research: Molecular diagnostic yield of whole-exome sequencing in a Turkish autism spectrum disorder cohort

Article Title: Whole-exome sequencing in a Turkish autism spectrum disorder cohort: a retrospective study of molecular diagnostic yield in isolated and complex presentations

Article References: Whole-exome sequencing in a Turkish autism spectrum disorder cohort: a retrospective study of molecular diagnostic yield in isolated and complex presentations. (n.d.). https://doi.org/10.1186/s12888-026-08739-x

Image Credits: AI Generated

DOI: 10.1186/s12888-026-08739-x

Keywords: autism spectrum disorder, whole-exome sequencing, molecular diagnosis, genetic testing, neurodevelopmental disorders, diagnostic yield, variants of uncertain significance, ClinGen, ACMG criteria, Turkish cohort, clinical genetics, developmental delay