Tandem repeat (TR) variation is associated with gene expression changes and over 50 rare monogenic diseases. Recent advances in sequencing have enabled accurate, long reads that can characterize the full-length sequence and methylation profile of TRs. However, despite these advances in sequencing technology, computational methods to fully profile tandem repeats across the genome do not exist. To address this gap, we introduce tools for tandem repeat genotyping (TRGT), visualization and an accompanying TR database. TRGT accurately resolves the length and sequence composition of TR regions in the human genome. Assessing 937,122 TRs, TRGT showed a Mendelian concordance of 99.56%, allowing a single repeat unit difference. In six samples with known repeat expansions, TRGT detected all repeat expansions while also identifying methylation signals, mosaicism, and providing finer resolution of repeat length. Additionally, we release a database with allele sequences and methylation levels for 937,122 TRs across 100 genomes.

Autism spectrum disorder is a neurodevelopmental condition characterized by deficits in social communication and repetitive behaviors. How specific anatomical alterations contribute to the clinical profile of autism spectrum disorder remains largely uncharacterized. We have previously shown that parvalbumin-positive Chandelier cells, a specific type of GABAergic interneuron, are reduced in number in the autism spectrum disorder prefrontal cortex. Here, we assessed the relationship between interneuron pathology with autism spectrum disorder symptom severity and comorbidity. We collected clinical records from autism ( n = 20) and control ( n = 19) brain donors, from whom we previously characterized GABAergic interneuron pathology in three regions of the prefrontal cortex (BA9, 46, and 47). We assessed the relationship between the severity of core symptoms, as indicated by Autism Diagnostic Interview—Revised scores, and Chandelier cell pathology in autism spectrum disorder, and also differences in interneuron pathology associated with autism spectrum disorder comorbidities. Total GABAergic interneuron number was significantly reduced in autism spectrum disorder cases with intellectual disability in the prefrontal cortex (PFC )—by 36.6% relative to autism spectrum disorder without intellectual disability and by 38.7% relative to neurotypical controls. The severity of autism spectrum disorder motor stereotypies was correlated with the severity of Chandelier cell loss in BA47, as indicated by reductions in parvalbumin+ interneurons and GABA transporter 1+ cartridges. Chandelier cell loss is associated with the core autism spectrum disorder symptom domain of restricted repetitive behaviors and likely plays a role in stereotypic motor mannerisms. Intellectual impairment in autism spectrum disorder reflects a more severe form of a common underlying neuropathology-cortical GABAergic interneuron loss. Lay Abstract Autism spectrum disorder is a neurodevelopmental condition characterized by deficits in sociability and communication and the presence of repetitive behaviors. How specific pathological alterations of the brain contribute to the clinical profile of autism spectrum disorder remains unknown. We previously found that a specific type of inhibitory interneuron is reduced in number in the autism spectrum disorder prefrontal cortex. Here, we assessed the relationship between interneuron reduction and autism spectrum disorder symptom severity. We collected clinical records from autism spectrum disorder ( n = 20) and assessed the relationship between the severity of symptoms and interneuron number. We found that the reduced number of inhibitory interneurons that we previously reported is linked to specific symptoms of autism spectrum disorder, particularly stereotypic movements and intellectual impairments.