{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Koesterich J"],"funding":["NIMH NIH HHS","NHGRI NIH HHS","National Institute of Mental Health","National Research Foundation of Korea","NIH","National Human Genome Research Institute","NIH HHS"],"pagination":["3509"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9959321"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["24(4)"],"pubmed_abstract":["Autism spectrum disorder (ASD) is a common, complex, and highly heritable condition with contributions from both common and rare genetic variations. While disruptive, rare variants in protein-coding regions clearly contribute to symptoms, the role of rare non-coding remains unclear. Variants in these regions, including promoters, can alter downstream RNA and protein quantity; however, the functional impacts of specific variants observed in ASD cohorts remain largely uncharacterized. Here, we analyzed 3600 de novo mutations in promoter regions previously identified by whole-genome sequencing of autistic probands and neurotypical siblings to test the hypothesis that mutations in cases have a greater functional impact than those in controls. We leveraged massively parallel reporter assays (MPRAs) to detect transcriptional consequences of these variants in neural progenitor cells and identified 165 functionally high confidence de novo variants (HcDNVs). While these HcDNVs are enriched for markers of active transcription, disruption to transcription factor binding sites, and open chromatin, we did not identify differences in functional impact based on ASD diagnostic status."],"journal":["International journal of molecular sciences"],"pubmed_title":["Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays."],"pmcid":["PMC9959321"],"funding_grant_id":["1S10OD010786-01","1U01MH116438","S10 OD010786","1UM1HG011966","R01 MH116999","U01 MH116438","R01 MH129751","NRF-2021M3E5D9021878","UM1 HG011966","NRF-2020R1C1C1003426","R00 MH117393"],"pubmed_authors":["Koesterich J","An JY","Kreimer A","Sanders SJ","Ahituv N","Inoue F","Sohota A"],"additional_accession":[]},"is_claimable":false,"name":"Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays.","description":"Autism spectrum disorder (ASD) is a common, complex, and highly heritable condition with contributions from both common and rare genetic variations. While disruptive, rare variants in protein-coding regions clearly contribute to symptoms, the role of rare non-coding remains unclear. Variants in these regions, including promoters, can alter downstream RNA and protein quantity; however, the functional impacts of specific variants observed in ASD cohorts remain largely uncharacterized. Here, we analyzed 3600 de novo mutations in promoter regions previously identified by whole-genome sequencing of autistic probands and neurotypical siblings to test the hypothesis that mutations in cases have a greater functional impact than those in controls. We leveraged massively parallel reporter assays (MPRAs) to detect transcriptional consequences of these variants in neural progenitor cells and identified 165 functionally high confidence de novo variants (HcDNVs). While these HcDNVs are enriched for markers of active transcription, disruption to transcription factor binding sites, and open chromatin, we did not identify differences in functional impact based on ASD diagnostic status.","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Feb","modification":"2026-04-08T14:09:13.296Z","creation":"2025-04-04T21:13:38.916Z"},"accession":"S-EPMC9959321","cross_references":{"pubmed":["36834916"],"doi":["10.3390/ijms24043509"]}}