{"doi":"10.1016/j.ajhg.2016.02.018","title":"Frequency and Complexity of De Novo Structural Mutation in Autism","abstract":"Genetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising 11 different classes. We found a high diversity of de novo mutations, the majority of which were undetectable by previous methods. In addition, we observed complex mutation clusters where combinations of de novo SVs, nucleotide substitutions, and indels occurred as a single event. We estimate a high rate of structural mutation in humans (20%) and propose that genetic risk for ASD is attributable to an elevated frequency of gene-disrupting de novo SVs, but not an elevated rate of genome rearrangement.","journal":"The American Journal of Human Genetics","year":2016,"id":316,"datarank":3.595436422829064,"base_score":4.68213122712422,"endowment":4.68213122712422,"self_citation_contribution":0.7023196840686331,"citation_network_contribution":2.893116738760431,"self_endowment_contribution":0.7023196840686331,"citer_contribution":2.893116738760431,"corpus_percentile":69.08055329536208,"corpus_rank":381,"citation_count":110,"citer_count":92,"citers_with_citation_signal":75,"citers_with_endowment":75,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6081,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2016-04-01","fair_score":37.1667,"fair_percentile":18.601583113456464,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":2971,"name":"Danny Antaki","orcid":"0000-0003-0381-7801","position":1,"is_corresponding":false},{"id":2972,"name":"Madhusudan Gujral","orcid":"0000-0001-5010-4826","position":2,"is_corresponding":false},{"id":2973,"name":"Amina Noor","orcid":null,"position":3,"is_corresponding":false},{"id":2974,"name":"Gabriel Rosanio","orcid":null,"position":4,"is_corresponding":false},{"id":2975,"name":"Timothy R. 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Brandler","orcid":"0000-0001-5280-325X","position":0,"is_corresponding":true}],"reference_count":44,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"27018473","pmcid":"PMC4833290","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":69.0,"fair_a":53.0,"fair_i":10.0,"fair_r":16.6667,"fair_zscore":-0.7277,"fair_rationale":{"fair_score":37.17,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":69.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper provides rich biological metadata (e.g., SV locus atlas, classes) but no structured machine-readable metadata, permanent identifiers, or formal descriptions for automated discovery."}]},"A":{"name":"Accessible","score":53.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"No data or code access protocol is mentioned; only a custom pipeline is described without specifying how others can retrieve the SV atlas or sequencing data."}]},"I":{"name":"Interoperable","score":10.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper uses some standard genomic identifiers (e.g., de novo SVs, nucleotide substitutions), but lacks systematic reference to standard ontologies, formats, or persistent identifiers for the compiled loci."}]},"R":{"name":"Reusable","score":16.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.167,"signal":null,"rationale":"No data-availability statement, license, or reproducibility measures (e.g., code repository, versioned dataset) are provided, limiting reuse beyond the described findings."}]}},"suggestions":["Deposit the SV atlas in a public repository with a persistent identifier (e.g., DOI) and machine-readable metadata (e.g., ISA-TAB, JSON-LD).","Provide a clear data access protocol in the paper, including URLs or accession numbers for the sequencing data and custom pipeline code.","Use standard genomics formats (e.g., VCF for SVs) and reference ontologies (e.g., SO, EFO) to improve interoperability."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"abstract_only"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"abstract_only","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:39:16.503855Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}