{"doi":"10.1038/s41467-026-68378-4","title":"Using the linear references from the pangenome to discover missing autism variants","abstract":"To better understand large-effect pathogenic variation associated with autism, we generated long-read sequencing (LRS) data to construct phased and near-complete genome assemblies (average contig N50 = 43 Mbp, QV = 56) for 189 individuals from 51 families with unsolved cases. We applied read- and assembly-based strategies to facilitate comprehensive characterization of de novo mutations, structural variants (SVs), and DNA methylation. Using LRS pangenome controls, we efficiently filtered >97% of common SVs exclusive to 87 offspring. We find no evidence of increased autosomal SV burden for probands when compared to unaffected siblings yet observe a suggestive trend toward an increased SV burden on the X chromosome among affected females. We establish a workflow to prioritize potential pathogenic variants by integrating autism risk genes and putative noncoding regulatory elements defined from ATAC-seq and CUT&Tag data from the developing cortex. In total, we identified three pathogenic variants in TBL1XR1, MECP2, and SYNGAP1, as well as nine candidate de novo and biallelic inherited homozygous SVs, most of which were missed by short-read sequencing. Our work highlights the potential of phased genomes to discover complex more pathogenic mutations and the power of the pangenome to restrict the focus on an increasingly smaller number of SVs for clinical evaluation.","journal":"Nature Communications","year":2026,"id":2133,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":37.91700569568755,"corpus_rank":716,"citation_count":2,"citer_count":2,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9244,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2026-01-23","fair_score":35.2083,"fair_percentile":17.282321899736147,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":24409,"name":"Jiadong Lin","orcid":"0000-0002-8116-5901","position":1,"is_corresponding":false},{"id":24410,"name":"Michelle D. Noyes","orcid":null,"position":2,"is_corresponding":false},{"id":19743,"name":"Young-Jun Kwon","orcid":"0000-0002-5024-2134","position":3,"is_corresponding":false},{"id":24411,"name":"Isaac Wong","orcid":"0000-0003-4877-5748","position":4,"is_corresponding":false},{"id":24412,"name":"Nidhi Koundinya","orcid":"0009-0008-7155-1287","position":5,"is_corresponding":false},{"id":19702,"name":"William T. Harvey","orcid":"0000-0003-0646-7528","position":6,"is_corresponding":false},{"id":24413,"name":"Mei Wu","orcid":null,"position":7,"is_corresponding":false},{"id":19716,"name":"Kendra Hoekzema","orcid":"0000-0002-8058-0177","position":8,"is_corresponding":false},{"id":19706,"name":"Katherine M. Munson","orcid":"0000-0001-8413-6498","position":9,"is_corresponding":false},{"id":24414,"name":"Gage H. Garcia","orcid":"0009-0005-2383-722X","position":10,"is_corresponding":false},{"id":24415,"name":"Jordan Knuth","orcid":"0009-0007-0176-7093","position":11,"is_corresponding":false},{"id":24416,"name":"Julie Wertz","orcid":"0009-0000-3747-3221","position":12,"is_corresponding":false},{"id":24417,"name":"Tianyun Wang","orcid":"0000-0002-5179-087X","position":13,"is_corresponding":false},{"id":24418,"name":"Kelsey M. Hennick","orcid":"0000-0002-6127-2400","position":14,"is_corresponding":false},{"id":24419,"name":"Druha Karunakaran","orcid":null,"position":15,"is_corresponding":false},{"id":24420,"name":"Rafael A. Polo Prieto","orcid":"0000-0002-8150-0757","position":16,"is_corresponding":false},{"id":24421,"name":"Rebecca Meyer-Schuman","orcid":null,"position":17,"is_corresponding":false},{"id":24422,"name":"Fisher Cherry","orcid":"0009-0001-7646-8422","position":18,"is_corresponding":false},{"id":24423,"name":"Davut Pehlivan","orcid":null,"position":19,"is_corresponding":false},{"id":24424,"name":"Bernhard Suter","orcid":"0000-0002-0127-7322","position":20,"is_corresponding":false},{"id":24425,"name":"Jonas A. Gustafson","orcid":"0000-0002-5748-905X","position":21,"is_corresponding":false},{"id":24426,"name":"Danny E. Miller","orcid":"0000-0001-6096-8601","position":22,"is_corresponding":false},{"id":24427,"name":"Human Pangenome Reference Consortium (HPRC)","orcid":null,"position":23,"is_corresponding":false},{"id":24428,"name":"Ivan A. Alexandrov","orcid":"0000-0003-4342-2003","position":25,"is_corresponding":false},{"id":24429,"name":"Jamie Allen","orcid":"0000-0002-8677-2225","position":26,"is_corresponding":false},{"id":24430,"name":"Alawi A. Alsheikh-Ali","orcid":null,"position":27,"is_corresponding":false},{"id":24431,"name":"Nicolas Altemose","orcid":"0000-0002-7231-6026","position":28,"is_corresponding":false},{"id":2358,"name":"Dmitry Antipov","orcid":"0000-0002-6087-0660","position":30,"is_corresponding":false},{"id":24433,"name":"Lucinda Antonacci-Fulton","orcid":null,"position":31,"is_corresponding":false},{"id":24434,"name":"Mobin Asri","orcid":"0000-0002-7194-5138","position":32,"is_corresponding":false},{"id":24436,"name":"Jennifer R. Balacco","orcid":null,"position":34,"is_corresponding":false},{"id":24437,"name":"Floris P. Barthel","orcid":null,"position":35,"is_corresponding":false},{"id":24438,"name":"Halle D. Bender","orcid":null,"position":36,"is_corresponding":false},{"id":24439,"name":"Andrew P. Blair","orcid":"0000-0002-3196-6233","position":37,"is_corresponding":false},{"id":24440,"name":"Davide Bolognini","orcid":"0000-0002-8735-8093","position":38,"is_corresponding":false},{"id":24441,"name":"Katherine E. Bonini","orcid":"0000-0001-7721-8137","position":39,"is_corresponding":false},{"id":23991,"name":"Christina Boucher","orcid":"0000-0001-9509-9725","position":40,"is_corresponding":false},{"id":30869,"name":"Konstantinos Billis","orcid":"0000-0001-8568-4306","position":41,"is_corresponding":false},{"id":24442,"name":"Silvia Buonaiuto","orcid":"0000-0002-7423-7110","position":42,"is_corresponding":false},{"id":24443,"name":"Shuo Cao","orcid":null,"position":43,"is_corresponding":false},{"id":19738,"name":"Mark J. P. Chaisson","orcid":"0000-0001-5395-1457","position":44,"is_corresponding":false},{"id":24445,"name":"Ann M. Mc Cartney","orcid":"0000-0003-3191-3200","position":45,"is_corresponding":false},{"id":30870,"name":"Mark J. P. Chaisson","orcid":null,"position":46,"is_corresponding":false},{"id":24447,"name":"Pi-Chuan Chang","orcid":"0000-0003-3021-6446","position":47,"is_corresponding":false},{"id":24449,"name":"Jitender Cheema","orcid":null,"position":49,"is_corresponding":false},{"id":1288,"name":"Haoyu Cheng","orcid":"0000-0002-9209-5793","position":50,"is_corresponding":false},{"id":24450,"name":"Claudio Ciofi","orcid":null,"position":51,"is_corresponding":false},{"id":42976,"name":"Katherine Fisher-Aylor","orcid":"0000-0003-3371-2947","position":52,"is_corresponding":false},{"id":24451,"name":"Sarah Cody","orcid":null,"position":53,"is_corresponding":false},{"id":24453,"name":"Holland C. Conwell","orcid":null,"position":55,"is_corresponding":false},{"id":30872,"name":"Daniel E. Cook","orcid":"0000-0003-3347-562X","position":56,"is_corresponding":false},{"id":16842,"name":"Mark Diekhans","orcid":"0000-0002-0430-0989","position":57,"is_corresponding":false},{"id":24455,"name":"Maria Angela Diroma","orcid":"0000-0003-1427-8946","position":58,"is_corresponding":false},{"id":24456,"name":"Daniel Doerr","orcid":"0000-0002-3720-6227","position":59,"is_corresponding":false},{"id":24457,"name":"Zheng Dong","orcid":null,"position":60,"is_corresponding":false},{"id":24458,"name":"Danilo Dubocanin","orcid":"0000-0003-0330-5814","position":61,"is_corresponding":false},{"id":2123,"name":"Richard Durbin","orcid":"0000-0002-9130-1006","position":62,"is_corresponding":false},{"id":2125,"name":"Evan E. Eichler","orcid":"0000-0002-8246-4014","position":64,"is_corresponding":false},{"id":6318,"name":"Jordan M. Eizenga","orcid":"0000-0001-8345-8356","position":65,"is_corresponding":false},{"id":24459,"name":"Parsa Eskandar","orcid":"0000-0001-7682-3140","position":66,"is_corresponding":false},{"id":24460,"name":"Eddie Ferro","orcid":null,"position":67,"is_corresponding":false},{"id":24461,"name":"Anna-Sophie Fiston-Lavier","orcid":"0000-0002-7306-6532","position":68,"is_corresponding":false},{"id":24462,"name":"Sarah M. Ford","orcid":null,"position":69,"is_corresponding":false},{"id":24463,"name":"Willard W. Ford","orcid":null,"position":70,"is_corresponding":false},{"id":21287,"name":"Giulio Formenti","orcid":"0000-0002-7554-5991","position":71,"is_corresponding":false},{"id":29021,"name":"Michael G. FitzGerald","orcid":"0000-0002-0488-0530","position":72,"is_corresponding":false},{"id":24464,"name":"Mallory A. Freeberg","orcid":null,"position":73,"is_corresponding":false},{"id":24465,"name":"Qichen Fu","orcid":null,"position":74,"is_corresponding":false},{"id":24466,"name":"Stephanie M. Fullerton","orcid":"0000-0002-0938-6048","position":75,"is_corresponding":false},{"id":1766,"name":"Robert S. Fulton","orcid":"0009-0006-6820-3404","position":76,"is_corresponding":false},{"id":6319,"name":"Yan Gao","orcid":"0000-0003-3814-5750","position":77,"is_corresponding":false},{"id":24467,"name":"Obed A. Garcia","orcid":null,"position":78,"is_corresponding":false},{"id":24468,"name":"Joshua M. V. Gardner","orcid":null,"position":79,"is_corresponding":false},{"id":62052,"name":"Nicholas F. Parrish","orcid":"0000-0002-6971-8016","position":81,"is_corresponding":false},{"id":24469,"name":"Nanibaa’ A. Garrison","orcid":"0000-0002-6228-3216","position":82,"is_corresponding":false},{"id":24470,"name":"John E. Garza","orcid":null,"position":83,"is_corresponding":false},{"id":24471,"name":"Margarita Geleta","orcid":"0000-0001-5823-9776","position":84,"is_corresponding":false},{"id":7649,"name":"Richard E. Green","orcid":"0000-0003-0516-5827","position":87,"is_corresponding":false},{"id":24473,"name":"Cristian Groza","orcid":"0000-0001-6624-5404","position":88,"is_corresponding":false},{"id":19201,"name":"Andrea Guarracino","orcid":"0000-0001-9744-131X","position":89,"is_corresponding":false},{"id":2972,"name":"Madhusudan Gujral","orcid":"0000-0001-5010-4826","position":90,"is_corresponding":false},{"id":24474,"name":"Maximilian Haeussler","orcid":"0000-0001-8721-8253","position":91,"is_corresponding":false},{"id":24475,"name":"Leanne Haggerty","orcid":"0000-0001-8843-3596","position":92,"is_corresponding":false},{"id":7658,"name":"Nancy F. Hansen","orcid":"0000-0002-0950-0699","position":94,"is_corresponding":false},{"id":24477,"name":"Yue Hao","orcid":null,"position":95,"is_corresponding":false},{"id":24478,"name":"Mohammad Amiruddin Hashmi","orcid":null,"position":96,"is_corresponding":false},{"id":14377,"name":"Steven J.M. Jones","orcid":"0000-0003-3394-2208","position":97,"is_corresponding":false},{"id":24479,"name":"Prajna Hebbar","orcid":"0009-0008-9817-5330","position":98,"is_corresponding":false},{"id":24480,"name":"Peter Heringer","orcid":null,"position":99,"is_corresponding":false},{"id":6314,"name":"Hickey, Glenn","orcid":"0000-0002-2280-9404","position":100,"is_corresponding":false},{"id":24481,"name":"Todd L. Hillaker","orcid":null,"position":101,"is_corresponding":false},{"id":24482,"name":"S. Nakib Hossain","orcid":null,"position":102,"is_corresponding":false},{"id":24483,"name":"Neng Huang","orcid":"0000-0001-7187-0749","position":103,"is_corresponding":false},{"id":19717,"name":"Sarah E. Hunt","orcid":"0000-0002-8350-1235","position":104,"is_corresponding":false},{"id":18874,"name":"Toby Hunt","orcid":"0000-0001-8377-0841","position":105,"is_corresponding":false},{"id":24484,"name":"Alexander G. Ioannidis","orcid":null,"position":106,"is_corresponding":false},{"id":24485,"name":"Nafiseh Jafarzadeh","orcid":"0000-0002-1816-2994","position":107,"is_corresponding":false},{"id":21329,"name":"Erich  D. Jarvis","orcid":"0000-0001-8931-5049","position":109,"is_corresponding":false},{"id":24486,"name":"Maryam Jehangir","orcid":"0000-0001-5121-770X","position":110,"is_corresponding":false},{"id":24487,"name":"Juan Jiang","orcid":"0000-0001-5056-5286","position":111,"is_corresponding":false},{"id":24488,"name":"Edward A. Belter","orcid":null,"position":112,"is_corresponding":false},{"id":24489,"name":"Jonathan LoTempio","orcid":"0000-0001-6897-5419","position":113,"is_corresponding":false},{"id":24490,"name":"Eimear E. Kenny","orcid":"0000-0001-9198-759X","position":114,"is_corresponding":false},{"id":21306,"name":"Juhyun Kim","orcid":"0000-0002-0321-9388","position":115,"is_corresponding":false},{"id":21308,"name":"Bonhwang Koo","orcid":"0000-0002-5181-6267","position":116,"is_corresponding":false},{"id":2118,"name":"Sergey Koren","orcid":"0000-0002-1472-8962","position":117,"is_corresponding":false},{"id":2103,"name":"Milinn Kremitzki","orcid":"0000-0001-7980-3153","position":118,"is_corresponding":false},{"id":24491,"name":"Charles H. Langley","orcid":null,"position":119,"is_corresponding":false},{"id":18148,"name":"Ben Langmead","orcid":"0000-0003-2437-1976","position":120,"is_corresponding":false},{"id":24492,"name":"Heather A. Lawson","orcid":"0000-0002-3550-5485","position":121,"is_corresponding":false},{"id":81146,"name":"Ashwinikumar Kulkarni","orcid":"0000-0003-0951-2427","position":122,"is_corresponding":false},{"id":30887,"name":"Alexandra P. Lewis","orcid":"0000-0002-6195-4786","position":123,"is_corresponding":false},{"id":24494,"name":"Wen-Wei Liao","orcid":null,"position":124,"is_corresponding":false},{"id":19692,"name":"Glennis A. Logsdon","orcid":"0000-0003-2396-0656","position":126,"is_corresponding":false},{"id":24496,"name":"Ryan Lorig-Roach","orcid":null,"position":127,"is_corresponding":false},{"id":24497,"name":"Hailey Loucks","orcid":"0009-0000-6956-9922","position":128,"is_corresponding":false},{"id":24498,"name":"Jane E. Loveland","orcid":null,"position":129,"is_corresponding":false},{"id":24499,"name":"Jianguo Lu","orcid":null,"position":130,"is_corresponding":false},{"id":24500,"name":"Shuangjia Lu","orcid":"0000-0001-8571-6902","position":131,"is_corresponding":false},{"id":24501,"name":"Julian K. Lucas","orcid":null,"position":132,"is_corresponding":false},{"id":19591,"name":"Kateryna D. Makova","orcid":"0000-0002-6212-9526","position":134,"is_corresponding":false},{"id":3673,"name":"Maximillian G. Marin","orcid":"0000-0002-9108-3328","position":135,"is_corresponding":false},{"id":19693,"name":"Peter Ebert","orcid":"0000-0001-7441-532X","position":136,"is_corresponding":false},{"id":6321,"name":"Tobias Marschall","orcid":"0000-0002-9376-1030","position":137,"is_corresponding":false},{"id":24504,"name":"Franco L. Marsico","orcid":null,"position":138,"is_corresponding":false},{"id":24505,"name":"Fergal J. Martin","orcid":"0000-0002-1672-050X","position":139,"is_corresponding":false},{"id":24506,"name":"Mira Mastoras","orcid":"0000-0001-6897-0116","position":140,"is_corresponding":false},{"id":53920,"name":"Brandy M. McNulty","orcid":null,"position":141,"is_corresponding":false},{"id":21289,"name":"Jack  A. Medico","orcid":"0000-0003-1855-0855","position":143,"is_corresponding":false},{"id":24509,"name":"Julian M. Menendez","orcid":null,"position":144,"is_corresponding":false},{"id":30894,"name":"Jennifer McDaniel","orcid":"0000-0003-1987-0914","position":145,"is_corresponding":false},{"id":24511,"name":"Anna Minkina","orcid":"0000-0002-7989-4478","position":146,"is_corresponding":false},{"id":24512,"name":"Matthew W. Mitchell","orcid":"0000-0002-6947-0495","position":147,"is_corresponding":false},{"id":24513,"name":"Saswat K. Mohanty","orcid":"0000-0002-1813-589X","position":148,"is_corresponding":false},{"id":24514,"name":"Younes Mokrab","orcid":"0000-0003-1611-6692","position":149,"is_corresponding":false},{"id":6315,"name":"Jean Monlong","orcid":"0000-0002-9737-5516","position":150,"is_corresponding":false},{"id":24515,"name":"Shabir Moosa","orcid":"0000-0003-2645-2497","position":151,"is_corresponding":false},{"id":24516,"name":"Avelina Moreno-Ochando","orcid":null,"position":152,"is_corresponding":false},{"id":24517,"name":"Shinichi Morishita","orcid":"0000-0002-6201-8885","position":153,"is_corresponding":false},{"id":24518,"name":"Njagi Mwaniki","orcid":null,"position":155,"is_corresponding":false},{"id":24519,"name":"Nasna Nassir","orcid":null,"position":156,"is_corresponding":false},{"id":24520,"name":"Chiara Natali","orcid":"0000-0002-0293-171X","position":157,"is_corresponding":false},{"id":24521,"name":"Shloka Negi","orcid":"0000-0002-9839-4030","position":158,"is_corresponding":false},{"id":30897,"name":"Maria Nattestad","orcid":"0000-0002-4796-2894","position":160,"is_corresponding":false},{"id":24523,"name":"Pilar N. Ossorio","orcid":"0000-0002-3495-7375","position":161,"is_corresponding":false},{"id":24524,"name":"Chie Owa","orcid":null,"position":162,"is_corresponding":false},{"id":24525,"name":"Sadye Paez","orcid":null,"position":163,"is_corresponding":false},{"id":30899,"name":"Nathan D. Olson","orcid":"0000-0003-2585-3037","position":164,"is_corresponding":false},{"id":2122,"name":"Adam  M. Phillippy","orcid":"0000-0003-2983-8934","position":166,"is_corresponding":false},{"id":24527,"name":"Brandon D. Pickett","orcid":"0000-0001-8235-4440","position":167,"is_corresponding":false},{"id":24528,"name":"Laura Pignata","orcid":"0000-0001-8835-5567","position":168,"is_corresponding":false},{"id":24529,"name":"Nadia Pisanti","orcid":null,"position":169,"is_corresponding":false},{"id":19696,"name":"David Porubsky","orcid":"0000-0001-8414-8966","position":170,"is_corresponding":false},{"id":24530,"name":"Pjotr Prins","orcid":"0000-0002-8021-9162","position":171,"is_corresponding":false},{"id":24531,"name":"Anandi Radhakrishnan","orcid":null,"position":172,"is_corresponding":false},{"id":24532,"name":"T. Rhyker Ranallo-Benavidez","orcid":null,"position":173,"is_corresponding":false},{"id":14954,"name":"Alexander Stark","orcid":"0000-0003-2611-0841","position":174,"is_corresponding":false},{"id":30918,"name":"Allison A. Regier","orcid":"0000-0002-1932-8714","position":175,"is_corresponding":false},{"id":24534,"name":"Alessandro Raveane","orcid":"0000-0002-8322-5461","position":176,"is_corresponding":false},{"id":24535,"name":"Luyao Ren","orcid":"0000-0002-4052-1148","position":177,"is_corresponding":false},{"id":21320,"name":"Arang Rhie","orcid":"0000-0002-9809-8127","position":178,"is_corresponding":false},{"id":24536,"name":"Fedor Ryabov","orcid":"0000-0001-8728-9465","position":179,"is_corresponding":false},{"id":24537,"name":"Samuel Sacco","orcid":"0000-0003-1227-8934","position":180,"is_corresponding":false},{"id":24539,"name":"Michael C. Schatz","orcid":"0000-0002-4118-4446","position":182,"is_corresponding":false},{"id":24540,"name":"Laura B. Scheinfeldt","orcid":null,"position":183,"is_corresponding":false},{"id":24541,"name":"Aarushi Sehgal","orcid":null,"position":184,"is_corresponding":false},{"id":24543,"name":"Mahsa Shabani","orcid":"0000-0001-7128-0474","position":186,"is_corresponding":false},{"id":24544,"name":"Kishwar Shafin","orcid":"0000-0001-5252-3434","position":187,"is_corresponding":false},{"id":24545,"name":"Shadi Shahatit","orcid":null,"position":188,"is_corresponding":false},{"id":24546,"name":"Ruhollah Shemirani","orcid":"0000-0003-1065-7244","position":189,"is_corresponding":false},{"id":24547,"name":"Vikram S. Shivakumar","orcid":null,"position":190,"is_corresponding":false},{"id":24548,"name":"Swati Sinha","orcid":"0000-0003-0795-8230","position":191,"is_corresponding":false},{"id":24549,"name":"Jouni Sirén","orcid":"0000-0001-5828-4139","position":192,"is_corresponding":false},{"id":21323,"name":"Linnéa Smeds","orcid":"0000-0002-8415-9259","position":193,"is_corresponding":false},{"id":24550,"name":"Steven J. Solar","orcid":"0000-0003-3051-9009","position":194,"is_corresponding":false},{"id":21290,"name":"Marco Sollitto","orcid":"0000-0002-0806-1460","position":195,"is_corresponding":false},{"id":24551,"name":"Nicole Soranzo","orcid":"0000-0003-1095-3852","position":196,"is_corresponding":false},{"id":11629,"name":"Andrew B. Stergachis","orcid":"0000-0002-1299-3674","position":197,"is_corresponding":false},{"id":18873,"name":"Marie-Marthe Suner","orcid":"0000-0002-0380-7171","position":198,"is_corresponding":false},{"id":19728,"name":"Arda Soylev","orcid":"0000-0003-2198-1920","position":200,"is_corresponding":false},{"id":24553,"name":"Ahmad Abou Tayoun","orcid":"0000-0002-9134-1673","position":201,"is_corresponding":false},{"id":17785,"name":"Jack A. S. Tierney","orcid":"0000-0002-5331-3604","position":202,"is_corresponding":false},{"id":24554,"name":"Chad Tomlinson","orcid":"0000-0001-9905-6159","position":203,"is_corresponding":false},{"id":24555,"name":"Francesca Floriana Tricomi","orcid":"0000-0002-6170-5499","position":204,"is_corresponding":false},{"id":24556,"name":"Mohammed Uddin","orcid":null,"position":205,"is_corresponding":false},{"id":24557,"name":"Matteo Tommaso Ungaro","orcid":"0000-0002-1107-3307","position":206,"is_corresponding":false},{"id":24558,"name":"Rahul Varki","orcid":"0009-0003-5721-9484","position":207,"is_corresponding":false},{"id":24559,"name":"Flavia Villani","orcid":"0000-0003-3633-0610","position":208,"is_corresponding":false},{"id":24560,"name":"Ivo Violich","orcid":null,"position":209,"is_corresponding":false},{"id":24561,"name":"Mitchell R. Vollger","orcid":"0000-0002-8651-1615","position":210,"is_corresponding":false},{"id":4363,"name":"Brian P. Walenz","orcid":"0000-0001-8431-1428","position":211,"is_corresponding":false},{"id":24562,"name":"Charles Wang","orcid":null,"position":212,"is_corresponding":false},{"id":24563,"name":"Lisa E. Wang","orcid":null,"position":213,"is_corresponding":false},{"id":24564,"name":"Ting Wang","orcid":"0000-0002-6800-242X","position":214,"is_corresponding":false},{"id":24565,"name":"Aaron M. Wenger","orcid":"0000-0003-1183-0432","position":215,"is_corresponding":false},{"id":24566,"name":"Conor V. Whelan","orcid":null,"position":216,"is_corresponding":false},{"id":24567,"name":"Zilan Xin","orcid":null,"position":217,"is_corresponding":false},{"id":24568,"name":"Zheng Xu","orcid":"0000-0002-5374-4121","position":218,"is_corresponding":false},{"id":14259,"name":"Kai Ye","orcid":"0000-0002-2851-6741","position":219,"is_corresponding":false},{"id":19700,"name":"DongAhn Yoo","orcid":"0000-0003-0033-3721","position":220,"is_corresponding":false},{"id":24569,"name":"Wenjin Zhang","orcid":"0000-0002-5979-0102","position":221,"is_corresponding":false},{"id":14882,"name":"Ying Zhou","orcid":"0000-0002-8107-3927","position":222,"is_corresponding":false},{"id":24570,"name":"Xiaoyu Zhuo","orcid":null,"position":223,"is_corresponding":false},{"id":24571,"name":"Giulia Zunino","orcid":null,"position":224,"is_corresponding":false},{"id":24572,"name":"Hanna Berk-Rauch","orcid":null,"position":225,"is_corresponding":false},{"id":21360,"name":"Tomasz J. Nowakowski","orcid":"0000-0003-2345-4964","position":226,"is_corresponding":false},{"id":21863,"name":"Aravinda Chakravarti","orcid":"0000-0002-4264-2285","position":227,"is_corresponding":false},{"id":24573,"name":"Huda Y. Zoghbi","orcid":"0000-0002-0700-3349","position":228,"is_corresponding":false},{"id":24574,"name":"Jamie L. Allen","orcid":null,"position":230,"is_corresponding":false},{"id":24575,"name":"Kaitlyn A. Sun","orcid":null,"position":231,"is_corresponding":false},{"id":21327,"name":"Paul  D. Waters","orcid":"0000-0002-4689-8747","position":232,"is_corresponding":false},{"id":24576,"name":"A J Carroll","orcid":null,"position":233,"is_corresponding":false},{"id":17704,"name":"Ying Chen","orcid":"0000-0001-8306-8083","position":235,"is_corresponding":false},{"id":24578,"name":"Claúdio Ciofi","orcid":"0000-0001-8537-8659","position":236,"is_corresponding":false},{"id":24579,"name":"Joana Damas","orcid":"0000-0003-4857-2510","position":237,"is_corresponding":false},{"id":24580,"name":"Chester Brown","orcid":"0000-0003-2828-7616","position":238,"is_corresponding":false},{"id":24581,"name":"Sheila Dodge","orcid":null,"position":239,"is_corresponding":false},{"id":24583,"name":"E. E. Eichler","orcid":null,"position":241,"is_corresponding":false},{"id":24584,"name":"Sarah Ford","orcid":"0009-0002-8855-3576","position":242,"is_corresponding":false},{"id":24585,"name":"W. L. Ford","orcid":null,"position":243,"is_corresponding":false},{"id":24586,"name":"Kin Fai Au","orcid":"0000-0002-9222-4241","position":244,"is_corresponding":false},{"id":24587,"name":"Mallory Freeberg","orcid":"0000-0003-2949-3921","position":245,"is_corresponding":false},{"id":24588,"name":"R J Fulton","orcid":null,"position":246,"is_corresponding":false},{"id":24589,"name":"Obed Garcia","orcid":"0000-0001-6150-6118","position":247,"is_corresponding":false},{"id":24590,"name":"Shihua Dong","orcid":"0000-0001-7020-8964","position":248,"is_corresponding":false},{"id":2128,"name":"Tina A. Graves-Lindsay","orcid":"0000-0002-0409-891X","position":249,"is_corresponding":false},{"id":24591,"name":"Cristian Alexandru Groza","orcid":null,"position":250,"is_corresponding":false},{"id":24592,"name":"Nima Mousavi","orcid":"0000-0003-1926-8982","position":251,"is_corresponding":false},{"id":30880,"name":"Thibaut Hourlier","orcid":"0000-0003-4894-7773","position":252,"is_corresponding":false},{"id":24593,"name":"M. Farhan Hanif","orcid":null,"position":253,"is_corresponding":false},{"id":24594,"name":"Simon Heumos","orcid":"0000-0003-3326-817X","position":254,"is_corresponding":false},{"id":24595,"name":"Todd Hillaker","orcid":null,"position":255,"is_corresponding":false},{"id":24596,"name":"Ian Korf","orcid":"0000-0001-5259-6182","position":256,"is_corresponding":false},{"id":24597,"name":"Harinder Singh","orcid":"0000-0002-6330-8526","position":257,"is_corresponding":false},{"id":24598,"name":"Wenwei Liao","orcid":null,"position":258,"is_corresponding":false},{"id":24599,"name":"T -C Liu","orcid":null,"position":259,"is_corresponding":false},{"id":13532,"name":"Eoghan Harrington","orcid":"0000-0002-4850-2486","position":260,"is_corresponding":false},{"id":24601,"name":"Jane E Loveland","orcid":"0000-0002-7669-2934","position":261,"is_corresponding":false},{"id":24602,"name":"Jianguo Lü","orcid":"0000-0002-3966-8812","position":262,"is_corresponding":false},{"id":24603,"name":"Julian K. Lucas","orcid":"0000-0001-9163-2756","position":263,"is_corresponding":false},{"id":14356,"name":"Geòrgia Escaramís","orcid":"0000-0002-5416-3177","position":264,"is_corresponding":false},{"id":24604,"name":"Franco Mársico","orcid":"0000-0002-0740-5516","position":265,"is_corresponding":false},{"id":24605,"name":"Julian Menendez","orcid":"0000-0002-0002-8543","position":266,"is_corresponding":false},{"id":24606,"name":"Njagi Moses Mwaniki","orcid":null,"position":267,"is_corresponding":false},{"id":24607,"name":"Ossorio Pn","orcid":null,"position":268,"is_corresponding":false},{"id":24608,"name":"Nadia P Pisanti","orcid":null,"position":269,"is_corresponding":false},{"id":24609,"name":"Laura Scheinfeldt","orcid":"0000-0001-6529-6701","position":270,"is_corresponding":false},{"id":24610,"name":"William Seligmann","orcid":"0000-0002-5762-3095","position":271,"is_corresponding":false},{"id":24611,"name":"Sergey Nurk","orcid":"0000-0003-1301-5749","position":272,"is_corresponding":false},{"id":24612,"name":"A Stergachis","orcid":null,"position":273,"is_corresponding":false},{"id":11776,"name":"Hazuki Takahashi","orcid":"0000-0001-7315-7349","position":274,"is_corresponding":false},{"id":24613,"name":"Flavia Galvão Villani","orcid":null,"position":275,"is_corresponding":false},{"id":24614,"name":"Charles H Wang","orcid":null,"position":276,"is_corresponding":false},{"id":20492,"name":" Ling Li","orcid":"0000-0002-9245-7387","position":277,"is_corresponding":false},{"id":24615,"name":"Juniper A. Lake","orcid":"0000-0001-7628-5645","position":278,"is_corresponding":false},{"id":24616,"name":"Yi Zhou","orcid":"0009-0009-1104-917X","position":279,"is_corresponding":false},{"id":24408,"name":"Yang Sui","orcid":"0000-0001-7285-8733","position":0,"is_corresponding":true}],"reference_count":71,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"41577710","pmcid":"PMC12909954","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":40.0,"fair_a":42.5,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":-0.9048,"fair_rationale":{"fair_score":35.21,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":40.0,"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":0.0,"signal":null,"rationale":"No machine-readable metadata (e.g., schema.org, JSON-LD) is provided in the paper text."}]},"A":{"name":"Accessible","score":42.5,"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":"The article states that data from HPRC and HGSVC are publicly available and mentions an open-access license, but does not specify a clear, standardized protocol for accessing the primary generated data or code."}]},"I":{"name":"Interoperable","score":25.0,"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 standard formats (e.g., VCF-like SV calls, GRCh38 reference) and identifiers (e.g., SFARI, ClinVar), but does not report using machine-readable vocabularies or formal ontologies for metadata."}]},"R":{"name":"Reusable","score":33.33,"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":0.5,"signal":null,"rationale":"A data-availability statement is implied by mentioning public pangenome resources and an open-access license (CC BY 4.0), but no explicit link to deposited data, code, or reproducibility instructions is provided in the text."}]}},"suggestions":["Include structured machine-readable metadata (e.g., Schema.org/Dublin Core) in the article header or supplementary.","Provide a dedicated data-availability section with persistent identifiers (e.g., DOI) for all generated datasets and code.","Deposit code and analysis pipelines in a public repository with a clear license and versioning.","Use formal ontologies (e.g., OBO foundry) for phenotypic and genomic variant annotations to enhance interoperability.","Provide a reproducible workflow container or detailed step-by-step documentation for rerunning analyses."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v1","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v1","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-17T23:00:07.780900Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}