{"id":"https://openalex.org/W7212229659","doi":"https://doi.org/10.64898/2026.09.07.749735","title":"A T2T Benchmark Reveals How Reference Choice Shapes Human Genome Interpretation","display_name":"A T2T Benchmark Reveals How Reference Choice Shapes Human Genome Interpretation","publication_year":2026,"publication_date":"2026-09-10","ids":{"openalex":"https://openalex.org/W7212229659","doi":"https://doi.org/10.64898/2026.09.07.749735"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.07.749735","doi":"https://doi.org/10.64898/2026.09.07.749735","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.07.749735","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/10/2026.09.07.749735.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/10/2026.09.07.749735.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5151326728","display_name":"Zhuo Huang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuo Huang","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China","University of Chinese Academy of Sciences; Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences; Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110703133","display_name":"Yanan Chu","orcid":"https://orcid.org/0000-0002-9349-4307","observed_orcids":["https://orcid.org/0000-0002-9349-4307"]},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanan Chu","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084202227","display_name":"Yabin Tian","orcid":"https://orcid.org/0009-0008-0820-0038","observed_orcids":["https://orcid.org/0009-0008-0820-0038"]},"institutions":[{"id":"https://openalex.org/I4210136676","display_name":"National Institutes for Food and Drug Control","ror":"https://ror.org/041rdq190","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210136676"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yabin Tian","raw_affiliation_strings":["State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China","institution_ids":["https://openalex.org/I4210136676"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009487011","display_name":"Changjun Shao","orcid":"https://orcid.org/0009-0007-5610-123X","observed_orcids":["https://orcid.org/0009-0007-5610-123X","https://orcid.org/0000-0002-5836-9447"]},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Changjun Shao","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122297554","display_name":"Jian Wang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Wang","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086731812","display_name":"Xueqi Zhang","orcid":"https://orcid.org/0000-0003-0345-0405","observed_orcids":["https://orcid.org/0000-0003-0345-0405"]},"institutions":[{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueqi Zhang","raw_affiliation_strings":["University of Chinese Academy of Sciences; Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Chinese Academy of Sciences; Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5151361891","display_name":"Jing Chen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Chen","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100594801","display_name":"Zheng Jia","orcid":"https://orcid.org/0009-0009-3665-9193","observed_orcids":["https://orcid.org/0009-0009-3665-9193"]},"institutions":[{"id":"https://openalex.org/I4210136676","display_name":"National Institutes for Food and Drug Control","ror":"https://ror.org/041rdq190","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210136676"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zheng Jia","raw_affiliation_strings":["State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China","institution_ids":["https://openalex.org/I4210136676"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100340046","display_name":"Lili Li","orcid":"https://orcid.org/0000-0001-7832-8688","observed_orcids":["https://orcid.org/0000-0001-7832-8688"]},"institutions":[{"id":"https://openalex.org/I4210136676","display_name":"National Institutes for Food and Drug Control","ror":"https://ror.org/041rdq190","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210136676"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lili Li","raw_affiliation_strings":["State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China","institution_ids":["https://openalex.org/I4210136676"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5151387391","display_name":"Jiale Li","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210136676","display_name":"National Institutes for Food and Drug Control","ror":"https://ror.org/041rdq190","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210136676"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiale Li","raw_affiliation_strings":["State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China","institution_ids":["https://openalex.org/I4210136676"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004708289","display_name":"Guigao Lin","orcid":"https://orcid.org/0000-0002-0406-9078","observed_orcids":["https://orcid.org/0000-0002-0406-9078"]},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210119648","display_name":"Beijing Hospital","ror":"https://ror.org/02jwb5s28","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210119648"]},{"id":"https://openalex.org/I4210146612","display_name":"National Center for Clinical Laboratories","ror":"https://ror.org/0530d6n45","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210146612"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guigao Lin","raw_affiliation_strings":["National Center for Clinical Laboratories, Beijing Hospital, National Center for Gerontology; National Clinical Research Center for Gerontology; The Key Laboratory of Geriatrics of NHC; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Clinical Laboratories, Beijing Hospital, National Center for Gerontology; National Clinical Research Center for Gerontology; The Key Laboratory of Geriatrics of NHC; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I4210119648","https://openalex.org/I4210146612"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137196731","display_name":"Kuo Zhang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210119648","display_name":"Beijing Hospital","ror":"https://ror.org/02jwb5s28","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210119648"]},{"id":"https://openalex.org/I4210146612","display_name":"National Center for Clinical Laboratories","ror":"https://ror.org/0530d6n45","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210146612"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kuo Zhang","raw_affiliation_strings":["National Center for Clinical Laboratories, Beijing Hospital, National Center for Gerontology; National Clinical Research Center for Gerontology; The Key Laboratory of Geriatrics of NHC; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Clinical Laboratories, Beijing Hospital, National Center for Gerontology; National Clinical Research Center for Gerontology; The Key Laboratory of Geriatrics of NHC; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I4210119648","https://openalex.org/I4210146612"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085581810","display_name":"Stylianos E. Antonarakis","orcid":"https://orcid.org/0000-0001-8907-5823","observed_orcids":["https://orcid.org/0000-0001-8907-5823"]},"institutions":[{"id":"https://openalex.org/I114457229","display_name":"University of Geneva","ror":"https://ror.org/01swzsf04","country_code":"CH","type":"education","lineage":["https://openalex.org/I114457229"]},{"id":"https://openalex.org/I206127235","display_name":"Academy of Athens","ror":"https://ror.org/00qsdn986","country_code":"GR","type":"education","lineage":["https://openalex.org/I206127235"]}],"countries":["CH","GR"],"is_corresponding":false,"raw_author_name":"Stylianos E. Antonarakis","raw_affiliation_strings":["Academy of Athens; Athens, 10670, Greece","Department of Genetic Medicine and Development, University of Geneva Medical Faculty; Geneva, 1211, Switzerland","Medigenome, Swiss Institute of Genomic Medicine; Geneva, 1207, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academy of Athens; Athens, 10670, Greece","institution_ids":["https://openalex.org/I206127235"]},{"raw_affiliation_string":"Department of Genetic Medicine and Development, University of Geneva Medical Faculty; Geneva, 1211, Switzerland","institution_ids":["https://openalex.org/I114457229"]},{"raw_affiliation_string":"Medigenome, Swiss Institute of Genomic Medicine; Geneva, 1207, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5140406783","display_name":"Yu Kang","orcid":"https://orcid.org/0000-0002-0999-8802","observed_orcids":["https://orcid.org/0000-0002-0999-8802"]},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu Kang","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China","University of Chinese Academy of Sciences; Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation; Beijing, 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences; Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5151294590","display_name":"Jie Huang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210136676","display_name":"National Institutes for Food and Drug Control","ror":"https://ror.org/041rdq190","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210136676"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Huang","raw_affiliation_strings":["State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Drug Regulatory Science, National Institutes for Drug Control; Beijing, 100050, China","institution_ids":["https://openalex.org/I4210136676"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5140406783"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699","https://openalex.org/I4210165038"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.98580002784729,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.98580002784729,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.006000000052154064,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.0027000000700354576,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/variant-calling-accuracy","display_name":"variant calling accuracy","score":0.703000009059906},{"id":"https://openalex.org/keywords/benchmarking","display_name":"benchmarking","score":0.39800000190734863},{"id":"https://openalex.org/keywords/hardy-weinberg-equilibrium","display_name":"Hardy-Weinberg equilibrium","score":0.7950000166893005},{"id":"https://openalex.org/keywords/variant-discovery","display_name":"variant discovery","score":0.34299999475479126},{"id":"https://openalex.org/keywords/chinese-individual","display_name":"Chinese individual","score":0.5040000081062317}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7854999899864197},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.7371000051498413},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6564000248908997},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5967000126838684},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5633000135421753},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.4916999936103821},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4869999885559082},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44699999690055847},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.42719998955726624},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.4027000069618225},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.38929998874664307},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3880999982357025},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3853999972343445},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34850001335144043},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3425999879837036},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.3312000036239624},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29490000009536743},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.2800999879837036},{"id":"https://openalex.org/C40583040","wikidata":"https://www.wikidata.org/wiki/Q1502105","display_name":"Human genetic variation","level":5,"score":0.27239999175071716},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26600000262260437},{"id":"https://openalex.org/C143191323","wikidata":"https://www.wikidata.org/wiki/Q118406","display_name":"Ploidy","level":3,"score":0.2639999985694885}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.07.749735","doi":"https://doi.org/10.64898/2026.09.07.749735","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.07.749735","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/10/2026.09.07.749735.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.07.749735","doi":"https://doi.org/10.64898/2026.09.07.749735","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.07.749735","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/10/2026.09.07.749735.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G7031067063","display_name":null,"funder_award_id":"2024YFC3405701","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7578743529","display_name":null,"funder_award_id":"32371537","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7212229659.pdf","grobid_xml":"https://content.openalex.org/works/W7212229659.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W2006921756","https://openalex.org/W2127495773","https://openalex.org/W2147733682","https://openalex.org/W2779975541","https://openalex.org/W2888300707","https://openalex.org/W2889664156","https://openalex.org/W2892014603","https://openalex.org/W2929354011","https://openalex.org/W2951331911","https://openalex.org/W2953263404","https://openalex.org/W3007365321","https://openalex.org/W3085758516","https://openalex.org/W3087389975","https://openalex.org/W3113162057","https://openalex.org/W3208186059","https://openalex.org/W4200597270","https://openalex.org/W4210887696","https://openalex.org/W4220999759","https://openalex.org/W4223416923","https://openalex.org/W4226151130","https://openalex.org/W4283210431","https://openalex.org/W4298109415","https://openalex.org/W4313250582","https://openalex.org/W4365513261","https://openalex.org/W4376133202","https://openalex.org/W4380730560","https://openalex.org/W4383186436","https://openalex.org/W4385856832","https://openalex.org/W4390500910","https://openalex.org/W4391383726","https://openalex.org/W4391925503","https://openalex.org/W4392500048","https://openalex.org/W4393870245","https://openalex.org/W4395667653","https://openalex.org/W4396907040","https://openalex.org/W4399781994","https://openalex.org/W4400564463","https://openalex.org/W4402459535","https://openalex.org/W4403075345","https://openalex.org/W4403508986","https://openalex.org/W4403526343","https://openalex.org/W4409995522","https://openalex.org/W4410363000","https://openalex.org/W4410498438","https://openalex.org/W4410498449","https://openalex.org/W4411983867","https://openalex.org/W4412600907","https://openalex.org/W4412929260","https://openalex.org/W4413020599","https://openalex.org/W4413066967","https://openalex.org/W4414403753","https://openalex.org/W4414807539","https://openalex.org/W4415033505","https://openalex.org/W4415306843","https://openalex.org/W4416716967","https://openalex.org/W4417199155","https://openalex.org/W4417261234","https://openalex.org/W7116113578","https://openalex.org/W7127604573","https://openalex.org/W7127646070","https://openalex.org/W7140045779","https://openalex.org/W7143329801","https://openalex.org/W7147353830","https://openalex.org/W7161701812","https://openalex.org/W7170083314","https://openalex.org/W7204450062"],"related_works":["https://openalex.org/W4385856832","https://openalex.org/W4414403753","https://openalex.org/W4225399233","https://openalex.org/W4413066967","https://openalex.org/W7166788126","https://openalex.org/W7213234163","https://openalex.org/W7211977859","https://openalex.org/W4414238232","https://openalex.org/W3177375819","https://openalex.org/W4408057065"],"abstract_inverted_index":{"Abstract":[0],"The":[1,59,137],"completion":[2],"of":[3,13,66,78,99,127],"telomere-to-telomere":[4],"(T2T)":[5],"human":[6,14,158],"genomes":[7],"has":[8],"expanded":[9],"the":[10,95,156],"accessible":[11],"landscape":[12],"genetic":[15],"variation,":[16],"yet":[17],"benchmark":[18,60],"resources":[19],"remain":[20],"limited":[21],"to":[22],"conventional":[23,135],"high-confidence":[24],"regions":[25,123],"defined":[26],"by":[27,49,134],"existing":[28],"reference":[29,57,84],"frameworks.":[30],"Here,":[31],"we":[32],"generated":[33],"a":[34,41,62,143],"near-perfect":[35,55],"diploid":[36,112],"T2T":[37,56,92],"genome":[38,88,107,149],"(T2T-LIN)":[39],"from":[40],"Chinese":[42],"individual":[43,100],"and":[44,74,103,113,120,139,151],"established":[45],"assembly-based":[46],"truth":[47],"sets":[48],"comparison":[50],"with":[51,69],"T2T-YAO,":[52],"an":[53],"ancestry-matched":[54,90],"genome.":[58,159],"showed":[61],"heterozygous/homozygous":[63],"SNV":[64],"ratio":[65],"~2,":[67],"consistent":[68],"expectations":[70],"under":[71],"Hardy\u2013Weinberg":[72],"equilibrium,":[73],"enabled":[75,104],"genome-wide":[76],"evaluation":[77],"reference-dependent":[79,148],"biases.":[80],"We":[81],"found":[82],"that":[83,131],"choice":[85],"substantially":[86],"influences":[87],"interpretation:":[89],"linear":[91],"references":[93],"provided":[94],"most":[96],"faithful":[97],"representation":[98],"genomic":[101],"variation":[102],"more":[105],"accurate":[106],"reconstruction":[108],"than":[109],"unmatched":[110],"linear,":[111],"graph-based":[114],"references.":[115],"Benchmarking":[116],"previously":[117],"inaccessible":[118],"repetitive":[119],"structurally":[121],"complex":[122],"revealed":[124],"substantial":[125],"limitations":[126],"current":[128],"variant":[129,152],"callers":[130],"were":[132],"masked":[133],"metrics.":[136],"T2T-LIN":[138],"YAO-LIN":[140],"benchmarks":[141],"establish":[142],"T2T-era":[144],"framework":[145],"for":[146],"evaluating":[147],"interpretation":[150],"discovery":[153],"across":[154],"nearly":[155],"complete":[157]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-12T00:00:00"}
