{"id":"https://openalex.org/W7213513191","doi":"https://doi.org/10.48550/arxiv.2609.17801","title":"GIA: Germline-Informed Aging with AlphaGenome Finds Genetically Regulated CpGs","display_name":"GIA: Germline-Informed Aging with AlphaGenome Finds Genetically Regulated CpGs","publication_year":2026,"publication_date":"2026-09-15","ids":{"openalex":"https://openalex.org/W7213513191","doi":"https://doi.org/10.48550/arxiv.2609.17801"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2609.17801","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.17801","pdf_url":"https://arxiv.org/pdf/2609.17801","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2609.17801","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5152010147","display_name":"Sean Lim","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lim, Sean","raw_affiliation_strings":["Wiess School of Natural Sciences , Rice University , Houston , Texas , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wiess School of Natural Sciences , Rice University , Houston , Texas , USA","institution_ids":["https://openalex.org/I74775410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5152010147"],"corresponding_institution_ids":["https://openalex.org/I74775410"],"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9951000213623047,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9951000213623047,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.002300000051036477,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0003000000142492354,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/epigenetic-clocks","display_name":"epigenetic clocks","score":0.949999988079071},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.9449999928474426},{"id":"https://openalex.org/keywords/germline-genetic-variation","display_name":"germline genetic variation","score":0.9120000004768372},{"id":"https://openalex.org/keywords/methylation-quantitative-trait-loci","display_name":"methylation quantitative trait loci","score":0.906000018119812},{"id":"https://openalex.org/keywords/alphagenome","display_name":"AlphaGenome","score":0.6740000247955322},{"id":"https://openalex.org/keywords/fhl2","display_name":"FHL2","score":0.75},{"id":"https://openalex.org/keywords/chromatin-accessibility","display_name":"chromatin accessibility","score":0.9359999895095825},{"id":"https://openalex.org/keywords/blood-dna-methylation","display_name":"blood DNA methylation","score":0.6880000233650208},{"id":"https://openalex.org/keywords/aging","display_name":"aging","score":0.4650000035762787}],"concepts":[{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.8474000096321106},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7742000222206116},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7445999979972839},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6740000247955322},{"id":"https://openalex.org/C109825262","wikidata":"https://www.wikidata.org/wiki/Q1139164","display_name":"Germline","level":3,"score":0.5472000241279602},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5374000072479248},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5109000205993652},{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.498199999332428},{"id":"https://openalex.org/C81941488","wikidata":"https://www.wikidata.org/wiki/Q853421","display_name":"Quantitative trait locus","level":3,"score":0.4925000071525574},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.3955000042915344},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3882000148296356},{"id":"https://openalex.org/C47042493","wikidata":"https://www.wikidata.org/wiki/Q265799","display_name":"Human genetics","level":3,"score":0.3330000042915344},{"id":"https://openalex.org/C84597430","wikidata":"https://www.wikidata.org/wiki/Q106227","display_name":"Locus (genetics)","level":3,"score":0.3305000066757202},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.3127000033855438},{"id":"https://openalex.org/C168393362","wikidata":"https://www.wikidata.org/wiki/Q5421706","display_name":"Expression quantitative trait loci","level":5,"score":0.2989000082015991},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.2985999882221222},{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.28769999742507935},{"id":"https://openalex.org/C2780336964","wikidata":"https://www.wikidata.org/wiki/Q3746807","display_name":"Flowering Locus C","level":5,"score":0.27950000762939453},{"id":"https://openalex.org/C38606739","wikidata":"https://www.wikidata.org/wiki/Q5121352","display_name":"Circadian clock","level":3,"score":0.2741999924182892},{"id":"https://openalex.org/C51255272","wikidata":"https://www.wikidata.org/wiki/Q550479","display_name":"Quantitative genetics","level":4,"score":0.2639000117778778},{"id":"https://openalex.org/C9287583","wikidata":"https://www.wikidata.org/wiki/Q5532883","display_name":"Genetic architecture","level":4,"score":0.2508000135421753}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2609.17801","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.17801","pdf_url":"https://arxiv.org/pdf/2609.17801","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2609.17801","doi":"https://doi.org/10.48550/arxiv.2609.17801","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2609.17801","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2609.17801","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.17801","pdf_url":"https://arxiv.org/pdf/2609.17801","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"score":0.46810001134872437,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7213513191.pdf","grobid_xml":"https://content.openalex.org/works/W7213513191.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1974047233","https://openalex.org/W1978813754","https://openalex.org/W2017502278","https://openalex.org/W2110065044","https://openalex.org/W2121091193","https://openalex.org/W2131442620","https://openalex.org/W2269937153","https://openalex.org/W2291827855","https://openalex.org/W2316537321","https://openalex.org/W2332043828","https://openalex.org/W2463513647","https://openalex.org/W2883262856","https://openalex.org/W2912654909","https://openalex.org/W2949100461","https://openalex.org/W2969128479","https://openalex.org/W3022131036","https://openalex.org/W3113754461","https://openalex.org/W3177165321","https://openalex.org/W4205358347","https://openalex.org/W4285492214","https://openalex.org/W4386226623","https://openalex.org/W4391027505","https://openalex.org/W4396773086","https://openalex.org/W4415849457","https://openalex.org/W4416704614","https://openalex.org/W7125967877"],"related_works":["https://openalex.org/W4405385114","https://openalex.org/W4415639507","https://openalex.org/W7167626955","https://openalex.org/W4403540848","https://openalex.org/W4407029004","https://openalex.org/W4414966627","https://openalex.org/W3112074028","https://openalex.org/W4386226623","https://openalex.org/W4391027505","https://openalex.org/W4300817285"],"abstract_inverted_index":{"Epigenetic":[0],"clocks":[1,69],"estimate":[2],"age":[3],"and":[4,77,144],"aging-related":[5,50],"phenotypes":[6],"from":[7,65],"DNA":[8],"methylation":[9,30,72,113,156],"at":[10,31,132],"selected":[11,64],"CpG":[12],"sites,":[13],"but":[14],"the":[15],"extent":[16],"to":[17,70,95,135],"which":[18],"these":[19],"inputs":[20],"are":[21,115],"influenced":[22,117],"by":[23,118,123,160],"germline":[24,119],"genetic":[25,46,80,120],"variation":[26,39,153],"is":[27,34],"unclear.":[28],"Because":[29],"many":[32],"CpGs":[33,63,88],"genetically":[35],"regulated,":[36],"some":[37],"between-person":[38],"in":[40],"clock":[41,87,108,172],"estimates":[42,173],"may":[43,154],"reflect":[44],"inherited":[45,152],"differences":[47],"rather":[48],"than":[49],"change":[51],"alone.":[52],"Here":[53],"we":[54],"developed":[55],"GIA":[56],"(Germline-Informed":[57],"Aging),":[58],"a":[59,129],"framework":[60],"that":[61,86,111],"maps":[62],"13":[66],"published":[67],"epigenetic":[68,161],"blood":[71,92,137],"quantitative":[73],"trait":[74],"loci":[75],"(meQTLs)":[76],"scores":[78],"associated":[79],"variants":[81,169],"with":[82],"AlphaGenome.":[83],"We":[84],"show":[85],"were":[89],"enriched":[90],"for":[91],"meQTLs":[93],"relative":[94],"matched":[96],"unused":[97],"Illumina":[98],"450k":[99],"probes":[100],"(62.7%":[101],"versus":[102],"39.6%;":[103],"OR":[104],"2.57),":[105],"across":[106],"multiple":[107],"families,":[109],"suggesting":[110],"age-informative":[112],"sites":[114],"heavily":[116],"variation.":[121],"Ranking":[122],"predicted":[124,134],"chromatin":[125,138],"effect":[126],"isolated":[127],"rs10190186,":[128],"cis-acting":[130],"variant":[131],"FHL2":[133,145],"increase":[136],"accessibility":[139],"(ATAC":[140],"+1.00;":[141],"DNase":[142],"+1.64)":[143],"RNA":[146],"(+0.30).":[147],"This":[148],"locus":[149],"illustrates":[150],"how":[151],"shape":[155],"features":[157],"repeatedly":[158],"used":[159],"clocks,":[162],"motivating":[163],"direct":[164],"tests":[165],"of":[166],"whether":[167],"such":[168],"shift":[170],"baseline":[171],"or":[174],"longitudinal":[175],"aging":[176],"trajectories.":[177]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-09-18T00:00:00"}