ArticleHGG advances2025
A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery.
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19citing papers in PubMed
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19 citing papers in PubMed.
- PhenoSS: phenotype semantic similarity-based approach for rare disease prediction and patient clustering.Journal of the American Medical Informatics Association : JAMIA · 2026Article
- A text mining and ontology-based approach using phenotypes to obtain relevant literature for rare diseases.iScience · 2026Article
- RankVar: machine learning-based variant ranking and reinterpretation for rare genetic diseases.Genome medicine · 2026Article
- PheBee: A Graph-Aware System for Scalable, Traceable, and Semantic Phenotyping.medRxiv : the preprint server for health sciences · 2026Article
- PhenoSS: Phenotype semantic similarity-based approach for rare disease prediction and patient clustering.medRxiv : the preprint server for health sciences · 2026Article
- Systematic benchmarking demonstrates large language models have not reached the diagnostic accuracy of traditional rare-disease decision support tools.European journal of human genetics : EJHG · 2026Article
- Phenotype-first patient matching with SimPheny identifies diagnostic candidates beyond curated gene associations.medRxiv : the preprint server for health sciences · 2026Article
- GA4GH phenopacket-driven characterization of genotype-phenotype correlations in Mendelian disorders.American journal of human genetics · 2026Article
- Performance of Information Theory Derived: Semantic Similarity Algorithms for Differential Diagnosis and Clustering.bioRxiv : the preprint server for biology · 2025Article
- RareLink: scalable REDCap-based framework for rare disease interoperability linking international registries to FHIR and Phenopackets.NPJ genomic medicine · 2025Article
- Consistent performance of large language models in rare disease diagnosis across ten languages and 4917 cases.EBioMedicine · 2025Article
- Oncopacket: integration of cancer research data using GA4GH phenopackets.Bioinformatics (Oxford, England) · 2025Article
- Inborn errors of immunity: Manifestation, treatment, and outcome-an ESID registry 1994-2024 report on 30,628 patients.Journal of human immunity · 2025Article
- PhenoDP: leveraging deep learning for phenotype-based case reporting, disease ranking, and symptom recommendation.Genome medicine · 2025Article
- Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework.BMC bioinformatics · 2025Article
- Consistent Performance of GPT-4o in Rare Disease Diagnosis Across Nine Languages and 4967 Cases.medRxiv : the preprint server for health sciences · 2025Article
- An ontology-based rare disease common data model harmonising international registries, FHIR, and Phenopackets.Scientific data · 2025Article
- Leveraging clinical intuition to improve accuracy of phenotype-driven prioritization.Genetics in medicine : official journal of the American College of Medical Genetics · 2025Article
- Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond.BMC bioinformatics · 2024Article
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Authors and funding
35 authors.
Daniel DanisBerlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington CT 06032, USA.
Michael J BamshadDepartment of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98195, USA.
Yasemin BridgesWilliam Harvey Research Institute, Queen Mary University of London, London, UK.
Andrés Caballero-OteyzaClinic for Immunology and Rheumatology, Hanover Medical School, Hanover, Germany; RESiST-Cluster of Excellence 2155, Hanover Medical School, Hanover, Germany.
Pilar CacheiroWilliam Harvey Research Institute, Queen Mary University of London, London, UK.
Leigh C CarmodyThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington CT 06032, USA.
Leonardo ChimirriBerlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
Jessica X ChongDepartment of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA 98195, USA.
Ben ColemanThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington CT 06032, USA.
Raymond DalgleishDepartment of Genetics, Genomics and Cancer Sciences, University of Leicester, Leicester, UK.
Peter J FreemanDivision of Informatics, Imaging and Data Science, The University of Manchester, Manchester, UK.
Adam S L GraefeBerlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
Tudor GrozaRare Care Centre, Perth Children's Hospital, Nedlands, WA 6009, Australia; SingHealth Duke-NUS Institute of Precision Medicine, 5 Hospital Drive Level 9, Singapore 169609, Singapore; Telethon Kids Institute, Nedlands, WA 6009, Australia.
Peter HansenBerlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
Julius O B JacobsenWilliam Harvey Research Institute, Queen Mary University of London, London, UK.
Adam KlocperkDepartment of Immunology, 2nd Faculty of Medicine, Charles University and University Hospital in Motol, Prague, Czech Republic.
Maaike KustersDepartment of Paediatric Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; University College London Institute of Child Health, London, UK.
Markus S LadewigDepartment of Ophthalmology, University Clinic Marburg - Campus Fulda, Fulda, Germany.
Allison J MarcelloDepartment of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA 98195, USA.
Teresa MattinaMedica Genetics University of Catania Italy, Catania, Italy; Morgagni Foundation and Clinic, Catania, Italy.
Christopher J MungallDivision of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Monica C Munoz-TorresDepartment of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Justin T ReeseDivision of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Filip RehburgBerlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
Bárbara C S ReisDepartment of Allergy and Immunology, National Institute of Women's, Children's and Adolescents' Health Fernandes Figueira, Rio de Janeiro, Brazil; High Complexity Laboratory, National Institute of Women's, Children's and Adolescents' Health Fernandes Figueira, Rio de Janeiro, Brazil.
Catharina SchuetzDepartment of Pediatrics, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; University Center for Rare Diseases, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; German Center for Child and Adolescent Health (DZKJ), partner site Leipzig/Dresden, Dresden, Germany.
Damian SmedleyWilliam Harvey Research Institute, Queen Mary University of London, London, UK.
Timmy StraussDepartment of Pediatrics, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; University Center for Rare Diseases, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
Jagadish Chandrabose SundaramurthiThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington CT 06032, USA.
Sylvia ThunBerlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
Kyran WissinkBerlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Utrecht University, Utrecht, the Netherlands.
John F WagstaffDepartment of Genetics, Genomics and Cancer Sciences, University of Leicester, Leicester, UK.
David ZoccheNorth West Thames Regional Genetics Service, Northwick Park & St Mark's Hospitals, London, UK.
Melissa A HaendelUniversity of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Peter N RobinsonBerlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington CT 06032, USA; ELLIS-European Laboratory for Learning and Intelligent Systems. Electronic address: peter.robinson@bih-charite.de.
Funding
UNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Hazel B Nichols · 2001 to 2026
$36.3MThe Monarch Initiative: Linking Diseases to Model Organism ResourcesR24OD011883 · OD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAENDEL, MELISSA A, MUNGALL, CHRISTOPHER J · 2012 to 2024
$16.0MUniversity of Washington Mendelian Genomics Research Center (UW-MGRC)U01HG011744 · NHGRI · UNIVERSITY OF WASHINGTON · PI MICHAEL Joseph BAMSHAD, Evan Eichler · 2021 to 2026
$15.8MImprovements to the LinkML framework to support the Phenomics First open science resourceRM1HG010860 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAENDEL, MELISSA A, MUNGALL, CHRISTOPHER J · 2020 to 2024
$10.3MThe Human Phenotype Ontology: Accelerating Computational Integration of Clinical Data for GenomicsU24HG011449 · NHGRI · JACKSON LABORATORY · PI Peter Nicholas Robinson · 2021 to 2026
$6.7MIncreasing the Yield and Utility of Pediatric Genomic Medicine with ExomiserR01HD103805 · NICHD · JACKSON LABORATORY · PI Valentina Cipriani, CHRISTOPHER J MUNGALL · 2021 to 2026
$4.3MA next-generation morbid map of the human genomeR35HG011297 · NHGRI · UNIVERSITY OF WASHINGTON · PI CHONG, JESSICA XIAO-LING · 2020 to 2024
$2.2MNHGRI NIH HHS R35 HG011297NHGRI NIH HHS RM1 HG010860NHGRI NIH HHS U01 HG011744NHGRI NIH HHS U24 HG011449NICHD NIH HHS R01 HD103805NIEHS NIH HHS P30 ES010126NIH HHS R24 OD011883
Abstract
The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 and approved by ISO as a standard for sharing clinical and genomic information about an individual, including phenotypic descriptions, numerical measurements, genetic information, diagnoses, and treatments. A phenopacket can be used as an input file for software that supports phenotype-driven genomic diagnostics and for algorithms that facilitate patient classification and stratification for identifying new diseases and treatments. There has been a great need for a collection of phenopackets to test software pipelines and algorithms. Here, we present Phenopacket Store. Phenopacket Store v.0.1.19 includes 6,668 phenopackets representing 475 Mendelian and chromosomal diseases associated with 423 genes and 3,834 unique pathogenic alleles curated from 959 different publications. This represents the first large-scale collection of case-level, standardized phenotypic information derived from case reports in the literature with detailed descriptions of the clinical data and will be useful for many purposes, including the development and testing of software for prioritizing genes and diseases in diagnostic genomics, machine learning analysis of clinical phenotype data, patient stratification, and genotype-phenotype correlations. This corpus also provides best-practice examples for curating literature-derived data using the GA4GH Phenopacket Schema.
Indexed as
GenomicsPhenotypeDatabases, GeneticHumansSoftwareglobal alliance for genomics and healthhuman phenotype ontologyphenopacket schema
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.