A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery
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.
Authors
- Pilar Cacheiro (ORCID: https://orcid.org/0000-0002-6335-8208)
- Chris Mungall (ORCID: https://orcid.org/0000-0002-6601-2165)
- David Zocche (ORCID: https://orcid.org/0000-0003-1390-0334)
- Andrés Caballero-Oteyza (ORCID: https://orcid.org/0000-0002-8892-1255)
- Anthony J. Marcello
- Damian Smedley (ORCID: https://orcid.org/0000-0002-5836-9850)
- Tudor Groza (ORCID: https://orcid.org/0000-0003-2267-8333)
- Bárbara Carvalho Santos dos Reis (ORCID: https://orcid.org/0000-0001-9725-9665)
- Markus S. Ladewig (ORCID: https://orcid.org/0000-0002-6601-4486)
- Raymond Dalgleish (ORCID: https://orcid.org/0000-0001-7667-187X)
- Timmy Strauß (ORCID: https://orcid.org/0000-0001-9969-9517)
- Peter N. Robinson (ORCID: https://orcid.org/0000-0002-0736-9199)
- Daniel Daniš (ORCID: https://orcid.org/0000-0003-0900-3411)
- Sylvia Thun (ORCID: https://orcid.org/0000-0002-3346-6806)
- Jagadish Chandrabose Sundaramurthi (ORCID: https://orcid.org/0000-0002-6670-9157)
- Melissa Haendel (ORCID: https://orcid.org/0000-0001-9114-8737)
- Jessica X. Chong (ORCID: https://orcid.org/0000-0002-1616-2448)
- J. Wagstaff (ORCID: https://orcid.org/0000-0002-9745-2462)
- Justin Reese (ORCID: https://orcid.org/0000-0002-2170-2250)
- Peter Freeman (ORCID: https://orcid.org/0000-0002-5838-5404)
- Julius O.B. Jacobsen (ORCID: https://orcid.org/0000-0002-3265-1591)
- Maaike Kusters (ORCID: https://orcid.org/0000-0001-7601-9822)
- Leonardo Chimirri (ORCID: https://orcid.org/0000-0002-6912-8518)
- Teresa Mattina (ORCID: https://orcid.org/0000-0001-6143-6682)
- Leigh Carmody (ORCID: https://orcid.org/0000-0001-7941-2961)
- Ben Coleman (ORCID: https://orcid.org/0000-0002-4422-1708)
- Adam Klocperk (ORCID: https://orcid.org/0000-0002-1526-4557)
- Yasemin Bridges (ORCID: https://orcid.org/0009-0002-1371-3782)
- Adam S L Graefe (ORCID: https://orcid.org/0009-0004-8124-8864)
- Filip Rehburg (ORCID: https://orcid.org/0009-0007-0457-5724)
- Kyran Wissink
- Peter Hansen (ORCID: https://orcid.org/0000-0001-5535-2845)
- Catharina Schuetz (ORCID: https://orcid.org/0000-0001-8731-8924)
- Monica C. Munoz-Torres
- Michael J Bamshad
Institutions
- Seattle Pacific University (US)
- University of North Carolina at Chapel Hill (US)
- Seattle Children's Hospital (US)
- Children’s Institute (US)
- Lawrence Berkeley National Laboratory (US)
- University of Leicester (GB)
- SingHealth (SG)
- Queen Mary University of London (GB)
- The Kids Research Institute Australia (AU)
- Utrecht University (NL)
- University of Washington (US)
- Charles University (CZ)
- Great Ormond Street Hospital for Children NHS Foundation Trust (GB)
- Princess Margaret Hospital for Children (AU)
- University of Manchester (GB)
- Medizinische Hochschule Hannover (DE)
- University of Catania (IT)
- University Hospital in Motol (CZ)
- Jackson Laboratory (US)
- Duke-NUS Medical School (SG)
- Brotman Baty Institute (US)
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
- William Harvey Research Institute (GB)
- Genomics (United Kingdom) (GB)
- St Mark's Hospital (GB)
- University Hospital Carl Gustav Carus (DE)
- University College London (GB)
- University of Colorado Anschutz Medical Campus (US)
- University of Tennessee at Knoxville (US)
- Technische Universität Dresden (DE)
Publication Details
- Journal
- Human Genetics and Genomics Advances
- Published
- 2024-10-10
- DOI
- https://doi.org/10.1016/j.xhgg.2024.100371
- Citations
- 11
- Primary Topic
- Genomics and Rare Diseases
- Type
- article
- Field-Weighted Citation Impact
- 6.05
Funders
- U.S. Department of Energy
- Alexander von Humboldt-Stiftung
- National Institutes of Health
- Office of Science
- Medical Research Council
- National Human Genome Research Institute
- National Institute of Child Health and Human Development
- Basic Energy Sciences
- Eunice Kennedy Shriver National Institute of Child Health and Human Development