TY - JOUR
T1 - A corpus of GA4GH phenopackets
T2 - Case-level phenotyping for genomic diagnostics and discovery
AU - Danis, Daniel
AU - Bamshad, Michael J.
AU - Bridges, Yasemin
AU - Caballero-Oteyza, Andrés
AU - Cacheiro, Pilar
AU - Carmody, Leigh C.
AU - Chimirri, Leonardo
AU - Chong, Jessica X.
AU - Coleman, Ben
AU - Dalgleish, Raymond
AU - Freeman, Peter J.
AU - Graefe, Adam S.L.
AU - Groza, Tudor
AU - Hansen, Peter
AU - Jacobsen, Julius O.B.
AU - Klocperk, Adam
AU - Kusters, Maaike
AU - Ladewig, Markus S.
AU - Marcello, Anthony J.
AU - Mattina, Teresa
AU - Mungall, Christopher J.
AU - Munoz-Torres, Monica C.
AU - Reese, Justin T.
AU - Rehburg, Filip
AU - Reis, Bárbara C.S.
AU - Schuetz, Catharina
AU - Smedley, Damian
AU - Strauss, Timmy
AU - Sundaramurthi, Jagadish Chandrabose
AU - Thun, Sylvia
AU - Wissink, Kyran
AU - Wagstaff, John F.
AU - Zocche, David
AU - Haendel, Melissa A.
AU - Robinson, Peter N.
N1 - Publisher Copyright:
© 2024 The Author(s)
PY - 2025/1/9
Y1 - 2025/1/9
N2 - 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.
AB - 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.
KW - global alliance for genomics and health
KW - human phenotype ontology
KW - phenopacket schema
UR - http://www.scopus.com/inward/record.url?scp=85207758619&partnerID=8YFLogxK
U2 - 10.1016/j.xhgg.2024.100371
DO - 10.1016/j.xhgg.2024.100371
M3 - Article
C2 - 39394689
AN - SCOPUS:85207758619
SN - 2666-2477
VL - 6
SP - 1
EP - 7
JO - Human Genetics and Genomics Advances
JF - Human Genetics and Genomics Advances
IS - 1
M1 - 100371
ER -