Development and application of a computable genotype model in the GA4GH Variation Representation Specification

Goar, Wesley; Babb, Lawrence; Chamala, Srikar; Cline, Melissa; Freimuth, Robert R.; Hart, Reece K.; Kuzma, Kori; Lee, Jennifer; Nelson, Tristan; Prlić, Andreas; Riehle, Kevin; Smith, Anastasia; Stahl, Kathryn; Yates, Andrew D; Rehm, Heidi L.; Wagner, Alex H.

doi:10.1142/9789811270611_0035

Cited by 1 publication

(2 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…11 The Phenopacket Schema integrates a version of the GA4GH Variant Representation Specification and is designed to be interoperable with other GA4GH standards, including those for pedigree data. 12 The Phenopacket Schema aims to represent data from different sources, including data from EHRs, research studies, data entry tools, or published case reports, in a consistent and computable format to enable the sharing and integration of structured clinical data. The core principles of the schema include composability, traceability (data provenance), the FAIR principles (Findable, Accessible, Interoperable, and Reusable), and computability.…”

Section: Main Textmentioning

confidence: 99%

See 1 more Smart Citation

A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery

Danis,

Bamshad,

Bridges

et al. 2024

Preprint

View full text Add to dashboard Cite

SummaryThe 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. Version 0.1.12 of phenopacket-store includes 4916 phenopackets representing 277 Mendelian and chromosomal diseases associated with 236 genes, and 2872 unique pathogenic alleles curated from 605 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.

show abstract

Section: Main Textmentioning

confidence: 99%

Section: Main Textmentioning

confidence: 99%