Pedigree Standard Roadmap Planning
- Do you feel like we’ve successfully reached our goals from the 2020 roadmap? What has been completed and can be removed?
- Is the product description from the 2020 roadmap still accurate?
- What needs further development or attention? What could we be doing better?
- What new activities would we like to pursue?
- Eg. This can include implementation/outreach activities like manuscripts, webinars, blog posts, etc.
FEEDBACK / IDEAS BOX
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Roadmap Template
Pedigree | ||
Technical Specification ❑ API ☑ Data Model / Ontology ❑ Protocol ❑ File Format Policy Framework ❑ Policy Framework | Resource ☑ Guide ❑ Technical Toolkit ❑ Ongoing Project ❑ Other (Please Specify) | |
Description | The GA4GH Pedigree Standard allows for the computable exchange of family health history as well as representation of larger, more complex families. The collection of specific clinical or genetic data is outside the scope of this deliverable, and is instead handled by other formats through references to individuals within the pedigree representation. It is intended to fit within the structure of other standards like HL7 FHIR and Phenopackets. The need for high quality, unambiguous, computable pedigree and family information is critical for scaling genomic analysis to larger, complex families. Pedigree data is currently represented in heterogeneous formats that frequently result in the use of lowest-common-denominator formats (e.g., PED) or custom JSON formats for data transfer. The HL7 FHIR standard core data models do not support pedigrees, but there is a draft extension to support genomic pedigrees that was evaluated. Standardizing the way systems represent family structure will allow patients to share this information more easily between healthcare systems and help software tools to use this information to improve genome analysis and diagnosis. | |
Source Driver Projects | Australian Genomics H3Africa GEM Japan Monarch Initiative BRCA Challenge | |
Other communities that will contribute to development | KidsFirst DRC Software vendors (PhenoTips, TrakGene...) | |
Proposed Implementations (at least 2) |
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Deliverables (add additional rows if required) (see taxonomy) | Description | Expected Completion Date (by quarter) |
Deliverable: Conceptual Model v1.0 | To support the interoperability of family health history data within and between existing standards (such as HL7 FHIR and Phenopackets), the GA4GH Clinical and Phenotypic Data Capture Workstream developed the Pedigree Conceptual Model. The Pedigree Conceptual Model defines core classes and their properties, and is based on A Recommendation for The Common Data Set for Family Health History (see below). The three main classes are Individual, Relationship and Pedigree. | Sept. 2022 |
Deliverable: KIN Ontology | The Kinship Ontology (KIN) is a family relations ontology developed as part of the Global Alliance for Genomics and Health Pedigree Standard project. It allows using an OWL reasoner to automatically validate a family history graph and infer new relations. The latest version of the ontology can be found at: http://purl.org/ga4gh/kin.owl The Ontology is open-source and managed in this GitHub repo: https://github.com/GA4GH-Pedigree-Standard/family_history_terminology | Sept. 2022 |
Deliverable: Common Dataset | The collection and use of family health histories span medical activities from genetic research to heritable risk assessment in patient care. For all the stakeholders in this process, the goal must be data that is accurate and coded for effective analysis, and transferable between systems. To achieve this, a globally accepted and universally implemented family health history (FHH) data set should be established as a benchmark. The purpose of the common dataset document is to create an updated recommended data set that can be used not only in both research and clinical settings, but to eliminate the gap between the two disciplines. This recommendation should also guide the development of research, clinical, and patient-facing FHH data and information collection tools, applications, and data repositories. This document should only be used as informative. | Sept. 2022 |
Deliverable: Implementation within existing models
| The working group will prepare implementations and implementation guides of the common dataset elements across commonly-used data modeling systems, specifically HL7 FHIR, Phenopackets, and RDF. This will support the use of interoperable pedigree data across these ecosystems.
| Sept. 2022 + additional implementations in 2023 |
Deliverable: Tools
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| Sept. 2022 Q2 2023 Q3 2023 |
Deliverable: Outreach/ Implementation Support
| Activities focused on promoting and supporting the use of the standard and common dataset within the broader community and ecosystem of vendors.
| Q1 2023 Q2 2023 Q2 2023 Q3 2023 |
Projected Submission Date | —--- | —--- |
2020/2021 Roadmap
Pedigree | ||
☑ In Progress/Planned (included on current Strategic Roadmap) ❑ New Version (approved deliverables where a new version is planned) ❑ New Deliverable (not on the current Strategic Roadmap) | ||
Description | The need for high quality, unambiguous, computable pedigree and family information is critical for scaling genomic analysis to larger, complex families. Pedigree data is currently represented in heterogeneous formats that frequently result in the use of lowest-common-denominator formats (e.g., PED) or custom JSON formats for data transfer. The HL7 FHIR standard core data models do not support pedigrees, but there is a draft extension to support genomic pedigrees that should be evaluated and potentially extended by the GA4GH. Standardizing the way systems represent family structure will allow patients to share this information more easily between healthcare systems and help software tools to use this information to improve genome analysis and diagnosis. | |
Source Driver Projects | AGHA Genomics England Monarch Initiative | |
Other communities that will contribute to development | KidsFirst DRC H3Africa EGA SPHN BRCA Challenge GEM Japan Software vendors (PhenoTips, ...) | |
Proposed Implementations (at least 2) |
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Expected Completion Date | 2021-09-01 | |
Milestone (add additional rows if required) (see taxonomy) | Description | Expected Completion Date (by quarter) |
Milestone 1: Landscape Analysis | Stakeholders engagement M1.1 Engagement of key pedigree data producers (EHRs, vendors) and consumers (projects, tools, analyses) within the GA4GH to motivate the need for export and interoperability M1.2 Compilation of difficult family history cases from stakeholders (e.g., 3-person IVF, 2 pairs of identical twins, multiple loops of consang., etc.) M1.3 Gap analysis of existing formats and APIs to represent these cases | 2020-Q1 |
Milestone 2: Draft specification | Development of a draft standard for pedigree data exchange M1.1 Creation of working group to incubate the technical standard development M1.2 Invite GA4GH stakeholders to join working group and participate in the early development and pilot implementation M1.3 Development of draft specification / implementation guide | 2020-Q3 |
Milestone 3: Implementation | Interoperability pilot M3.1 Compliance test suite implementation M3.2 Two implementations of draft specification that pass compliance tests (potential parties: EHR, patient-facing vendor, clinical-facing vendor, CDS, research system); shoot for end-to-end: patient survey → clinical system → CDS → clinical system → research system | 2021-Q3 |
Projected Submission Date | 2021-09-01 | 2021-Q3 |