Representing Personal Genomic History

Type	Standard / Implementation Specification	Standards Process Maturity	Implementation Maturity	Federally required	Cost	Test Tool Availability
Standard for observations	Human Phenotype Ontology (HPO)	Final	Production	No	Free	No
Standard for observations	HGVS Nomenclature	Final	Production	No	Free	No
Standard for observations	HUGO Gene Nomenclature Committee	Final	Production	No	Free	No
Standard for observations	LOINC®	Final	Production	No	Free	No
Standard for observations	SNOMED CT® U.S. Edition	Final	Production	No	Free	No

Limitations, Dependencies, and Preconditions for Consideration	Applicable Value Set(s) and Starter Set(s)
The Assistant Secretary for Technology Policy (ASTP), in partnership with the National Institutes of Health (NIH), created Sync for Genes to strengthen genomic data sharing, a key component of the Precision Medicine Initiative. This project is also aligned with the recommendations made by the Precision Medicine Task Force under the Health IT Standards Committee (HITSC) to advance data standards, address relevant privacy policies, and advance innovations in health IT that support precision medicine. Sync for Genes is the first step toward integrating clinical genomics into the point-of-care by expediting the use of standards, such as Health Level 7 (HL7) Fast Healthcare Interoperability Resource (FHIR), to enable and improve patient’s ability to seamlessly share their genomics information via point-of-care applications, such as application programming interfaces (APIs). Sync for Genes supports a critical element of sharing genomic data amplifying the ability to seamlessly share genomic information for research and commercial purposes. Below are the HL7 FHIR Clinical Genomic profiles that were tested as part of the Sync for Genes work: Family Health History Genetics https://www.hl7.org/fhir/pushpull.html Sequencing Quality and Regulatory Genomics https://www.hl7.org/fhir/STU3/sequence.html https://www.hl7.org/fhir/STU3/bundle.html https://www.hl7.org/fhir/STU3/capabilitystatement.html Activities with Global Alliance for Genomics and Health (GA4GH) is an international community dedicated to advancing human health through genomic data. They build technical standards and policy frameworks and tools that will expand responsible, voluntary, and secure use of genomic and other related health data. Categorical Variation Representation Specification (Cat-VRS) Variant Annotation Specification (VA-Spec). The Monarch Initiative maintains the Human Phenotype Ontology (HPO) which provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality. The Human Genome Organization (HUGO) Gene Nomenclature Committee maintains the HUGO Gene Nomenclature and approves gene names and symbols (short-form abbreviation) for each known human gene. The Human Genome Variation Society (HGVS) Variant Nomenclature Committee (HVNC), under the auspices of the HUGO Gene Nomenclature committee maintains the HGVS Nomenclature. The National Library of Medicine National Center for Biotechnology Information (NLM NCBI) maintains the Reference Sequence Database - a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic DNA, transcripts, and proteins. NLM NCBI maintains dbVAR, a database of human genomic structural variation. Implementation information for Personal Genomic History exchange can be found in Content/Structure	For genomic data: Specified data elements of genomics include the following: Gene Studied Variant Data Variant Interpretation Variant Type Molecular Consequence Variant Clinical Significance

Limitations, Dependencies, and Preconditions for Consideration

Applicable Value Set(s) and Starter Set(s)

The Assistant Secretary for Technology Policy (ASTP), in partnership with the National Institutes of Health (NIH), created Sync for Genes to strengthen genomic data sharing, a key component of the Precision Medicine Initiative. This project is also aligned with the recommendations made by the Precision Medicine Task Force under the Health IT Standards Committee (HITSC) to advance data standards, address relevant privacy policies, and advance innovations in health IT that support precision medicine. Sync for Genes is the first step toward integrating clinical genomics into the point-of-care by expediting the use of standards, such as Health Level 7 (HL7) Fast Healthcare Interoperability Resource (FHIR), to enable and improve patient’s ability to seamlessly share their genomics information via point-of-care applications, such as application programming interfaces (APIs). Sync for Genes supports a critical element of sharing genomic data amplifying the ability to seamlessly share genomic information for research and commercial purposes. Below are the HL7 FHIR Clinical Genomic profiles that were tested as part of the Sync for Genes work:
- Family Health History Genetics
  - https://www.hl7.org/fhir/pushpull.html
- Sequencing Quality and Regulatory Genomics
Activities with Global Alliance for Genomics and Health (GA4GH) is an international community dedicated to advancing human health through genomic data. They build technical standards and policy frameworks and tools that will expand responsible, voluntary, and secure use of genomic and other related health data.
- Categorical Variation Representation Specification (Cat-VRS)
- Variant Annotation Specification (VA-Spec).
The Monarch Initiative maintains the Human Phenotype Ontology (HPO) which provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality.
The Human Genome Organization (HUGO) Gene Nomenclature Committee maintains the HUGO Gene Nomenclature and approves gene names and symbols (short-form abbreviation) for each known human gene.
The Human Genome Variation Society (HGVS) Variant Nomenclature Committee (HVNC), under the auspices of the HUGO Gene Nomenclature committee maintains the HGVS Nomenclature.
The National Library of Medicine National Center for Biotechnology Information (NLM NCBI) maintains the Reference Sequence Database - a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic DNA, transcripts, and proteins.
NLM NCBI maintains dbVAR, a database of human genomic structural variation.

Implementation information for Personal Genomic History exchange can be found in Content/Structure

For genomic data: Specified data elements of genomics include the following:

Form Guide

1. Optional: Background Text / Cover Letter

The "Optional Background Text / Cover Letter" field provides space for additional context or introductory information related to your comment.

This field is entirely optional and serves the following purposes:

Provides context for reviewers
Serves as an introduction if submitting multiple comments
Functions as a cover letter for formal submissions

If you are submitting a single comment for a specific data class or element, you may leave this field blank. For multiple comments, this space is useful for explaining the overall purpose or connection between your comments.

Fig 1 The "Optional Background Text / Cover Letter" field allows users to provide contextual information or introductory remarks for their comment submission.

2. Complete the Comment Form

The comment form contains several fields that require your input:

ISA Content: This field is automatically populated based on the page you are currently viewing. No action is required.

Standards and Implementation Specifications: This drop-down menu is pre-selected based on the topic you're commenting on. The selection reflects the relevant standard or implementation specification for your current page.

Subject: Enter a concise title that summarizes the focus of your comment. This helps reviewers quickly understand the nature of your feedback.

Comment: This is the main field where you provide your detailed feedback, concerns, or suggestions. The comment box includes a text editor with formatting options that allow you to:

Format text as bold or italic
Insert hyperlinks
Create bullet points
Create numbered lists
Apply strike-through formatting
Attach images
Insert tables

Use these formatting options as needed to clearly present your information.

Fig 2 The comment text editor toolbar provides formatting options including bold, italic, links, lists, tables, and image insertion capabilities.

3. Optional: Add Additional Comments

If you need to provide feedback on multiple aspects of the ISA content, you can add additional comments:

After completing your first comment, locate and click the link labeled "Comment on another interoperability need" at the bottom of the form.
A new comment section will appear, allowing you to enter details for your additional comment.
For this new comment section, the "ISA Content" and "Standards and Implementation Specifications" fields will not be automatically populated. You must select the appropriate content and specification from the drop-down menus for each additional comment.
Complete all required fields for your additional comment.
Repeat this process for each additional comment you wish to submit.

Fig 3 The "Comment on another interoperability need" link enables users to add multiple comments within a single submission.

4. Optional: Upload Supporting Files

The platform allows you to upload supporting documentation to enhance your comment:

Locate the "File Upload" section at the bottom of the comment form.
Click to upload any files (such as PDFs or documents) that provide additional context, evidence, or clarification for your comment.

Important: If you have already entered your comments using the form fields, there is no need to upload duplicate content in PDF format. The file upload feature is intended for supplementary materials only. Please avoid uploading files that contain the same information already provided in your comment text.

Fig 4 The "File Upload" section permits users to attach supporting documentation that supplements their written comments.

5. Optional: Save and Exit

If you need to pause your work and return to complete your comment later:

Click the "Save and Exit" button at the bottom of the form.
Your comment will be saved as a draft that you can access and complete later.
When you return to the platform, you will see a red triangle with an exclamation mark next to the "Return to saved Comment" button, indicating that you have saved comments in draft status.
Click the "Return to saved Comment " button to continue working on your draft.
You will be taken to a review page where you can:
1. Select "Submit Comment" to officially submit your feedback.
2. Click "Edit" to return to the comment form and make changes
3. Select "Discard Draft" to delete the saved draft and start fresh

Fig 5 A red triangle with exclamation mark indicator appears next to the "Return to saved Comment" button when draft comments are saved in the system.

6. Review and Submit

Once you have completed your comment:

Click the "Review and Submit" button at the bottom of the form.
This will take you to a review screen displaying your comment(s) in full.
Review all information for accuracy and completeness.
On this review screen, you have three options:
1. Click "Submit Comment" to officially submit your feedback
2. Click "Edit" to return to the comment form and make changes
3. Click "Discard Draft" to delete the comment and start fresh
The review screen also includes a "Print" button that allows you to create a printed copy of your comments for your records.
If you choose to submit, your comment will be recorded in the system and made available for review by the appropriate stakeholders.