View raw Markdown
type: resourceresource: GenomicStudy

GenomicStudy

Introduction

[%stu-note dstu%] The material on this page is currently undergoing work to be refactored in a future release as further analysis is done. Reviewers are encouraged to provide their comments and feedback about the example codes for terminology binding purposes. [%end-note%]

Scope and Usage

GenomicStudy resource aims at delineating relevant information of a genomic study. A genomic study might comprise one or more analyses, each serving a specific purpose. These analyses may vary in method (e.g., karyotyping, CNV, or SNV detection), performer, software, devices used, or regions targeted.

GenomicStudy describes relevant information including the reasons, purpose, and performers of the study. It also provides technical endpoints to access these data. It could be a logical aggregator for complex genomic analyses.

A GenomicStudy might be based on one or more service requests or care plans. The reasons for performing a genomic study might be driven by specific Conditions or Observations. Although the genomic study subject is the focus of the study, the analysis-level focus could be used to specify other relevant subjects or specimens. For example, trio testing may involve three subjects: the proband, and both parents. The proband would be the subject listed directly under the genomic study, while each of the analyses could represent proband, mother, and father genomic analyses.

In clinical use, the study interpreters use all the results of these various analyses to provide diagnostic and therapeutic insights for the patient. Where performers are listed according to their participation in each genomic analysis. Each analysis may be based on a set of defined protocols that may differ from the performed protocols.

The regionStudied and regionCalled elements can refer to DocumentReference instances carrying BED files. Other types of files used in an analysis can be provided similarly, and listed either as inputs or outputs.

Detailed information about the results of the analyses may be represented by Observations and gathered in a DiagnosticReport. Both resources may refer back to the originating GenomicStudy to allow navigation.

Boundaries and Relationships

A main function of GenomicStudy is to provide additional metadata for one or more clinical genomic analysis pipelines where DocumentReference instances are used to track inputs and outputs of those pipelines. Device is used to represent both hardware and software used in the sequencing and in the analyses.

It is intended that this resource be referenced by Observation and DiagnosticReport in the same way that ImagingStudy is currently referenced on those resources. Of note, the results of the study would be captured in Observations and referenced on a DiagnosticReport.

Important contextual references include Patient, Specimen, Encounter, ServiceRequest, Practitioner, and Organization.

Observation or Condition instances may also be referenced from genomic study to designate a given reason for performing the study.

GenomicStudy can support the event-definition workflow pattern by referencing PlanDefinition via the instantiatesCanonical relationship when implementers wish to describe more specifics of the pipelines and devices used in the analysis.

Notes

Example Codes

GenomicStudy uses many example codes for terminology binding. Reviewers and implementers are strongly encouraged to provide their comments and feedback about the example codes for terminology binding purposes.

The attributes and example bindings are listed below. Links are included to indicate where the example codes were pulled from.

GenomicStudy.type

The type example codes were based on discussions by Clinical Genomics Workgroup.

GenomicStudy.analysis.methodType

The methodType example codes were pulled from National Library of Medicine-Genetic Testing Registry (NCBI-GTR) and describe testing methods on various levels: major method category, method category, and primary methodology.

GenomicStudy.analysis.input.type and GenomicStudy.analysis.output.type

The input and output type example codes were pulled from Integrative Genomics Viewer Documentation by Broad Institute.

GenomicStudy.analysis.changeType

The changeType example codes were based on discussions by Clinical Genomics Workgroup.

Implementation Notes

Handling markdown

The description is a markdown datatype, and implementers should carefully consider how to appropriately handle this attribute. The characters in markdown formatting can conflict with those commonly used in descriptions of genomic data. In particular, descriptions that contain mentions of "star alleles" (widely used in the pharmacogenomics and HLA domains) could be munged in a way that prevents accurate interpretation. For example, consider this text:

This genomic study analyzes CYP2D6*1 and CYP2D6*2

If the system producing this data treats this as a simple text string with no special processing, but a receiving system processes this via a markdown rendering engine, the two '*' characters would be processed as markdown formatting characters. This would italicize the text between '*' characters, and not display '*' characters. This could cause an inaccurate interpretation of the study description.

There are several ways data producers can ensure content is appropriately rendered by receiving systems without requiring the content to be formatted as markdown prior to sending. Here are three basic approaches to consider:

Use Cases

The attributes subject and analysis.focus can reference many resource types besides Patient such as Group, BiologicallyDerivedProduct, or Substance. In addition, it can provide more details about involved genomic files as inputs or outputs. These various options allow the GenomicStudy resource to cover many use cases besides direct patient care, e.g., research studies that involve multiple patients or environmental samples. Through the following subsections, some of these use cases are described.

Trio studies

Trio studies involve a proband and two more subjects such as proband’s mother and father for a de novo mutation detection study. GenomicStudy would list the proband as subject because it is the main subject of the study. Each of the study participants, i.e., proband, mother, and father, may have their own analysis entry. When an analysis was performed on an entity other than the subject, the analysis.focus attribute would reference that entity. If a analysis entry documented the analysis of all participants of the trio, each participant would be referenced by analysis.focus.

The analysis.input lists various files that may be used for each individual analysis, their types, and their generation context. analysis.input.file may link these files to DocumentReference resources to provide details about each individual file. One of the main details is the subject of a file. If a file is linked to a specific patient, the corresponding DocumentReference.subject may reference this Patient Resource. If the file contains data from multiple persons, the corresponding DocumentReference.subject may reference a Group resource that lists these persons, and their relationship to each other if available.

Somatic mutation detection studies

Somatic mutation studies may use multiple samples from the patient to support mutation detection, e.g., tumor-normal sample pair. analysis may describe conducted analyses per each sample, where analysis.specimen elements may provide details about each individual specimen. In addition analysis.input can list relevant input files, where the DocumentReference referenced by analysis.input.file can list the specific specimen this input file is related to using DocumentReference.subject as a Specimen resource instance.

EHR access to genomic studies

StructureDefinition

Elements (Simplified)

Mappings

Resource Packs

list-GenomicStudy-packs.xml

<?xml version="1.0" encoding="UTF-8"?>

<List xmlns="http://hl7.org/fhir">
  <id value="GenomicStudy-packs"/>
  <status value="current"/>
  <mode value="working"/>
</List>

Search Parameters

Full Search Parameters

Examples

Full Examples

Mapping Exceptions

genomicstudy-event-mapping-exceptions.xml

Divergent Elements

Unknown does not represent "other" - one of the defined statuses must apply. Unknown is used when the authoring system is not sure what the current status is.

Unmapped Elements

genomicstudy-fivews-mapping-exceptions.xml

Unmapped Elements