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Motivation and scope

The purpose of this CDA Implementation Guide (IG) is to specify a standard for Genetic Testing Reports. In this project, the Clinical Genomics Work Group develops a CDA Implementation Guide (IG) for genetic testing reports, with the support of the Structured Documents Work Group.

Genetic tests have recently become an important tool in clinical care that further personalizes the care processes based on the patient individual genetic makeup. Genetic testing methods are diverse and span from testing for known germline mutations in the context of single-gene disorders, to full sequencing of genes in tumor tissues looking for somatic variations in cancer cells. We also see the emerging use of gene expression testing in clinical care and it is expected to see a growing use of research techniques adjusted to healthcare. As a consequence of that diversity and the constantly growing number of techniques yielding new result formats less familiar to clinicians, we see existing report formats having emphasis on detailed but easy-to-understand interpretations of the testing results along with recommendations. These interpretations may originate from the laboratory or they may be created by a clinician specializing in genetic/genomic medicine. This work also supports, communication within the report itself, detailed information on the tests performed including references to the appropriate scientific studies and publications in a format that looks quite often like a short abstract in a scientific journal. In some realms, the second transmission of this data (EHR to EHR/PHR) is performed using the CCD message model (a constrained version of the CDA model). As such for the healthcare specific message, this implementation guide will minimally detail how certain data sets defined in the above mentioned implementation guide would be included using the CDA model as appropriate to the level of granularity of this human-readable report. Note: The producers of GTR documents include genetic labs as well as clinical geneticists or any clinician who needs to create a report summarizing genetic testing results (and is capable and authorized to do so). In addition, all roles in a research environment that needs to summarize genetic assays are included in the scope.

GTR latest spec

This spec has passed DSTU ballot but is still being refined based on reconciliation of negative ballot comments. Early adopters are welcome but should be aware that final spec could be different than the current version.

Four complete GTR samples are provided in the ballot package containing the guide. Portions of these samples are automatically extracted by the MDHT (Model-driven Health Tool - a CDA Template editor)tool and placed as figures demonstrating the various templates of this guide. Nevertheless, not all templates are extracted from the samples and a few extractions may not be accurate. Therefore, for best viewing of the XML snippets, it is recommended to first go through the complete samples provided in the ballot package.

The September 2011 ballot package (including sample instances):‎

Reconciled ballot spreadsheet of Freida Hall: Media:CDAR2_IG_GENTESTRPT_R1_O3_2011SEP_f_hall_20110906105628_reconciled_v3.xls

The May 2012 package (for internal review): Media:Genetic_Testing_Report_(GTR)

GTR section outline discussion

The GTR section outline represents the rendering of the GTR for human readability. This includes the sections order, nesting, titles & codes.

The sections are currently organized by genetic testing type (i.e., Genetic Variations, Cytogenetics, Gene Expression, etc.) but alternatively it could have been organized by locus, e.g., all observations related to the same gene will appear in the same section, whether these are variations, expression or other type of testing.

Note that the structured data conveys the same semantics regardless the section outline. This is achieved by using the Clinical Genomic Statement template as described in the GTR spec.

We are analyzing the various recommendations found in the literature for section outlines of genetic testing reports. This analysis is summarized in the following outline comparison table.