Clinical Report
With emedgene's reporting solution, creating comprehensive Clinical Reports is a piece of cake.✨ All the relevant case- and variant-level information is automatically populated to the corresponding sections of the report.
Clinical Report layout and information sources
1) Case Information
Case Information includes (numbers indicate data sources which can be found at the bottom of the article):
a. Patient details: Patient's name [1], date of birth [2], sex [2] and MRN [1];
b. Technical sample details: Specimen's type [1] and quality [3], dates collected [1] and received [1];
c. Provider details: Lab number [1], ordering physician's name [1];
d. Report date [3];
e. Case type [2];
f. Clinical information: Indication for testing [2] or, if it's not available, Proband's phenotypes [2]; Secondary findings requested [2]: Yes/No.
2) Results summary
Results summary gives a general overview of the test result:
a. Test result summary [4];
b. Secondary ACMG findings summary [4];
c. Interpretation summary [4];
d. Recommendations [4].
3) Detailed results
Detailed results highlight the genetic testing findings:
a. Basic sequence variant details include:
Gene
[3],Genomic location
[3],Variant
[3](HGVS description relative to the transcript selected as a reference in the Clinical Significance section of the Variant Page),Zygosity/Inheritance
[3](Zygosity in Proband and their relatives),Classification
[6](Pathogenicity),Condition
[7](Disease and Inheritance mode if available).
b. Basic copy number variant details include:
Chromosome region
[3],Type: DEL/DUP
[3],Genes
[3],Zygosity/Inheritance
[3](Zygosity in Proband and their relatives),Minimum length
[3],Classification
[6](Pathogenicity).
c. Individual sequence variant interpretations include:
Basic variant details
[3]: gene, genomic location, coding sequence and protein sequence change HGVS notations, exon involved, variant's main effect, Prediction, Conservation and Splice Prediction scores, gnomAD population statistics,Associated diseases
[3]- all the diseases known to be associated with the gene,Quality
[3]: Zygosity, base quality, depth in Proband and their relatives,Summary
[8].
d. Individual copy number variant interpretations include:
Chromosome region
[3],Type: DEL/DUP
[3],Minimum length
[3],Zygosity in Proband
[3],Classification
[6](Pathogenicity),Summary
[8].
e. Gene interpretation [4]
4) Test details
Test details include:
Test methodology
[5];Test limitations
[5].
5) References
The References [9] section lists all the PubMed citations mentioned in the report. References will be auto-formatted if the PMID is supplied in the report.
6) Signatures
The Signatures section documents who and when generated the report [3].
Generating a Clinical Report
After you completed the Case interpretation flow, you may want to have a look at the Report Preview before finalizing a case. To do this, click on the eye button located rightmost on the Individual case page Top bar, select a template and click Preview.
You can download the report preview in a .pdf or .odt format.
After you changed Case status to Finalized, you can Generate Report. All the generated reports are saved per case. Click on the printer button on the Individual case page Top bar, select Create New or choose a previously generated report (if any), then select a template and click Generate.
You can download the report in a .pdf or .odt format.
Data sources:
[1] - API;
[2] - filled in while adding a new case; displayed in Case Info; editable for non-finalized cases;
[3] - automatically inferred by emedgene,
[4] - filled in in the Case Interpretation widget while finalizing the case,
[5] - fixed text,
[6] - manually assigned in the Pathogenicity box of the Evidence section of the Variant Page,
[7] - depends on the evidence generated on the Evidence page,
[8] - automatically or manually filled in in the Variant Interpretation notes of the Evidence section of the Variant Page,
[9] - in any of the free text fields you can add PMIDs in one of the following formats: PMID1234, PMID 1234, PMID:1234.
Note: emedgene offers the capability of customizing Clinical Reports upon request. We tailor Report templates for any use case according to your SOPs and aesthetic sense.
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