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.


Exemplary Clinical Report layout and information sources

Case Information

Includes (numbers indicate data sources):

  1. Patient details: Patient's name [1], date of birth [2], sex [2] and MRN [1];

  2. Technical sample details: Specimen's type [1] and quality [3], dates collected [1] and received [1];

  3. Provider details: Lab number [1], ordering physician's name [1];

  4. Report date [3];

  5. Case type [2];

  6. Clinical information: Indication for testing [2] or, if it's not available, Proband's phenotypes [2]; Secondary findings requested [2]: Yes/No.

Results summary

Results summary gives a general overview of the test result:

  1. Test result summary [4];

  2. Secondary ACMG findings summary [4];

  3. Interpretation summary [4];

  4. Recommendations [4].

Detailed results

Detailed results highlight the genetic testing findings:

  1. Basic sequence variant details:

    1. Gene [3],

    2. Genomic location [3],

    3. Variant [3] (HGVS description relative to the transcript selected as a reference in the Clinical Significance section of the Variant Page),

    4. Zygosity/Inheritance [3] (Zygosity in Proband and their relatives),

    5. Classification [6] (Pathogenicity),

    6. Condition [7] (Disease and Inheritance mode if available).

  2. Basic copy number variant details:

    1. Chromosome region [3],

    2. Type: DEL/DUP [3],

    3. Genes [3],

    4. Zygosity/Inheritance [3] (Zygosity in Proband and their relatives),

    5. Minimum length [3],

    6. Classification [6] (Pathogenicity).

  3. Individual sequence variant interpretations:

    1. 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,

    2. Associated diseases [3] - all the diseases known to be associated with the gene,

    3. Quality [3]: Zygosity, base quality, depth in Proband and their relatives,

    4. Summary [8].

  4. Individual copy number variant interpretations:

    1. Chromosome region [3],

    2. Type: DEL/DUP [3],

    3. Minimum length [3],

    4. Zygosity in Proband [3],

    5. Classification [6] (Pathogenicity),

    6. Summary [8].

  5. Gene interpretation [4]

Test details

Test details:

  1. Test methodology [5];

  2. Test limitations [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.

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.


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.

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