# Reporting

With reporting solution provided by Emedgene, creating comprehensive reports is a piece of cake. All the relevant case- and variant-level information is automatically populated to the corresponding sections of the report.

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**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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## Exemplary report layout and information sources

### **Case Information**

Includes (numbers indicate [data sources](#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.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-ece96c60231b4f99ee04a1d8dea348eccfe6fdd0%2Fclinical_report_1_image.png?alt=media)

### **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].

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-4479ceb8cc4db6f400b5511c5cf1bc688a2923df%2Fclinical_report_2_image.png?alt=media)

### **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](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section) [section](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section) of the [Variant Page](https://help.emedgene.com/en/collections/2457718-manual#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]

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-05e80b33f6f6e71269e1399a02760561d4fcdd40%2Fclinical_report_3_report_new.gif?alt=media)

### **Test details**

Test details:

1. Test methodology \[5];
2. Test limitations \[5].

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-3e9629af58b4833df5dccd594caeefa036c35972%2Fclinical_report_4.gif?alt=media)

### **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.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-0cc11ae9e54a4e4272f85c352a9f9c2cfe7a9e0e%2Fclinical_report_5.png?alt=media)

### **Signatures**

The Signatures section documents who and when generated the report `[3]`.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-92ea64d5c113b2f274030c4034ff4bb65c5e03a6%2Fclinical_report_6.png?alt=media)

***

## Generating a Report

{% tabs %}
{% tab title="Previewing 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.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-cdaa939ebcefe5a42171675f1b3952c574d87e0c%2Fclinical_report_7.gif?alt=media)

You can download the report preview in a .pdf or .odt format.
{% endtab %}

{% tab title="Generating report for a finalized case" %}
After you changed [Case status](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/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.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-4424ba2c45525bbfaefd129724b5ea19f03811fd%2Fclinical_report_8.gif?alt=media)

You can download the report in a .pdf or .odt format.
{% endtab %}
{% endtabs %}

***

## Data sources

\[1] - API;

\[2] - filled in while adding a new case; displayed in [Case Info](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/getting_around_the_platform/cases_tab/case_details); [editable](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/editing_an_existing_case) for non-finalized cases;

\[3] - automatically inferred by Emedgene,

\[4] - filled in in the Case Interpretation widget while [finalizing the case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/case-completion-and-reporting/finalizing_a_case),

\[5] - fixed text,

\[6] - manually assigned in the Pathogenicity box of the [Evidence](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section) [section](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section) of the Variant Page,

\[7] - depends on the evidence generated on the [Evidence page](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/evidence_page),

\[8] - automatically or manually filled in in the Variant Interpretation notes of the [Evidence](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section) [section](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/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.