You've done your job, the case is solved, and the only thing left is to generate a report.

Then you see "Failed to generate report". If you are experiencing issues with report preview or generation in a particular case, don't panic.

The error is most likely caused by an unsupported character, most commonly the "&" sign.

Look for it:

• in Variant Interpretation paragraphs for variants selected for reporting;

• in (Interpretation notes, Gene interpretation, Recommendations).

Having found the culprit, replace it with "and" or another suitable alternative and try generating the report again. 🤞

Can't find any ampersands (& signs) or the report generation fails even after you got rid of them?

Time for a serious investigation. Don't hesitate to reach out!

But if you're curious, go on and check if you have added any PMIDs in the fields mentioned above. If the PMID links to a very old paper, it may be absent from our database used to populate citations in the report. This also causes a rendering error.

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Yes, Emedgene supports the recommended interpretation flow for Illumina Complete Long Reads.

Illumina Complete Long Reads interpretation flow in Emedgene includes:

1. Ingesting combined output of long-read/short-read callers for both SVs and SNVs, along with the long-read BAM files. Short-read callers from VCF (CNV read-depth and STR) can be additionally used starting from DRAGEN 4.2;

2. ICLR calling by the BSSH application;

3. Ingesting VCF and BAM files through the existing BSSH integration;

4. Explainable AI shortlisting of ICLR variants and automated ACMG classification, when relevant.

Current limitations:

• Complex SV variants like inversions and translocations are not yet supported for interpretation.

• ICLR cases must be start from VCF files; Emedgene does not support case accessioning from both VCF and FASTQ sources.

1. Click on your initials or profile picture on the top right to access the Settings.

2. In the My settings tab scroll down to the Organization section on the left. Under the title Organization, you'll see the name of the organization you're currently in.

3. Click on the Select Organization text box and select the organization from the dropdown menu or search for it by typing its name.

4. Press Save. You will be transferred to the requested account.

5. Refresh your page and that's it!

Our systems are synchronized using a Cloud Time Sync Service to ensure accurate timekeeping and consistent log timestamps.

To run mtDNA variant analysis on Emedgene, you need to upload:

a. FASTQ files, or

b. VCF file(s) created with / / / using the mtDNA genome reference or a full genome reference that includes rCRS (e.g., hs37d5).

In case of an end-to-end analysis starting from FASTQ files, mtDNA SNV/indel variants will be mapped to rCRS and called by DRAGEN with improved variant quality calculation.

CNV calling from exome FASTQ is done automatically! A prerequisite for this is defining a Panel of Normals (PON) per each enrichment kit you're using.

A PON aids to set a baseline coverage pattern and account for recurrent technical artifacts that are specific to your workflow. Depth of coverage per each sequenced region is averaged across PON samples; if a significant increase or decrease from this baseline is detected in a test sample, a CNV is called.

Recommendations for creating a PON to call CNVs from exome data:

1. Samples for a PON should be derived from healthy individuals.

2. In our experience, a PON of at least 40-50 samples yields the best results. A smaller PON is better than nothing, but keep in mind that you may encounter more false positives.

3. You should aim at preparing samples for a PON in a unified manner to avoid the batch effect. Please log differences in library preparation (if any).