Case Information

Case information is shown when opening a case page from the case listing and the case information page consist of:

• Case header: always shown on case page when scrolling through the results, visualising basic case identifiers and information as well as reporting functionality

• Information sections: divided into Clinical and Analysis information

• Download results button: allows downloading the results in a tsv format.

Case header

Fixed case header contains the following information and actions:

• Case ID

• Sex and Age of the patient

• Edit the case summary - Write your case report summary. This summary will be shown in the exported report. Case summary is needed in order to generate a report.

• Generate a report - Once you mark one/several relevant variant(s) and add a report summary, you can download a PDF with a summary of the case here.

• Date of submission & submitter - The date for the submission of the case to AION, and the user who submitted the case

• Assign case - Allowing you to assign the case for yourself or a colleague

• Version history - you can visualize the version history of the case.

  

Information sections

Clinical information

• Symptoms of the patient. You may edit the patient symptoms through the Edit button. This will launch a re-analysis with the new list of HPOs and the current analysis pipelines and algorithms.

• Case type (singleton/trio)

• Parents affected status in case of a trio.

  
  
  

Analysis information

• Uploaded data for this case. Original files names can be reviewed through “Show” button

• The reference genome version information: The reference genome used by AION analysis pipeline for analysing the results. This should match the input reference genome of your files. The supported reference genomes are GRCh38/hg38 and GRCh37/hg19. Reference: Exome variant discrepancies due to reference-genome differences

• The in silico gene panels used in the analysis

• AION DB (database) statistics refreshing: shows date and time in which the statistics in AION DB have been been updated. The "Refresh" of the statistics can be manually performed every 30mins for cases with GRCh37/hg19 reference genome. The refresh action can is active if there are cases submission after the submission of the current case.  For more information visit AION variant statistics.

  

Gene coverage 

Gene based coverage data extracted from the BAM file can now be uploaded to AION in tsv format. This data is then transformed by AION in a user friendly xlsx file allowing easy visualisation, sorting and filtering for instance by a list of genes of interest. The xlsx file is available for download for all cases where this data exist under the download results dropdown:

If you are using Nostos Genomics secondary analysis for the creation of the gene coverage data the region to define for a gene to be fully covered depend on the sample type and is the following; 

• WES/Panel: Canonical transcripts, coding sequence (CDS) only, +- 5bp padding
  • where, canonical transcript definition depends on the reference genome build and is for 
    
    • hg19: ensembl 
    • hg38: MANE 

• WGS: Ensembl all transcripts, all exons and UTRs, +- 50bp padding

Download results

Small variants:

• Annotation file: table containing all the annotated variants submitted to AION in tsv format.

• Prioritizer file: table containing the prioritized variants available in the AION results tab. This file (tsv) also contains symptoms (and their corresponding HPO codes) used to perform the prioritization.

CNVs:

• Annotated variants - VCF file name: table containing the annotated CNV pipeline results. CNV results are sorted by relevance, showing the most relevant candidate CNVs at the top of the downloadable file.