The Shortlist presents all variants that are considered to be of interest for a specific analysis.
Both the variants selected by the automated Moon analysis pipeline, and variants that were manually selected in the Filter view, are displayed. The Shortlist can be accessed via the corresponding tab on top of the sample screen.
For each of the shortlisted variants, several annotations are provided in the overview table and in the variant card. The variant card can displayed by clicking the information icon on the right of the variant in the overview.
The Shortlist screen consists of the following elements, as also visible in the screenshot below:
Name of the sample when running the current analysis ('Proband_demo' on the screenshot).
Status of the analysis ('Completed' on the screenshot).
Overview of the patient info for this analysis (gender, age of onset, list of HPO terms).
For a family analysis: family information entered through the Patient info screen (family member’s sample name, relation and status) with confirmation of family relations.
Menu that allows to close the case as either Negative, VUS or Solved (see on the right of the screenshot), or indication of how the case was closed.
Reanalysis button that allows to manually start reannotation and reanalysis of the sample.
In case results of a previous analysis are being reviewed, the 'Close as' and 'Reanalysis' buttons will not be visible. Instead, a message will indicate that you are reviewing results of a previous analysis.
Below the patient information, the variants of relevance are divided over tabs.
Variants in the shortlist are organised in tabs, each presenting a (ranked) list of a subset of variants. The following tabs are present:
SNVs: This tab displays the ranked list of SNVs that were outputted by the automated pipeline. For variants to be displayed in this tab, it is required that the genotype of the variants is in accordance with the inheritance pattern of the associated disorder.
MT SNVs: This tab displays the ranked list of SNVs in mitochondrial (MT) genes that were outputted by the automated pipeline. If no MT SNVs were shortlisted by Moon, this tab is not shown.
Carrier SNVs: This tab displays a similar ranked list of variants as the SNV tab. However, all variants presented here have a heterozygous genotype (0/1 call in VCF) in association with an autosomal recessive inheritance of the associated disorder.
SV/CNVs: This tab displays the ranked list of SV/CNVs outputted by the automated pipeline, in case a file with this kind of genetic variation was provided as input.
Manually Filtered: This tab displays the variants that were manually added to the Shortlist from within the Filter view. Variants in this list are not ranked.
Each variant in the Shortlist is presented with a Variant summary display. In this display, the three icons on the right allow to perform an action for the variant.
Clicking the icon on the left allows to add the variant in question to the lab's Knowledge base.
The icon in the middle allows to add a variant to the Report of that specific analysis.
Clicking the info icon on the right brings up the Variant card with more extensive variant annotations.
Hovering over the icons, will bring up a tooltip explaining each icon.
For each sample, you can review the results and reports for all analyses performed over time. Via the menu at the bottom of the Shortlist screen, an analysis of choice can be selected. Previous results are displayed similarly to results from new analyses. The patient info for previous analyses is displayed based on the info that was inputted in Moon at the time of that specific analysis.
Annotations sources used by Moon for the analysis for which the results are displayed, can be reviewed using the Annotations sources.
