SNV Genome browser

The Moon SNV genome browser, which can be opened from the Gene region section within the variant card, includes three levels of visualisation: an overview of the exon-intron structure of the gene, an exon-level detail, and a nucleotide-level display. Light grey lines connect the different levels of visualisation.

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On top of the screen, the gene name and currently visualised transcript are shown. You can easily change the displayed transcript by selecting the transcript ID of choice in the drop-down menu next to the gene name.

Open

At all three levels of visualisation, functional protein annotations such as domains, repeats, regions and motifs (thereafter referred to as domains) are shown in blue (from UniProt) and green (from Pfam).

Gene-level display

This view shows a high-level overview of the selected transcript of the gene of interest.

The gene/transcript is always displayed in the 5' to 3' direction and the visualisation includes UTR regions (light grey boxes), coding exons (dark grey boxes) and intronic regions (dark grey lines).

The red arrow on top of the visualisation indicates the position of the variant that was detected in the patient’s sample. You can re-centre the browser to that variant’s position at any time by clicking this red arrow.

The grey arrow indicates the position you are currently exploring. You can slide this grey indicator or use the arrow keys to move to another position within the gene. Switching between exons is possible by using the Alt+arrows keys. Hovering over any exon brings up a tooltip that indicates the exon rank of that specific exon.

A high-level visualisation of the position of the protein annotations is also displayed under the exons.

Exon-level display

A more detailed view of the exon you are exploring, is shown below the gene/transcript overview.

Begin and end locations are shown at the border of the displayed exon. The exon rank is indicated. The grey arrow again indicates the position you are currently exploring and can be moved by sliding the arrow or using the arrow keys.

Colour-coded lines within the exon mark the location of previously classified variants in either ClinVar or the lab’s internal knowledge base (KB). Variants are coloured according to the legend shown below the gene visualisation.

The position of protein domains from both UniProt (blue) and Pfam (green) are displayed under the exon. Rounded caps indicate the beginning and end of a domain.

Nucleotide-level display

The nucleotide level display is the most detailed level of visualisation. It shows the nucleotide sequence at the position of interest, with location indication on top.

When exploring coding regions, individual nucleotides are grouped in codons, with the corresponding amino acids displayed below. Hovering over a specific nucleotide brings up a tooltip with information on the genomic location of the nucleotide, c. location and p. location.

When moving over the nucleotide sequence, the currently hovered-over position with corresponding annotations in the tracks below are highlighted in blue. Five annotation tracks are displayed:

• UniProt and Pfam tracks: Display functional protein annotations from both sources for transcripts for which this info is available. Hovering over domains brings up a tooltip indicating their name and p. location. Clicking on them opens their corresponding UniProt and Pfam entries for further exploration.

• ClinVar track: Shows the location of variants reported in ClinVar, colour-coded according to their pathogenicity classification. Clicking the coloured dots in this track redirects you to the ClinVar page of interest.

• Mastermind track: Displays the number of scientific articles published that mention the specific variants located in the corresponding positions. Clicking the Mastermind annotation shows how many publications there are per alternative allele, and allows you to open the Mastermind Search Engine for the variant change of interest.

• Knowledge base track: Shows variants previously reported within the lab’s internal KB, colour-coded according to their pathogenicity. Clicking this annotation opens this variant in the KB, where additional information can be explored, or the classification can be updated.

• Observations track: Displays the number of observations of a certain allele in the lab account. Clicking the observations annotation shows details on the number of homo/hemizygous or heterozygous observations and allows you to open the Observations page for the variant change of interest.