Case repository
Moon creates a case repository based on all samples that are uploaded in a specific Moon lab account. This allows to take advantage of the knowledge of observations of variants in other samples in your account, for interpretation of variants in new samples.
The information derived from the case repository is displayed as an additional annotation source for each variant, and can be used during manual review of variants. This information is not used for the automated analysis in Moon.
Variant card
The Lab’s allele frequency and number of occurrences of alleles, grouped by zygosity, are displayed in the variant card. Clicking any of these info fields, opens the Observations page for this variant.
If a Lab account contains samples from different genome builds, case repository info will be genome-build specific.
The Lab % and number of observations are calculated at the time of analysis, which is reflected by the CaseRepoSample date in the ‘Annotation sources’. Therefore, it is possible that indicated values for the case repo are not up to date anymore for analyses that have been run in the past. Reanalysing the case will update these annotations based on all currently analysed samples in the lab account.
For new samples uploaded after the initial creation of the Case repository, a check is performed to not take into account duplicate samples for calculating Lab frequency and variant observations. For samples that were already uploaded prior to creation of the Case repository, duplicates are not specifically removed.
Observations page
The observations page allows users to explore observations of a variant of interest. This page can be accessed either from within the variant card, or via the Observations track in the SNV Genome browser (see below).
On top of the observations page, the variant of interest is displayed, including its genomic position.
Below, samples in your Moon Lab account in which this particular variant has been observed are listed. Samples are grouped based on the zygosity in which the variant occurred in each sample (homozygous, hemizygous, heterozygous occurrences).
For each sample observation, the following information is indicated:
Sample name; clicking the sample name redirects you to the latest analysis of this sample.
Healthy or affected status of the sample:
For affected samples, the age of onset (AOO) and gender, as inputted on the patient info screen of the sample, are displayed.
For healthy samples, Moon displays the gender of the sample based on the family relation inputted on the Patient info screen.
Clicking the field with info on Affected status, AOO and gender reveals the HPO terms that were used as input to analyse each affected sample. This allows for easy comparison of HPO terms between samples carrying the same variant.
‘Shortlisted’ indicates whether this variant was Shortlisted in any analysis on a particular sample.
‘Reported’ indicates whether this variant was Reported in any analysis on a particular sample.
Filter view
Variants can be filtered based on Lab frequency, by using the Lab frequency slider or free input field to adapt the threshold. The Lab frequency filter can be turned off by setting the slider at 2%.
The Lab frequency will be unreliable if the total number of samples in your Moon account is low. In the Filter view, setting the frequency threshold at a low value in a Lab with few samples, can lead to inappropriately filtering out of variants of potential interest.
Genome browser
The Observations track in the SNV genome browser, displays the number of observations of a certain allele in the lab account. Clicking the observations annotation shows details on the number of homozygous, hemizygous or heterozygous observations per Alt allele and allows you to open the Observations page for the variant of interest.