Some of the screenshots shown below have undergone censoring of participant information. This can include file names, references to plate-key's and participant id's, reported sex, and phenotypes and disorders. Within the Research Environment you will be able to view the information without issue.
For the Rare Disease programme, the Case Interpretation is the most relevant of the IVA’s components for Clinical Scientists. All the cases and its associated data can be found in the Case Portal within the Case Interpretation tab. You can access the space from the top-tab or from the central display of the screen (as highlighted in the picture with red arrows).
Once in the Case Portal grid, you can find all the cases. The gross of the cases within Rare Diseases Studies are Family Cases, where you can encounter genomic information about one proband along with its relatives whose genomes have been sequenced (usually father and mother, but it could include siblings and other relatives).
You can filter the cases, or find the case you'd like to explore, by applying the filters showed in the picture above. Thus, you can find a case by looking for its id, its associated sample id, proband id, family id, or disorders. Similarly to the Variant Browser, extended information about the case and the proband can be found below the main table when you select the row corresponding to a case, as showed below. Phenotypical information about the proband individual of the selected case can be found in the Proband Info tab scrolling down through the main case portal.
Once you select a case from the main table of the case portal, the following sub-components will appear:
Provides general information about the case and the data about the proband for who the case was created (id, sex, DOB, disorders, phenotypes).
Provides general QC metrics (this part is under current active development) and Sample Stats.
Sample stats include aggregated information about the variants in the sample associated with the case, like the aggregated genotypes, VCF filters, depth, variant type, INDEL size, variants per chromosome, consequence type, biotype and ClinVar clinical significance.
Sample Variant Browser
The sample variant browser provides an interface to browse over the variants presented in the samples associated with the case. Similarly to the Variant Browser, it is possible to apply different filters to retrieve the variants of interest for each use case.
The main difference comes from the Sample Genotype filter (shown below).
There, you can filter the variants based on the genotypes of the individuals included in the case. This can be useful, among other use cases, for guessing the phase of some of the variants (e.g: father 0/0, mother 0/1, we can conclude that , in the proband, the allele carrying the variant came from the mother).