Gene panels

Everything in ELLA revolves around gene panels, and they're an essential part of the configuration. Note that a gene panel doesn't have to be a targeted panel in the traditional sense, but can include all genes in the exome if desired.

For details on how gene panels suitable for ELLA should be made, see the Gene panel builder (GPB) (opens new window) repository and GPB docs (opens new window).

To add a new gene panel, run the following command:

ella-cli genepanels deposit <path to gene panel directory or JSON file>

See the Gene panel store (opens new window) repository for examples of complete gene panels.

For additional commands related to gene panel handling, see ella-cli genepanels --help.

Transcripts shared between gene panels

A transcript (e.g. NM_000059.4) is stored once and shared by all gene panels that include it. When a gene panel is deposited, transcripts already in the database get all their fields (e.g. MANE status, coordinates, gene) from that gene panel, in all gene panels using them. This changes the filtering of ongoing and reopened analyses on those gene panels; completed interpretation rounds keep their filter results. Deposit gene panels in the order they were made, as an older gene panel deposited later puts its values back. The command lists the updated transcripts and their changed fields (not with --replace), and its output is stored in the database (clilog table).

--replace overwrites all fields of the gene panel's transcripts, also for other gene panels using them. These changes are not compared or listed. To update the transcripts from the current gene panels without waiting for new versions, deposit the current versions again with --replace.