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Patients & samples

Patients

The Patients page lists every patient (study ID) with counts of samples and available result types. Click a study ID to open the patient, which has five tabs:

  • Overview — identity plus clinical/outcome placeholders (populated in a later slice).
  • Summary — all of the patient's samples merged into one set of per-result-type tables. Every row shows which sample it came from (name, type, timepoint, site) and links to that sample's page, plus a Run link back to the upload that produced it — useful for comparing results across samples/timepoints at a glance, or tracing a value back to its source.
  • Samples — every sample belonging to the patient. Each row links to that sample's page.
  • Data availability — which result types exist for this patient, and how many.
  • Cohorts — every cohort this patient belongs to, each linking to that cohort's page.

Samples

The Samples page is segmented by sample type — most work happens within one type at a time:

  • Fresh frozen
  • FFPE
  • Organoid
  • Ascites
  • Plasma

Use the type tabs to switch, and the toolbar to filter by patient or timepoint (diagnosis / interval / relapse). Sort any column by clicking its header.

A single sample

Opening a sample shows three tabs: Overview (metadata — type, timepoint, anatomical site, parent/derivatives, state — and a link back to its patient), Results (typed + generic results, below), and Logistics (current storage location + move control, state + history, QC records, and a scannable QR code — see Sample logistics for the full picture: freezers, the visual box picker, batches, and shipments).

Typed results

If this sample has any of the four typed result kinds (see Typed results), they render first with their own dedicated columns:

  • Somatic variants — gene, variant (HGVS), VAF, caller. The gene links to OncoKB and the variant links to ClinVar.
  • Germline variants — gene, variant, classification, zygosity.
  • Copy number — chromosome, start–end, gene (if known), copy number, type.
  • HRD score — score, HRD/HRP status, method.

Every typed-result row shows a verification status badge (draft/verified/rejected) and, for reviewers (postdoc/superuser), inline ✓/✕ buttons to verify or reject it directly. A row with more than one version shows a v2 ▾ button that opens its full version history — see Verification workflow for what versions and "current" mean.

Generic results

Below the typed sections, ad-hoc results land per result type, same as Slice 1:

  • Sequencing logistics — event, facility, date.
  • QC flags and HR status — value plus method/notes, colour-coded (e.g. HRD in green, "not suitable" in red).
  • Any other ad-hoc result type registered via CSV upload.

Every result row (typed or generic) links to the run it came from.