Register a patient and sample#

This page explains how to register a new clinical case in Reporter. Registering creates the patient, order, biosample, and supporting records that the downstream analysis and reporting stages use.

Before you start#

  • Confirm that you have the ReporterDataEntryOperator role. If the Add Sample area is not available, ask your administrator to check your assigned role.

  • Gather the required identifiers and clinical information for the case.

  • Verify that the assay or test type is configured for your organization.

Required information#

Reporter’s Add Sample page collects the following sections. All mandatory fields must be complete before you can submit.

Section

What to enter

Why it matters

Lab test / Order

Order or test identifiers, assay selection, ordered date.

Links the biosample to the requested test.

Biosample

Sample ID, sample type, collection date, handling information.

Identifies the physical specimen being analyzed.

Personal (Individual)

National ID, Medical record number, Name, Alias Name (optional), Date of birth, Ethnicity, Gender.

Identifies the patient and supports report generation.

Phenotypic Features

Observed phenotypes, searched by term.

Provides clinical context for interpretation and reporting.

Ordering physician

Physician name, institution, contact information.

Required for report attribution and communication.

Field formats#

  • National ID and Medical record number are free-text identifiers; there is no fixed pattern, but they should follow your organization’s identifier scheme so duplicate-detection is reliable.

  • Sample ID (in the Biosample section) is also free text, but must be unique within your organization. Reporter rejects a submission if the Sample ID already exists.

  • Gender is a single-select of Female, Male, or Unknown.

  • Ethnicity is a fixed dropdown (for example North American, East Asian, European, African, and similar categories) rather than free text.

  • Phenotypic Features uses a type-ahead search over HPO terms: type at least 3 characters of a clinical description (for example “seizure”) and select one or more matching HPO terms as chips. It is not free text and not a static dropdown.

Linking to an existing patient#

Use the Import button at the top of the Personal section to search for and select an existing Individual record instead of creating a duplicate patient. Selecting an existing individual auto-fills and locks the Personal fields (National ID, Medical record number, Name, Alias Name, Date of birth, Ethnicity, Gender) from that record; leave the section blank and fill it in manually to create a new Individual.

How to register a single sample#

  1. In Reporter, open Add Sample.

  2. Fill in each section on the form. The timeline on the right shows which sections are still invalid.

  3. When all sections are valid, click Submit.

  4. Reporter creates the records and places the sample in the PENDING state.

How to register samples in batch#

The Batch button opens the Batch Sample Registrator, a 3-step wizard:

  1. Accession / Copy-Paste Data. Copy 16 columns from Excel or a CSV file and paste them into the text box, or click Download Excel Template (.xlsx) to start from a blank template. The columns, in order, are:

    #

    Column

    Mandatory

    1

    Assay Name

    Yes

    2

    Sample ID

    Yes

    3

    Sample Type

    Yes

    4

    Time of Collection

    Yes

    5

    Primary Cancer Type

    No

    6

    Sampled Tissue

    No

    7

    Person Name

    Yes

    8

    National ID

    Yes

    9

    Medical Record Number

    Yes

    10

    Date of Birth

    Yes

    11

    Ethnicity

    Yes

    12

    Gender

    Yes

    13

    Phenotypes (comma-separated HPO IDs, for example HP:0100013,HP:0000769)

    No

    14

    Order Date

    Yes

    15

    Hospital Name

    Yes

    16

    Physician Name

    Yes

  2. Review & Edit Spreadsheet. Reporter parses the pasted data into an editable grid and runs a real-time audit: missing mandatory fields, duplicate Sample IDs within the batch, and invalid dates are flagged per cell. You can add rows manually, use Autofill Order Details to copy shared order-level values (order date, assay, sample type, diagnosis) across rows, or remove failed rows.

  3. Verify & Submit to System. Submission is blocked until the error count is zero. Each valid row creates a Biosample and Phenopacket independently, so a single row’s failure (for example a duplicate Sample ID) does not block the rest of the batch.

Validation and duplicate prevention#

  • Mandatory fields are enforced before submission, both for single-sample registration and for batch rows.

  • Sample IDs are checked for uniqueness within the organization; a duplicate Sample ID is rejected with an error naming the conflicting ID. If a duplicate is detected, verify whether the sample is a rerun, re-collection, or data-entry error before proceeding.

  • Batch rows are also checked for duplicate Sample IDs against each other within the same paste.

  • Phenotype terms are restricted to HPO terms returned by the built-in search; there is no free-text phenotype entry.

What happens after submission#

  • The sample appears in the PENDING lane of the Management view.

  • The sample is listed in Sample List.

  • No analysis has started yet; the next step is to upload sequencing data and launch the pipeline. See Import sequencing data and start analysis.

Troubleshooting#

Problem

Possible cause

Action

Submit button is disabled

A required field is missing or invalid.

Review the timeline indicators and complete each section.

Duplicate identifier warning

The patient or sample ID already exists.

Verify the identifier or mark the case appropriately.

Assay not available

The assay is not configured for your organization.

Contact your SeqsLab administrator.