Sample attributes

Sample Name

(Required)

The unique name of the sample.

Use any combination of alphanumeric characters, plus spaces, periods (.), hyphens (-), and underscores (_).

This attribute is used by Ion Reporter™ Software.

A 255‑character limit must be followed for Ion Reporter™ Software name validation. If you are using Ion Reporter™ Software, and the actual sample name already exists in that software, a string such as _v1 or _v2, and so on, is added to the sample name.

Sample External ID

(Optional) If you manage samples in an external system, for example, a Laboratory Information Management System (LIMS), enter the identifier from that system.

Barcode Kit

The name of the barcode kit used to make a library from the sample. The same barcode kit must be used for all samples in a Sample Set.

Barcode

The name of the specific barcode in the selected barcode kit. Assign a unique barcode to each sample in a Sample Set.

Sample ID

A unique identification code (SampleID) for each barcode in a sample. This helps to track samples or possibly identify misassignment between samples and barcodes in a sequencing run. The SampleID is passed to Ion Reporter™ Software.

If you manage samples in an external system (for example, a LIMS), you can use the identifier from that system.

This attribute cannot be changed.

Control Type

The control type used when preparing the sample. If blank, the sample is not a control type sample.

Description

Typically one or two sentences that describe the sample.

Nucleotide Type

• Unspecified

• DNA

• RNA

• TNA

• Fusions

Sample Source

The source from which the sample is extracted.

• Blood

• FFPE

• Other

Panel Pool Type

Reserved for future use.

• Dual Pool

• Single Pool

Gender

The biological gender of the sample.

This attribute is used by Ion Reporter™ Software.

• Female

• Male

• Unknown

Type

The relationship type for this sample. Type is used in conjunction with Relationship Group, described below. For example, a relationship group can contain two samples, one with a type Tumor and another with a type Normal.

The following sample relationships are supported by Ion Reporter™ Software:

• Control

• Father

• Mother

• Normal

• Sample

• Self—Use Self for both a single sample and for the proband sample in a trio. A single sample is not related to other samples and is analyzed by itself.

• Tumor

Relationship Group

Use Relationship Group to designate a group of multiple related samples within the same Sample Set. For example, DNA and RNA samples from the same sample would have the same Relationship Group number.

Use a whole number to define a sample as part of a relationship group. It is used in conjunction with Type. For example, a Sample Set can contain 6 samples, consisting of 3 groups of 2 related samples each (of types Tumor and Normal). In this case, you would designate the two samples in each group as part of group 1, 2, or 3. This is identical to the Set ID in the IonReporterUploader plugin.

Sample Collection Date

The date that the blood sample was drawn.

Sample Receipt Date

The date that the laboratory received the blood sample.

Cancer Type

The type of cancer that is present in the sample.

Population

The super population code assignment for a sample, as defined by the human 1000 genomes project ( www.internationalgenome.org/faq/which-populations-are-part-your-study/). The population is relevant to the analysis of samples by the TCRB-LR assay workflow in Ion Reporter™ Software. The TCRB-LR analysis workflow produces a haplotype group assignment for samples having a population attribute of "European".

Mouse Strains

The name of a mouse strain. Choose from a select number of the most common strains. In Ion Reporter™ Software 5.12, the selected mouse strain will not affect Ion Reporter™ Software analysis workflows.

Cellularity %

The percentage of tumor cells in the sample. This is a whole number between 1 and 100.

Biopsy Days

The timepoint post-fertilization at which the biopsy was taken from an embryo. This is a whole number.

Cell Number

The cell count of the biopsied material.

Couple ID

An identifier for the couple. For use with the Reproductive research application.

Embryo ID

An identifier for the embryo. For use with the Reproductive research application.

<user defined>

If you create additional sample attributes, each attribute is listed here and in the CSV file. Attributes that are marked as mandatory must be entered for each sample. If you create an attribute of type integer, only numeric characters (whole numbers) can be entered for that attribute.