Sample Sheet Input

The input sample sheet provides patient-related sample information including the sample type and sex chromosomes reporting status. The system requires complete sample information before sequencing pools can be generated.

The input sample sheet must be a tab-delimited text file (*.txt). The header column names in the file must match the header column names exactly as they appear in the following table.

Header Column	Data Type	Requirement	Description
batch_name	String/Blank	Required	Indicates the batch name of the sample. Must match the batch name entered into the calling method (Workflow Manager) to confirm that the input sample sheet is associated with the correct batch. There is a 26-character maximum. A column may be left blank. Sample sheets without a batch_name column will not be accepted.
sample_barcode	String	Required	Barcodes on blood sample tubes loaded onto the ML STAR. If an integer value is used as a sample barcode, it should not exceed 15 digits. An alphanumeric sample barcode can be a maximum of 32 characters. Use only numbers, letters, dashes (-), and underscores (_). The sample barcode is not case-sensitive. Case-sensitive barcodes are not considered unique. The sample barcode must be unique and must not differ only in capitalization. For example, the sample names Sample01 and sample01 are not unique.
sample_type	String	Required	Indicates the sample type for analysis. Allowed values are Singleton, Twin, Control, and NTC.
sex_chromosomes	String	Required	Indicates the fetal sex chromosomes reporting. Allowed values are yes (report), no (do not report), and sca (report only for sex chromosome aneuploidies).
screen_type	String	Required	Indicates the type of screening for analysis. Allowed values are "basic" and "genomewide".

The input sample sheet is uploaded during plasma isolation or pooling and can be uploaded using the Batch Manager. The system automatically applies barcodes, screen type, sample type, and sex reporting for NTCs. Different information is required based on if the sample sheet is uploaded during plasma isolation or pooling.

Sample information can be changed throughout by using Batch Manager.

Sample information is confirmed during the sample uploading process. During pooling, the system requests any missing sample information not uploaded during plasma isolation, even for NTCs (ie, sex chromosome and screen type).

To avoid errors, do not include sample information or rows for NTCs in the sample sheet during the plasma isolation step.

You can control sample loading for all samples in a batch generated by the LIMS, or for specific samples that require retesting. If loading samples for retest purposes, fill the remaining open positions with available samples.

Choose from the following strategies for using sample sheets:

•

Predefined batches (LIMS created batches)

•

Ad hoc batches (VeriSeq NIPT Workflow Manager created batches)

Predefined Batches

You can use the LIMS to create batches before sample processing begins. In predefined batches, all samples are already associated with a batch before they are loaded onto the ML STAR. The sample sheet uploaded during plasma isolation includes every sample in the batch, along with all sample information. Sample sheets for batches created in a LIMS must include values in the Batch ID column. Including the batch ID helps to make sure that the correct batch ID name was manually entered into the Workflow Manager at the start of processing.

The predefined batch approach locks down the exact samples loaded because the system requires that all samples in the sample sheet be in the batch. No further information is required. The lab can proceed to the final report without additional data input.

Features and requirements of the predefined batches approach are as follows.

•

Allows for complete control of batch contents.

•

Prevents the loading of unwanted samples.

•

Requires a system for creating batches from inventory (advanced LIMS).

•

Can require lab personnel to retrieve the correct samples from storage. Alternatively, this requires an advanced sample storage system.

Ad Hoc Batches

You can create batches in the lab by physically collecting sample tubes and loading them onto the ML STAR during plasma isolation. No prior sample-to-batch association is required. You determine which samples to include in the batch.

When prompted by the Workflow Manager, select No Sample Sheet during plasma isolation. The Workflow Manager associates the loaded samples with the manually entered batch ID and generates a batch initiation report.

Features and requirements of the ad hoc batching approach are as follows.

•

No LIMS or sample sheet is required.

•

You can modify the batch initiation report with information on sample type, screen type, and sex reporting for upload during pooling. You can add samples at any time.

•

There is no automated control over which samples are included in the batch. You can load an unwanted sample.

•

Sample data must be uploaded during pooling.

Edit Sample Attributes

Before starting a sequencing run, you can use the VeriSeq NIPT Batch Manager to change individual sample sex chromosome reporting, screen type, and sample type attributes.

Access the Batch Manager. For details, refer to Access Batch Manager.

Enter the batch ID and user name or operator initials, and then select OK.

On the batch plate diagram, select the well position associated with a sample.

Confirm that the correct sample is displayed, and then select a sample type attribute from the Sample Type drop-down list.

Select a sex reporting attribute from the Sex Reporting drop-down list.

Select a screen type attribute from the Screen Type drop-down list.

Select Edit.