VeriSeq NIPT Assay Software Tasks

The VeriSeq NIPT Assay Software performs both automated and user-initiated tasks.

The VeriSeq NIPT Assay Software completes the following automated tasks:

• Sample preparation log collation and storage—Produces a set of output files at the end of each step and stores them in the ProcessLogs folder located in the Output folder. Refer to Reports File Structure for an overview and Process Reports for details.
• Alert, email, and report notification generation—Monitors the validity status of the batch, pool, and sample during the Sample Preparation steps and QC of the sequencing data and analysis results per sample. Based on these validation checks, the VeriSeq NIPT Assay Software determines whether to continue with the process and if the results are to be reported. The VeriSeq NIPT Assay Software terminates the process when a batch or a pool is invalidated based on QC results. An email notification is sent to the user, a report is generated, and an alert is logged on the web UI.
• Sequence data analysis—Analyzes the raw sequence data for each sample multiplexed in the pool using the integrated NIPT Analysis Software. The VeriSeq NIPT Assay Software determines the aneuploidy score for each sample. The system does not report results for samples invalidated or canceled. For samples that fail the QC criteria, an explicit rationale for the failure is provided; however, results for the failed sample are suppressed. For more information, refer to NIPT Report.
• Results file generation—Provides sample results in a tab-separated value file format, which is saved to the Output folder. For more information, refer to NIPT Report.
• Report generation— The VeriSeq NIPT Assay Software generates supplementary result information, notifications, and process reports. For more information, refer to VeriSeq NIPT Assay Software System Reports.
• Sample, pool, and batch invalidation
– Sample invalidation—The VeriSeq NIPT Assay Software marks individual samples as invalid when the user:
• Explicitly invalidates the sample.
• Invalidates the whole plate during library preparation before the pools are created.

When a sample is marked as invalid, a Sample Invalidation Report is automatically generated, refer to Sample Invalidation Report.

– Pool and batch invalidation report generation—Pools and batches can only be invalidated by the user. Invalidated pools are not processed by the system. Pools already created from an invalid batch are not automatically invalidated and can be further processed by the system. However, new pools cannot be created from an invalidated batch. When a pool is invalidated, the system issues a Pool Retest Request Report under the following conditions:
• The batch is valid.
• There are no more available pools for this batch.
• The number of allowed pools from the batch has not been exhausted.

For more information, refer to Pool Retest Request Report.

• Retest management
– Pool failures—Failed pools are typically pools that failed the Sequencing QC metrics. The VeriSeq NIPT Assay Software does not proceed with processing failed pools if the run is terminated. Resequence using a second pool aliquot.
– Sample failures—The software allows failed samples to be retested if needed. Failed samples must be incorporated into a new batch and reprocessed through assay steps.
– Reruns—The system does not reanalyze pools with samples that have been processed previously and reported successfully. Rerun a sample by replating the sample on a new batch.

The VeriSeq NIPT Solution v2 – RUO enables you to perform tasks as follows.

Using the Workflow Manager:

• Mark the following as invalid:
– An individual sample.
– All samples within a batch.
– All samples associated with a pool.
• Mark a given sample as canceled. The VeriSeq NIPT Assay Software then marks the result as canceled in the final results report.

Using the VeriSeq NIPT Assay Software:

• Configure software to be installed and integrated into the laboratory network infrastructure.
• Change configuration settings such as network settings, shared folder locations, and user account management.
• View system and batch status, result and batch processing reports, activity and audit logs, and assay results.

The ability to perform tasks depends on user permissions. For more information, refer to User Roles.