N_xClinical

As new cases are added to NxClinical for analysis and review, a database of all historical cases is automatically created.  This valuable knowledge base is available and utilized as reference (along with integrated public databases) in interpretation of new cases.  When reviewing a case, similar events found in other samples in the in-house database are displayed in the interactive browser alongside the events in the sample under review. The graphical representation of these past cases also includes indicators depicting how this variant was previously classified and this information from previous cases is used in the automated Variant Interpretation Assistance (VIA) system to pre-classify events in new cases.

A centralized database storing all information as well as role-based access maintains consistency across different users and machines. Administrator defined protocol-based settings ensure processing consistency across samples of the same type. Automated workflows mirror a lab’s interpretation rules and/or regional guidelines (e.g. ACMG) providing a controlled environment adhering to reporting guidelines. The system includes other features that help adhere to such guidelines; e.g. confirmation of biological relationships for family-based analysis as recommended by ACMG guidelines. Enhanced filtering options include virtual gene panels to avoid detection of incidental findings.

NxClinical has a Variant Interpretation Assistance (VIA) system that incorporates lab classification rules to automatically pre-classify events. Automated processes reduce errors often introduced by routine manual tasks.  The VIA also “learns” from previous interpretation of events in your database to automatically classify events in new cases.

All data in NxClinical is maintained in a secure, centralized database providing efficient multi-user and remote access.  Assigned user roles and privileges ensure appropriate access and control of data. Notes and comments from different reviewers are tracked and instantly shared with colleagues.  Extensive audit trailing allows for traceability to meet potential regulatory demands.

NxClinical maintains all data in a single, centralized database that can be installed on the cloud or on-site within an institution’s own network. Multiple users can access the same data without causing inconsistencies and instant updates to the database allows all users to access the latest information immediately. The central database also houses information from external databases such as OMIM®, DECIPHER, CIViC, ClinGen, and more providing the same reference and annotation data to all users accessing the system.

BioDiscovery’s MSR algorithm makes it possible to obtain copy number from a variety of NGS data (WES, WGS, targeted panels, shallow sequencing).  This allows one to get the most out of a single NGS assay – getting copy number, AOH, and sequence variants from the same assay streamlines the process and saves both time and money. It also enables easier management of tools with the need for only one analysis and interpretation tool and training on only one software system. In addition to time and cost savings, this paradigm also increases the diagnostic yield allowing for detection of compound events that may otherwise have been missed if analyzed via a test for a single modality.

CNV, SNV, and AOH derived from one NGS assay viewed in NxClinical simultaneously with display of BAM depth and individual BAM reads along with reference data tracks, and BAF and CNV pseudo-probes plots.

NxClinical is unique in that it stores both microarray and NGS data in the same database. Storing CNV and sequence variant data in a single database software system allows review and interpretation of all events (CNV, AOH, and sequence variants) simultaneously for a single sample.  This can help uncover synergistic events (e.g. a deletion of a recessive gene that also has a LOF mutation) which may not be easily revealed when using different software for each modality.

Case showing a compound event on TP53 – single base deletion (blue lollipop on browser at the top and indicated by purple arrows in the BAM reads track) and AOH (gold bar); plus the results table at the bottom.