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The long-awaited NxClinical update is here! NxClinical 6.0 is packed with over 500 features and improvements - too many to talk about here but below are some highlights.

Want to dive deeper into these and other new capabilities in NxClinical 6.0? Register for our tech tour series to see NxClinical in action. These 30-minute sessions introduce new guidance to improve your daily workflow as an analyst or a reviewer.

1. Knowledgebase

Eases the interpretation and reporting process and enhances consistency in reporting

A new database within NxClinical, called the “Knowledgebase” (KB), stores information about a variant or genomic region allowing users to create their own personal database of syndromes, cytogenetic regions, or pathogenic variants. The database allows for multiple different KBs split between constitutional and oncology which can then also specify between CNV and AOH events as well as genome-wide profiles for oncology.

  • Specifically for constitutional, annotations such as inheritance mode, event interpretation, PubMed references, evidence level, and phenotypes can be added.

  • For oncology cases, the KB stores cancer-specific information such as cancer type from the WHO and OncoTree ontologies, gene functions (tumor suppressor/oncogene), and AMP-ASCO-CAP classifications. The KB also links to relevant publications through a PubMed ID which provides important information on diagnostic, therapeutic, and prognostic content.

Knowledgebase profile record(click image to enlarge in a new tab)

2. Variant Details View

Collated information on a variant in a single easy-to-digest view allows rapid and accurate interpretation of variants

A new Variant Details user interface pulls together and displays collected information for a variant in an easy-to-read single view. The layout automatically adjusts for different modalities (CNV, AOH, or SeqVar) and type of sample (Oncology vs. Constitutional) to present the most relevant information in a concise format to help quickly and confidently interpret the variant.

Variant details view displays a constitutional sample copy number loss(click image to enlarge in a new tab)

Variant details view displays oncology sequence variant(click image to enlarge in a new tab)

3. Oncology Profiles

Visualize genome-wide CNV and AOH profile of oncology samples and compare to stored cancer-specific profiles stored in the knowledgebase

Somatic samples exhibit many copy number and AOH events across the genome. Certain cancer types have very specific “signature” profiles that are both diagnostic and prognostic. In NxClinical 6.0, you can now create genome-wide profiles by grouping various samples together (e.g. all AML cases). These profiles can be added to the Knowledgebase with extensive annotation support (references to publications, important genes, interpretation, etc.). Users can also import oncology profiles (e.g. TCGA profiles) and utilize these to aid in diagnosis and interpretation. The Global Similarity function compares a new case against these stored and annotated CNV and AOH profiles and ranks them to show which profiles are the most similar. A sample can also visually be compared to select stored profiles. The function allows for rapid verification of tumor type and can also indicate a different origin for the sample than the one reported.

oncology profile and global similarity plot(click image to enlarge in a new tab)

4. Inheritance Pattern filter enhancements 

Allows application of all inheritance models simultaneously rather than one at a time with the union of the results displayed

The inheritance pattern filter has now expanded to include CNV events in addition to SeqVar events.  Another new filter allows display of only those variants where the inheritance model is consistent with the OMIM inheritance model (e.g. only displaying homozygous variants for OMIM recessive genes).

5. Customized Views

Enables individual users to create a view that is optimal for their specific role within the review process allowing for stronger case-review collaboration

Enhanced customizations for layouts and views allow creation of multiple different views consisting of specific tracks, filters, etc. that can be specific to a user, to an individual sample, or can be shared among users. For example, a case level view can be shared among users allowing each reviewer to see the same filter settings and visual components used for interpretation. An “Interpretation View” containing many tracks (OMIM Morbid, DECIPHER Syndromes, etc.) and multiple fields can be used during the interpretation process and a “cleaned up” view, “Final Report View”, with just a few relevant tracks and fields can be used for reporting.

This release is packed with new and improved features that make the interpretation process much more efficient and pain-free.

Join our tech tour and see NxClinical 6.0 in action.

Our experts lead 30-minute webinar sessions, offering practical information and guidance to improve your daily workflow as an analyst or a reviewer. We explore a variety of application areas, including constitutional genetics, oncology, molecular genetics, and preimplantation genetics. Use the button below to learn more and register.

Join the tech tour