We are ringing in the new year with a webinar on what’s new in NxClinical. We have three webinar sessions (schedule below) on the upcoming NxClinical 5.0. There are many new features that will be available in version 5 and here are some highlights.
Enhanced support for mosaicism including aberrant cell fraction calculation
Multiple new features and enhancements have been added to support detection, visualization, and reporting of mosaic events. Some of these are
- Events can now be marked as mosaic either manually, or automatically during processing based on whether it meets the user-defined threshold.
- Aberrant cell fraction can automatically be calculated using the log R and BAF (when available) using a platform-specific conversion algorithm. The values can be calculated for all one-copy CNV events as well as copy neutral AOH events. The reviewer may manually change the value if desired and any such change will be documented.
- Mosaic events can be spotted easily in the browser as the event indicator bars for these will be displayed with a texture fill.
- The log R plot can now also be displayed as copy number values and easily switched back
Phenotype-based Gene Panel Design
To aid with interpretation, a phenotype-based “virtual panel” filter can be applied to individual cases to take into consideration the relevance of a gene to the phenotype
- Gene panel automatically populates with genes associated with phenotypes of the case under review
- The genes in the panel are listed based on the most relevant gene first using a significance score that uses the number of phenotypes and their position in the HPO ontology. The most relevant genes can be selected based on a significance threshold.
- The significance score takes into account the contribution (as interpreted by a clinician) of an individual phenotype to the diagnosis. A phenotype that the clinician feels would be more relevant will get a higher weight than other phenotypes in this calculation.
Significance Associated with Phenotype (SAP) score
This new score improves upon the existing Evidence Score value. Phenotypes associated with all the genes in an aberrant region are compared with the list of sample phenotypes using a statistical measure to arrive at the SAP score.
Multiple Improvements to Support Panels
In addition to phenotype-based gene panels described above, many other enhancements have been added for panel support including
- Import of regions covered by a panel (can be imported as specific transcripts or just genes/regions) and expected minimum coverage. The software automatically measures the coverage and provides a warning if some areas are not sufficiently covered thus avoiding potential false-negative results.
- Ad-hoc panel report per sample allowing the reviewer to upload any arbitrary list of genes or regions as a panel to filter or review a specific sample.
- Locking of event display and reporting so that only regions specified as a panel will be displayed (e.g. prevents incidental findings)
Enhancements to Sequence Variant Annotations
- Sequence variants can now be annotated directly from within NxClinical allowing for streamlined and hassle-free loading and processing of VCF files for sequence variant analysis without the need for external pre-processing using a variant annotator.
- A new custom VCF parser allows import of custom fields from the VCF file.
- Additional in silico predictions (Mutation Assessor, FATHMM, MetaSVM, and MetaLR) have been added.
There are many other enhancements such as improvements to estimation of CNV from very small panels as well as estimation of CNV from WGS without a reference file . Most of the features listed above and some others not listed will be covered in the webinar so sign up now to see what's coming in NxClinical 5.0.
Jan. 16 at 5:00pm PST Jan. 17 at 9:00am CST(Beijing)| 12:00pm AEST
Jan. 17 at 7:30am PST | 10:30am EST
Jan. 17 at 10:00am PST | 1:00pm EST