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These tutorials are for NxClinical admins and users who setup workflows, processing parameters, sample types as well as user profiles. We also have sessions dedicated for reviewing and signing out cases.
This tutorial should review the structure and content of the existing tracks in NxClinical (provided by BDI) and then show how users (Admin) can add custom tracks. The user should be shown how to organize tracks into folders (best practice: create a separate folder to house custom tracks); note that tracks are build specific. The basic BED file format should be shown to create a functional track and what that would look like in the UI. Then the user should be shown how to add additional elements such as color coding and links to the files and how these would look in the UI.
This tutorial should review the source for genes in this track, source for transcripts, bold/canonical indicators in the UI for transcript selection and how to select a different transcript. Users should also be shown that they can link out to external db via right click and how to change the options to their favorite dbs. This tutorial can also show users how to change the transcript source to use transcripts from HGMD, for example.
This session will demonstrate how to review a somatic cancer case and the importance of genome-wide CNV and AOH from NGS panels.
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This session will go through the various areas of the Admin tab in an overview fashion to cover all the things the admin can do. For example, will show the Users tab and explains how to create, assign privileges, and inactivate users.
We will provide an overview of setting up initial preferences for different sample types and why this should be done.
At the end of this session, the attendee will have a good idea on all the capabilities of the admin role.
This session is a basic introduction to the NxClinical system with the main focus on the home tab and its layout. It will cover the various query limits that can be set from the filter drop down lists (e.g. Sample Types, Phenotypes, etc.) as well as how to query for samples based on name, attributes, processing dates, etc.
We will cover the basics of how the load, duplicate, delete functions work as well as the multi-sample view. Finally, we will cover the information that can be seen for each sample including the hyperlinked sample type and processing type, the various QC metrics visible and how to edit sample attributes and get more information from the sample info window.
At the end of this session, the attendee will know how to perform relevant queries to quickly locate samples, understand all the fields in the query results, and how to get more information about a sample.
This session will cover both the Self-Reference Algorithm as well as the MSR (multiscale reference) method.
We will cover the basic ideas behind the approaches and dive into the reference builder, its parameters, how to use it and how to load the reference into NxClinical. We will also cover how to set parameters for panels, WES, and WGS data and gender matching. Quality measures (e.g. capture bias, various read counts) will also be discussed.
At the end of this session, the user will have a good idea on when to use each algorithm and the pros and cons of each, how to create reference files and process samples in NxClinical using these methods to get CNV and AOH data.
This session will cover the SNP-FASST2 and SNP-Rank algorithms for CNV and AOH detection. At the end of this session, the user will understand how the different parameters in the SNP-FASST2 and SNP-Rank algorithms impact the sensitivity and specificity of the CNV and AOH detection from SNP array data.
This session will cover how the Variant Interpretation Assistance (VIA) system is designed to increase the efficiency of the case review process by pre-classifying CNV and AOH events.
Some examples will be shown (e.g. how previously classified events can be used to pre-classify recurrent events as artifact, how overlap with certain regions or gene content can help in classification). We will demonstrate how the admin can create multiple trees and test all of them in parallel against a test sample and how to make adjustments and retest the tree.
At the end of this session, the admin will be able to create and edit a decision tree before deploying it for use with different sample types.
This session will give a brief overview of how the SAP score is calculated for single genes as well as CNV/AOH events that cover multiple genes and how to use it to identify the most relevant variant.
The genes and SAP scores in the panel tab will be covered along with color coding of genes in the panel tab.
Constitutional singleton case review - Cytogenetic workflow (from raw data to final report)
Constitutional singleton case review - Combined Cyto and Molecular analysis using NGS and array data (from raw data to final report)
This session will focus only on trio analysis and will cover the parent of origin column for SNP arrays as well as how to use inheritance pattern filtering in both CNV and NGS data.
This session will cover how the admin can create and load different panels for each sample type and also how a similar process can be done by the user in ad-hoc fashion. It will cover how to specify transcripts or regions in the panel and how to use the coverage QC measures for NGS data.
We will also cover validation of the regions and how the admin can re-validate regions if required.
This session will cover how the whole genome view should be reviewed to detect low level mosaic events that might not have been called. We will also show how to merge mosaic events with many small calls clustered in an area and how to convert an alleleic event into a mosaic AOH.
We will also cover the aberrant cell fraction and estimated copy number columns and how to interpret these values.
This session will demonstrate a “typical” end-to-end case review process for CNV/AOH data. We will start at the point where sample is already loaded and processed in the system and and walk through the review process (filtering, pre-classification, variant prioritization...) to end at the final report.
This session is intended to give a “typical” end-to-end case review process for CNV/AOH/Seq Var data. At least one example should show a combination of array and NGS. It should follow similar flow as the cyto but should include cases where there is only pathogenic Seq var data as well as potential combination of Seq Var and CNV/AOH (I think the p53 case from CHLA would be very nice here as the last example)