Database Providing:
• Accessibility
• Security
• Quality Control Review
• Variant Review
• Historical Library
• Variant Pathogenicity Prediction
• Laboratory Reporting
• Exportation to LIMS
Geneticist Assistant NGS Interpretative Workbench has been developed in collaboration with Mayo Clinic, departments of Laboratory Medicine, Information Technology and Health Science Research to provide a multi-tool electronic database to create significant informational efficiency in laboratories utilizing Next Generation Sequencing. The database is compatible with standard .BAM, .VCF and .BED files as well as custom databases. Geneticist Assistant Workbench includes tools for ascertaining if NGS sequencing has met user defined quality parameters; logs all found variants by individuals and test panel, develops a historical overview by test panel and variant; provides pathogenicity prediction scoring from multiple databases, color codes pathogenicity calls and links to confirmatory scientific articles such as PubMed, dbSNP and others.
Geneticist Assistant Workbench additionally develops actionable lists of novel variants, low coverage regions or variants requiring confirmatory Sanger Sequencing, or variants that require pathogenicity verification and confirmation.
Security and user access is managed through Geneticist Assistant Workbench’s user management control module, which can be used to limit access by function to groups or individuals. Geneticist Assistant Workbench tracks and records all changes which can be recalled by user and user groups. Additionally the Workbench encrypts all data with a SSL connection.
User Management
Access to the various functionalities of Geneticist Assistant Workbench is managed through the embedded user management tool; The Workbench administrator assigns individuals or groups access to various functionalities of the program by username and password. The Workbench
automatically records log on/log off times, edits or other changes made to data. Activity reports can be generated by authorized personnel.
Workbench Input/output
Geneticist Assistant Workbench accepts standard .BAM, .VCF, .BED and custom panel inputs. Workbench automatically applies the sequencing .BAM file and .VCF file to the test panel, which can be limited by utilization of a .BED file. NextGENe® software users have the capability of creating an automatic link between NextGENe and Geneticist Assistant Workbench creating a seamless Analysis/QC/Variant Interpretation/Reporting pipeline. Finalized laboratory reports can be saved electronically in .PDF format or exported to LIMS as comma delimited text files.
Quality Control
Geneticist Assistant automatically reviews sequencing files comparing to user defined quality control metrics. Each region, as defined by .BED files, is reviewed, and areas failing to meet user defined quality parameters can be flagged for further review or placed on an Action List for resequencing or Sanger sequencing.
Quality metrics include: Acceptable minimum and average coverage across .BED region; percent of the region covered; distribution of quality scores, overall GC% of sample, GC% per base position and read length distribution.
Sequencing Action List
Regions failing to meet user defined quality parameters are easily added to an Action List, for further review, resequencing or Sanger Sequencing. Report includes start and end positions for primer chemistry, reason for failure, as well as further actions required.
Simple Operation
Recently submitted Next Generation Sequencing runs are automatically listed in Geneticist Assistant. To view additional information for any new runs, simply double click on the run of interest. Automated pipeline is easily created by users of NextGENe software, and importation of analyses by other software programs can be automated by creating a simple importation script.
All samples included in the sequencing run are listed in the run tab, each includes sample ID; run date and time; run name; test panel name; reference used; number of regions included in panel; patient ID; current status such as passed or failed Quality Control, ready for review, ready for pathogenicity calling, ready for laboratory reporting etc. as well as any entered comments. After each stage of review, the status of a particular sample can be updated.
Genome Viewer
Geneticist Assistant workbench includes an interactive genome viewer that provides a review of all regions defined by the .BED file, a list of the panel regions with quality control settings and sample metrics, found sample variants, as well as an interactive read pile-up. Clicking on a region or variant centers the variant in the pile up view for rapid manual visualization.
Historical Knowledge Base Development
Detailed information regarding each found variant can be reviewed including annotation, prediction information, previous pathogenicity status and other samples where the same variant was found. Following pathogenicity review and confirmation, variants can be sorted bringing only those considered damaging to the top of the list. As historical information is developed fewer novel variants will be noted, significantly reducing pathogenicity review time and resources.
Geneticist Assistant includes pre-calculated pathogenicity scores from the dbNSFP database, which includes several algorithms including LRT, PolyPhen2, SIFT, Mutation Taster and Mutation Assessor as well information from the COSMIC database. Custom or other similar databases can easily be imported into Geneticist Assistant Workbench.
Pathogenicity supporting information such as scientific articles, PubMed articles, and dbSNP information are easily linked to the pathogenicity call allowing quick and easy review.
Pathogenicity can easily be selected via a drop down menu, speeding recognition for future samples. Geneticist Assistant automatically develops a “variant card” for each found variant speeding pathogenicity review. Variants that are pending pathogenicity call can be confirmed by authorized users and are recorded and locked. Geneticist Assistant automatically records the date, time and personnel that set the pathogenicity of the variant. Supporting information from various sources such as PubMed, dbSNP and others are easily linked to the variant card.
Variant Confirmation Action List
Novel variants are easily exported to an Action List indicating that further review or confirmation by Sanger Sequencing is required.
Variant Confirmation Action List
Laboratory Report Generation
Laboratory Report Generation
Laboratory reporting is simple and direct within Geneticist Assistant, simply highlight variants and information of interest, select report format and click to save. Program will automatically print in pdf form, CSV or other formats.
Accessibility
Geneticist Assistant Workbench provides extremely flexible accessibility from just a single dedicated computer to access over the internet. The workbench can be utilized by single departments, multiple departments within an institution or by multiple collaborating institutions via a SSL internet connection. A single workbench server can easily be accessed by multiple clients.
Export to LIMS
All data contained Geneticist Assistant Workbench can easily be exported to LIMS systems in .CSV format. For complete automation, please contact us to develop an export script.
SoftGenetics
Oakwood Centre
100 Oakwood Avenue
Suite 350
State College PA 16803 USA
info@softgenetics.com
www.softgenetics.com
© 2013 Registered Trademarks are property of their respective owners. For Clinical Research
Recommend Hardware Requirements
Server and Database: 4 cores
8 GB RAM
2TB hard drive space available (expandable)
64bit Linux (Ubuntu 10.04 or higher is recommended) or Windows Vista, 7, 8 or Server 2003 through Server 2012 OS Client:
4 cores 8 GB RAM 500 GB hard drive
64bit Windows Vista, 7, 8, Server 2003 through Server 2012 OS
