1486503577_Clinical_Analysis

GENOMIC LABORATORIES

Variantyx offers genomic labs a comprehensive clinical NGS interpretation and reporting solution

Variantyx provides NGS labs with an end-to-end solution for translating sequencing data into a clinical report - accurately and in a cost and time effective manner.

Translating NGS data into a high quality clinical report is a complex process, one that requires highly skilled personnel, up-to-date variant curation databases and top of the line bioinformatic and report generation tools. Yet the competitive marketplace dictates a high level of operational efficiencies.

Genomic Intelligence® achieves the highest level of operational efficiency by integrating all necessary components with process automation and  your Lab Management System (LIMS). A simple to use online console allows for rapid and accurate variant selection and report generation, without the need for on-premise hardware or software. Variantyx Genomic Intelligence® is the most accurate and efficient solution for any size assay - from single gene analysis to WGS.

Variantyx Genomic Intelligence® automates your NGS sequenced data processing interpretation and reporting. Conduct multiple assays, each with its specific pulldown kit gene list, BED file, coverage statistics, customized variant classification and filtration criteria, branded report format and knowledge base, based on your lab’s unique specifications. Seamless integration to LIMS and sequencer further streamlines processing of NGS assays. Gold standard annotation databases ensure high quality, accurate reports, all with a click of a button.

Logistics and process management

Bioinformatics

Variantyx’s Genomic Intelligence® platform utilizes the best of the available public and proprietary tools, resources and databases, as well as in-house developed tools, to detect and report clinically relevant disease causing, predisposing and carrier risk genetic variants. This ensures rapid high diagnostic yield results. The platform is comprised of the following major building blocks:

  • Core bioinformatics
  • NGS data CNV and tandem repeats analysis
  • Gold standard annotation databases
  • Data quality control
  • Data retention

CORE BIOINFORMATICS
Bioinformatic pipeline validated with 1000s of samples

Variantyx maintains an up-to-date gold standard bioinformatic pipeline. Integration and on-going updates of tools and databases is carried out at the highest standards of data quality control and regression testing.

features

  • Up-to-date custom-tuned variant detection using gold standard Broad Institute tools and best practices combined with our proprietary methods
  • Incoming data QC - Coverage statistics, gender and pedigree concordance, and more
  • Identification of uncovered loci with clinical significance
  • Compound Heterozygosity identification and analysis for family trios
  • Structural variant and CNV analysis

Benefits

  • Accurate Test results
  • High diagnostics yield
  • Repeatability and audit trail

NGS data CNV and tandem repeats analysis

Genomic Intelligence® bioinformatic pipeline detects Copy Number Variants in NGS data based upon read-depth analysis, breakpoint detection, and triple repeat region assembly.

features

  • Read-depth analysis on WGS/WES/Panel assays
  • State of the art breakpoint and triple repeat region assembly in WGS sequence data.

Benefits

  • Replace multiple assays with one NGS test
  • Increase the diagnostic yield
  • Multiple CPT codes in one assay

Integration with world leading sequencing partners

Our platform is integrated with a global network of world-leading CLIA / CAP certified labs and sequencing partners. This integration allows for a frictionless process from the sample custody chain through the management of the sequencing process, quality control, and data management.

Gold standard curation databases

To ensure high diagnostic yield, Variantyx maintains a comprehensive gold-standard set of genotype to disease mapping and pharmacogenomic databases. Genomic Intelligence®  annotates the variants using a wide array of public and commercial curated variant and gene databases, as well as numerous severity prediction tools. This ensures rich, comprehensive and up-to-date annotated data per variant for high quality diagnosis.

features

  • Virtual gene panel analysis
  • Variants annotated using the latest versions of a comprehensive set of phenotype/disease and pharmacogenomic databases, including:
    • HGMD® professional and Genome Trax
    • PGMD® professional
    • Clinvar
    • OMIM
    • Orphanet
    • TransFAC
    • Proteome
    • Many others
  • Multiple population allele frequency databases, including:
    • EVS/NHLBI
    • 1000 Genomes project
    • ExAc
    • DGV (for copy number variants)
    • GenBank (for mitochondrial analysis)
    • Variantyx allele frequency database
  • The latest variant severity prediction tools, including: SIFT, MutationAssessor, Mutation Taster, GWAVA, PolyPhen2, FATHMM, Silva, LRT, MetaLR
  • Conservation score prediction tools, including: SiPhy, GERP++, PhyloP, PhastCons
  • Comprehensive gene level annotation databases

DATA QUALITY CONTROL

Genomic Intelligence® provides a comprehensive set of tools for sequenced data quality control prior to the bioinformatic analysis, to verify sufficient coverage and overall quality of the test.

features

  • FastQC checks
  • FLAGSTAT to determine percentage of mapped reads, properly paired reads, QC failed reads and duplicate reads.
  • Check sequencing depth statistics to ensure SLA met

Benefits

  • Verify high data quality
  • Time saving

Data retention

Variantyx maintains its own multi-site fully redundant data centers to guarantee the highest levels of data retention, security and compliance.

features

  • Long term data retention for re-analysis and compliance with regulatory requirements
  • HIPAA compliant

Benefits

  • Compliance with regulatory requirements
  • Cost saving

Automation

Variantyx Genomic Intelligence® is a highly automated NGS diagnostic platform. It significantly lowers the time it takes to run a genomic test, diagnose a case and compile a report. Variants are pre-annotated against a comprehensive set of databases, which allows for rapid variant selection by the diagnosing physician. Customizable workflow and approval process, with a full audit trail, ensure repeatable and auditable results.

Assay specific solutions

Automate Each assay

Assay-specific customization provides further automation and streamlining of your lab’s processes. Work with our team to define, for each assay, the list of target genes, variant classification and filtration criteria and an assay-specific report format. 

features

  • Coverage statistics on your assay gene list
  • Multiple predefined filters based on your clinical team’s criteria
  • Custom report format with your Medico-Legal language.

Benefits

  • High level of customization
  • Operational efficiencies
  • Based on your specifications

LIMS integration

Variantyx integrates to your labs management system, for automation of process control and management.

features

  • Automate all normal processing between sequence data creation and your clinicians use of the Genomic Intelligence® Only exceptions need attention.
  • No per test overhead -  improves operational efficiencies.

Benefits

  • Improved consistency, lower cost, lower turnaround time.

Validation management

Whenever Sanger validation is required, Genomic Intelligence ® provides automation to support the process.

features

  • One-click work order generation
  • Results are integrated into the report

Benefits

  • Streamlined Sanger validation process

Genomic diagnostics platform

Console and Reports

Genomic Intelligence ® is a cloud platform hosted by Variantyx, with a web based diagnostic console user interface. Using the platform does not require any on-premise hardware or software, offering enhanced security, high availability and maintenance-free operation.

 

The user-friendly diagnostic console allows for variant selection and report generation with a few button clicks.

Online diagnostic console

Genomic Intelligence ® is accessible and operated via a highly secure, HIPAA compliant, always on web based diagnostic console. It allows for

Multilayer system presents the diagnosing clinician with the most relevant information for the case diagnosis and report compilation. Drill-down capabilities allow the clinician to navigate through the available rich information, down to the PubMed article,

features

  • From variant selection to report generation with a few button clicks.
  • Layered content presents the most relevant information

Benefits

  • Operational efficiencies
  • Accuracy

Customized reports

Powerful report generation tool allows for customization of reports per assay. Customizations include your specific branding, medico-legal language and content from a comprehensive set of available data.

features

  • Customizable reports per assay

Benefits

  • High quality reports custom tailored to your clinical teams requirements
  • High level of automation

Knowledge base

An integrated knowledge base further improves report automation for high volume assays by storing variant-specific comments and follow-up recommendations, preserving the organization's domain expertise knowledge base.

features

  • Codification of the lab’s best recommendations
  • Variant level analysis knowledge base
  • Patient follow up recommendation knowledge base

Benefits

  • Further automation
  • Allows rapid ramp-up of new clinical staff
  • Consistent, high quality clinical recommendations

Patient’s report generation

Genomic intelligence® integrated report generation tool allows clinicians to efficiently produce information rich clinical diagnostic reports with a high level of automation.

features

  • Integrated patient report generation tool

Benefits

  • Findings and recommendations rolled up into one concise document
  • Time saving
  • Medico-legal Compliant
  • Exportable, post editable

Variants classification, filtration and diagnostics tools

Variantyx’ interactive and easy to use web front-end allows clinicians and bioinformaticians to rapidly identify variants of interest then rapidly access further details, such as the PMID article where the variant was reported.  Our platform aids diagnosis through the utilization of proprietary phenotype-disease-genotype mapping algorithms.  The most likely causative variants relating to the patient’s phenotypes are highlighted for prioritization of candidate causative variants, leading to rapid and accurate diagnosis.

features

  • Interactive, multi-level filtration by the physician and/or bioinformatician with drill-down capabilities using web links to leading genomic resources
  • Proprietary algorithms to convert human curated databases to machine readable formats
  • Proprietary Mode Of Inheritance (MOI) database
  • Proprietary phenotype-disease-genotype mapping algorithms; highlighting most likely causative variants relating to patient phenotypes

Benefits

  • Rapid, accurate diagnosis
  • High diagnostic yield

Collaboration tools

Genomic intelligence® provides hospitals with collaboration tools, allowing bioinformaticians and clinicians to collaborate effectively while maintaining privacy and security segregation based on hospital defined rules.

features

  • Custom security and sharing rules between clinicians and bioinformaticians for collaboration

Benefits

  • Effective collaboration
  • Operational efficiency
  • Rapid diagnostics
  • HIPAA compliance

Periodic reanalysis of unsolved cases

Genomic Intelligence® provides automation tools for periodic re-analysis of unsolved cases. The system can be configured to re-run the cases on a predefined schedule or based on clinical databases updated. New findings can trigger notification to clinicians and/or bioinformaticians for reanalysis of the case if need be.

features

  • Automated re-annotation and announcement of new scientific findings
  • New findings are reported to physician / Bioinformatician

Benefits

  • Improved case closure rate
  • Higher diagnostic yield

Diagnostics and clinical interpretation services

Variantyx’s team, consisting of highly skilled bioinformaticians and US Board certified clinical geneticists, is available to work closely with our customers for diagnosis or second opinion of clinical cases.

features

  • In-house bioinformatician or Variantyx professional services team can work hand in hand with the clinician
  • Variantyx Clinical diagnosis and/or second opinion provided by US board certified clinical geneticists
  • Fully insured

Benefits

  • Allows the patient’s clinician who is most familiar with the case to conduct the diagnosis
  • Augmented by Variantyx’ clinical team for time savings or second opinion
  • Rapid and accurate diagnostics

Custom tools and services

Genomic Intelligence® web front-end provides an interactive and easy to use interface for rapid diagnostics, supporting singleton analysis as well as small family cohorts with known pedigree. In addition to the web front end, Variantyx provides customizable research tools for large cohorts and complex queries. A high performance variant database, supported by Variantyx’s professional services team, utilizes modern database querying tools for custom analysis of larger cohort sizes. 

features

  • High performance database with sophisticated database querying tool for complex custom queries
  • Supported by Variantyx’ professional services team

Benefits

  • High flexibility for complex research analysis