Hospitals

Hospitals

Variantyx offers hospitals a complete solution for Genomic diagnosis of rare genetic disorders.

Our Genomic Platform as a Service™ provides the basis for an in-house Whole Genome diagnostics core, without the capital and operating expenses of an NGS core, overcoming any disadvantage associated with remote diagnosis.

Running an in-house clinical NGS core has the potential to be beneficial for medical centers, as it promises better diagnostics than traditional technologies. However, the complexity and cost of in-house testing makes it prohibitive for the vast majority of the clinical community worldwide. Outsourcing tests to third party genomic centers disconnects the physician diagnosing the case and the patient, resulting in lower diagnostic yield, long turnaround time and high cost.

We help hospitals build a genomic diagnostic core using our Genomic Intelligence®, an end-to-end diagnostic platform, from sample collection to diagnostic report generation. Genomic Intelligence® enables hospitals to conduct WES/WGS diagnostics in house without the need to own and operate an NGS core. The result is the best of both worlds, as it brings together a high quality diagnosis at a reduced cost and rapid turnaround time.

Logistics and process management

Medico-Legal and Records Management framework

Genomic Intelligence® automatically generates all necessary locale-specific forms needed for the particular medical test and stores the signed forms in a single, easy to access location. These include an electronic patient questionnaire, patient informed consent, physician disclaimer, research and clinical use documentation and territory specific materials. Throughout the process, the CLIA chain of custody is maintained. Forms can be customizable per customer, and provide the necessary audit trail required.

features

  • Automatic generation of Electronic Record Management and Medico-Legal forms for compliance with clinical and other regulations
  • CLIA and HIPAA compliant
  • Audit trail and custody chain maintenance

Benefits

  • Compliance with clinical regulations
  • Time savings
  • Cost savings

Sample collection, logistics and custody chain management

Genomic Intelligence® provides a comprehensive set of tools for the management, shipping and tracking, chain of custody, and automation of the lab and logistics processes, including:

 

  • Sample collection kits optimized for international shipping and tracked to avoid use of kits past their expiration date.
  • Unique identification (barcode) stickers pre-assigned to each account and labeling each sample and accompanying medico-legal paperwork for tracking.
  • Automatic generation of international shipping documents (Air-waybill, pro-forma invoice, non-hazardous materials declaration)
  • Chain of custody tracking and management tools for audit trail

features

  • Pre-packaged sample collection kits
  • Automation of logistics and international shipping
  • Integrated chain of custody process with sequencing partners

Benefits

  • Hassle free
  • Time saving
  • Cost saving
  • Visibility and audit trail
  • Compliant with regulatory requirements

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.

Test selection optimization

Genomic Intelligence® allows for optimal choice of sequencing company and test type (Clinical Exome, WES , WGS), at the correct coverage and relevant specifications to best fit the case.

The platform allows for entry of patient phenotypes (based on HPO nomenclature) and/or suspected diseases. A list of genes of interest is then generated (in-silico virtual panel) for pre-sequencing coverage analysis. Genomic Intelligence® maintains up-to-date coverage analysis statistics for several major sequencing companies, sequencing equipment used and the industry leading pull-down kits.  Based on this coverage analysis databases and the list of genes of interest, Genomic Intelligence® compares multiple sequencing options for the user to optimize coverage, cost, and time.

features

  • Virtual panel compilation based on list of phenotypes/diseases
  • Coverage statistics database for the industry leading pull-down kits, sequencing equipment, and sequencing companies
  • Marketplace of sequencing partners - We contract with world leading CLIA/CAP certified labs and Israeli ministry of health certified labs, all of which provide both clinical and research products.

Benefits

  • Allows users to optimise test selection accounting for coverage in regions of interest, turnaround time, and cost

DNA extraction and Quality Control management

To ensure high quality sequencing and sufficient coverage, we track the DNA quality and quantity, as well as provide DNA extraction services from various tissue sample types. This reduces the need for PCR cycles or the need to re-sequence. Genomic Intelligence® provides tools to track the sample quality from extraction through sequencing. An audit trail of the sample quality control results ensures a high quality sequencing, saves time, and reduces unnecessary cost.

features

  • Management and quality control of DNA sample from extraction to sequencing
  • Integrated process with ecosystem partners for DNA extraction and quality control
  • Maintained custody chain and audit trail

Benefits

  • Guaranteed high quality sequencing
  • Efficient resolution of exceptions
  • Time saving
  • Cost saving

NGS sequencing services

Variantyx works closely with world leading sequencing vendors to offer a wide range of competitively priced and high quality sequencing services. These include targeted Whole Exome and Whole Genome options.  Our platform is integrated to the sequencers’ Laboratory Information Management System (LIMS) and Data plane. This ensures automated, secure and compliant data download services. We pass on all volume discounts maintained with our sequencing partners.

features

  • Marketplace of world leading sequencing partners
  • Full suite of targeted, whole exome and whole genome sequencing products with various coverage levels and different pulldown kits
  • Available for both clinical and research application

Benefits

  • Wide range of products from which to choose
  • Competitive pricing
  • High throughput processing, not limited by in-house capacity, eliminates the need for buying and maintaining expensive sequencing equipment

NGS sequencing management tools

Genomic intelligence® provides tools for the automation and management of the sequencing process, whether performed in-house or by a third party through Variantyx. These tools guarantee repeatable high quality results by managing the sequencing specifications, such as processing facility selection, Sequencing Machine, Pull-down kit, coverage, number of bases read, read length and many other parameters.

features

  • Tools for tracking and management of the sequencing process

Benefits

  • Efficient communication with sequencing companies
  • Guaranteed high quality of sequencing
  • Audit trail
  • Time saving
  • Cost saving

Data handling and retention

Genomic Intelligence® service platform is integrated with multiple sequencing partners for automated, rapid, low cost and secure data transfer. Sequenced data is directly downloaded into Variantyx’s data centers, eliminating the challenges of courier shipping of hard disk drives with clinical data. Variantyx maintains its own multi-site fully redundant data centers to guarantee the highest levels of data retention, security and compliance.

features

  • Integration to partners’ LIMS and data download tools
  • Automated, rapid, and secure data download from sequencing partners to our systems
  • Long term data retention for re-analysis and compliance with regulatory requirements
  • Licensed genetic database by the Israel ministry of justice

Benefits

  • Hassle free handling
  • Rapid results
  • Secure, HIPAA compliant process
  • Cost saving

Validations

Variantyx and its ecosystem partners provide an end-to-end service for Sanger validation of variants of interest. Extracted DNA is stored by the sequencing partners for a pre-defined period to allow for Sanger validation of clinically actionable results.

Genomic intelligence® provides management and automation tools for the validations process to ensure rapid and accurate validations while maintaining audit trail and chain of custody.

features

  • One click integrated process for results validation
  • Full workflow integration with wet bench partners
  • Results interpretation

Benefits

  • Rapid, accurate, compliant process

Genomic diagnostics platform

A highly automated WES/WGS diagnostics platform significantly lowers the time it takes to diagnose a case, resulting in lower cost and turnaround time.

Gold standard bioinformatic analysis and clinical databases.

Intuitive, interactive, and easy to use web console for clinicians.

Sequenced data quality control

Genomic Intelligence® provides a comprehensive set of tools for sequenced data quality control prior to the bioinformatic analysis. Among others, these include:

  • MD5 and FastQC checks to validate downloaded fastq files
  • FLAGSTAT run to determine percentage of Mapped Reads, Properly Paired Reads, QC Failed Reads and Duplicate Reads. For example, a high duplication rate can identify that DNA may have undergone too many rounds of PCR before sequencing, resulting in coverage bias.
  • Check mean and median read depth vs. requested sequencing depth to ensure sequencing to requested standards
  • Coverage analysis of all sequence target based on pull-down kit BED files and panel genes of interest coverage in particular
  • Aneuploidy analysis
  • Verify predicted gender of sequenced data vs. reported patient gender as a check on correct clinical data entry and sample matching
  • Verify whether the reported pedigree is in concordance with sequenced data as a check on correct clinical data entry and sample matching

features

  • Comprehensive quality control of incoming data
  • Assurance of correct data entry and sample handling and matching

Benefits

  • Guaranteed high quality sequencing
  • Overcomes human errors
  • Time saving

Bioinformatic analysis

Variantyx’ 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 disease causing and other clinically relevant genetic variants. This ensures rapid high diagnostic yield results. The platform is comprised of the following major building blocks:

  • Core bioinformatics
  • Genotype to disease mapping tools and databases
  • Variant classification, filtration, and diagnostic tools
  • Collaboration tools
  • Custom tools and services

Core bioinformatics

Variantyx maintains an up-to-date gold standard bioinformatic pipeline, as detailed in the Genomic Intelligence® appendix. For each bioinformatic analysis the system logs the tools and databases that have been used, providing diagnostic repeatability and audit trail. 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 variant detection using gold standard Broad Institute tools and best practices
  • Incoming data QC - Gender and pedigree concordance, coverage and more
  • Identification of uncovered loci with clinical significance
  • Compound Heterozygosity identification and analysis for family trios
  • Structural variant analysis for Whole Exome Sequencing / Whole Genome Sequencing

Benefits

  • State of the art gold standard core bioinformatics
  • Test repeatability and audit trail
  • High diagnostics yield

Genotype to disease mapping tools and 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
    • Proteome
    • Many others
  • Multiple population allele frequency databases, including:
    • EVS/NHLBI
    • 1000 Genomes project
    • ExAc
    • 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

Benefits

  • Up to date Genotype to disease mapping tools and databases for gold standard diagnosis
  • High diagnostics yield

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

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

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