Technology

Genomic Intelligence®

Proprietary technology driving advanced diagnostics

Our algorithms

Many benefits are inherent in whole genome sequencing (WGS) technology. PCR-free DNA preparation methods eliminate amplification-related issues producing better coverage of amino acid coding regions. In addition, comprehensive coverage of intronic and intergenic regions ensures the identification of potentially relevant transcription factor binding site, enhancer and other regulatory variants. Importantly, WGS provides unique opportunities for detection of more complex variants.

Our algorithms, used on WGS data, uniquely identify and analyze four types of variants:

  • Small sequence changes (SNVs and indels)
  • Structural variants, including CNVs
  • Trinucleotide repeat expansions
  • Mitochondrial variants

These clinically validated, technological advances form the basis of our Variantyx Unity™ test for rare genetic disorders and the components of our lab solutions which are enabled by our Genomic Intelligence® NGS data analysis and interpretation platform.

Our platform

Developed to handle WGS data, our proprietary Genomic Intelligence® platform provides sample to clinical report generation and automation for genomic tests at any size or scale. All aspects of the NGS testing process are seamlessly integrated to deliver the highest level of operational efficiency coupled with superior diagnostic results.

Our Genomic Intelligence® platform integrates and automates:

  • Sample collection and test selection
  • DNA extraction, QC and sequencing
  • Data QC, analysis and annotation
  • Interpretation and clinical reporting

The HIPAA-compliant platform can be used from end-to-end, or select components can be used to perform dedicated NGS analysis and intepretation tasks such as clinical report generation.

Collect Sample

Sequence

Call Variants

Annotate & Filter

Interpret

Clinical Report

Sample collection and test selection

Prepackaged sample collection kits make it easy to initiate the testing process while maintaining patient privacy and full compliance with regulatory requirements. Each kit uses a unique barcode. When a barcode is activated, relevant shipping documents are automatically generated. An audit trail is initiated, tracking custody chain and progress of the sample through the entire testing process.

A wide and ever growing menu of industry-leading pull-down kits provides full flexibility to select the most appropriate test for the patient. Panel, whole exome and whole genome options are available. The ordering physician has the ability to input information about the patient’s phenotype in order to further guide the analysis.

DNA extraction, QC and sequencing

The Genomic Intelligence® platform is integrated with world-leading sequencing partners. DNA extraction and sequencing are performed to the highest standards as ensured by rigorous QC processes. Pre-negotiated discounts guarantee competitive pricing with no minimum volume required. This results in a per-sample cost significantly below what can be achieved with locally hosted infrastructure. The integrated workflow simultaneously ensures an unbroken audit trail and ongoing oversight of the sample’s progress at all times.

Customized integration with existing laboratory management system (LIMS) and sequencer is also available.

Data QC, analysis and annotation

Raw sequence data is securely transferred to Variantyx’s cloud-based, HIPAA-compliant Genomic Intelligence® platform. The bioinformatic pipeline provides rapid, accurate data analysis and annotation employing:

  • Extensive data QC including determination of mapped read percentage, properly paired reads, QC failed reads, duplicate reads, coverage statistics, gender and pedigree concordance
  • Gold-standard algorithms and best practices for alignment and variant calling
  • Proprietary methods for calling structural variants, trinucleotide repeat expansions and mitochondrial variants
  • Best-in-class public and commercial variant and gene annotation databases
  • Multiple population allele frequency databases
  • Proprietary mode of inheritance data and phenotype-disease-genotype mapping algorithm
  • In silico panels
  • Widely accepted variant severity and conservation prediction tools

Variantyx’s multi-site, fully redundant data centers guarantee the highest levels of data retention, security and compliance while keeping operational costs low.

Interpretation and clinical reporting

Sequenced, analyzed and annotated data are automatically transferred to your team for expert data interpretation and review. The multi-layer Genomic Intelligence® diagnostic console provides a summary of variants passing the default filter settings.

Variants are evaluated against known patient phenotypes and ethnicity. Clinical geneticists drill into each variant individually, reviewing rich details including links to supporting literature for annotated variant-disease and gene-disease associations. They can adjust the filters as desired to expand or contract the variant list. Once satisfied, the clinical geneticist simply selects the variant(s) to be reported and enters any comments and/or follow-up recommendations. A single button click automatically generates a clinical report. If desired, Sanger sequencing validation can be ordered automatically.

Report templates can be customized with an institution’s branding and medicolegal language. In addition, variant-specific comments and follow-up recommendations can be stored in a custom database for reuse with new samples. Automated tools for optional periodic reanalysis of unsolved cases lead to even greater diagnostic yields. Finally, our board-certified medical geneticists are available to help with data interpretation, or to provide a second opinion.

 

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