Clinical Interpretation

Technology & Capabilities

RareCODE

Solve more cases by identifying novel candidate genes/variants and validating with instant raw sequence visualization

RareCODE, our rare disease clinical interpretation system enables, users to quickly analyze their data through a clinically intuitive interface. It can identify novel and de novo mutations, provide instant validation through unrivaled raw sequence, and allows custom knowledge base creation.

Solve Cases Faster

Shave days from once-tedious workflows, filtering variants by frequency, impact and mode of inheritance. Scan for de novo variants and validate immediately by viewing in raw sequence. Easily toggle between individual case and clinical data collections. Generate provisional reports or review final reports all from within the system.

Increased Diagnostic Yield

Our system has proven power for identifying novel variants, thanks to our unique genomic data architecture and a knowledge base including comprehensive, constantly updated key global reference datasets. Perform novel de novo mutation detection while controlling for whole genome or whole exome read-depth and direct analysis of aligned read files, improving both sensitivity and specificity.

Integrate and Collaborate

Integrate with existing systems and use our ecosystem to collaborate with colleagues and institutions around the world. Leverage full-resolution data without moving big files. Cross-match any prioritized variant to all sequenced patients in your own institution and to your partner institutions and build your own knowledge base.

End-to-End Capabilities

We offer a full suite of other products and services from patient collection data management, sequencing and secondary analysis. When integrated with our CancerCODE system, we offer an unmatched comprehensive solution.

Hardware is Optional

Run our system in the cloud to get elastic scalability, compliance and the best-in-class security (powered by DNAnexus). Pay only for the compute time and storage you need.

Features



  • Diagnoses for one patient, one trio or a whole family at a time
  • An integrated HPO coding system
  • Simultaneous analysis of WGS, WES, RNAseq and arrayCGH data
  • Novel de novo mutation detection directly on raw sequence
  • Customized case-control studies with attribute visualization
  • Cross-family analysis for rare or extreme phenotypes
  • Gene-based association analysis with GAVA
  • Detection of novel variants with allelic frequencies down to 0.01%
  • Shared homozygosity and LOH analysis
  • A knowledgebase that includes all key global reference datasets, constantly updated, as well as the ability to create your own custom knowledgebase.
  • Filtering by sequence quality, variant frequency, impact, mode of inheritance and more
  • Ability to scan entire patient collections for carriers of a candidate variant
  • Immediate visualization of raw sequence reads in genome browser

The Brown Vialetto van Laere Case

Two sisters, ages 3 and 5, had progressive blindness and deafness. Over many years they had tested negative for many single-gene retinal and hearing disorders. In just 5 minutes using our system our CSO, Dr. Jeffrey Gulcher, analyzed their WGS data for all mutation types, narrowed the search to 423 variants occurring with < 1 % frequency, screened for autosomal recessives and reduced the number to 6 candidates. The top hit identified was SLC52A2 , a duplication of SLC52A3, a gene involved in riboflavin transport not previously known to cause Brown Vialetto Van Laere Syndrome. Dietary supplements to address this hypothesis arrested the progression of the disease in both sisters.

WuXi NextCODE Powered Testing

The most comprehensive test available for inherited rare diseases provides a phenotype-focused clinical report reviewed by board-certified clinical geneticists. Partnering institutions include Claritas Genomics and Fudan University Children’s Hospital.

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claritas

cancercode

CancerCODE

Uncover new cancer-related associations, find novel drug response markers and generate reports to guide treatment

The CancerCODE interpretation system empowers you to scan WGS data derived from tumors/germlines for mutations and structural variations. Our system facilitates identifying cancer-related variants and rapidly comparing them with genomic data from other sources, including array-CGH, and RNA-seq.

Easy To Use

Our system was designed to be intuitive, allowing standard analyses to be performed quickly while offering a bioinformatics workbench solution that provides flexible tools for more-advanced and scalable analyses. High sensitivity and specificity comes from access to different population allelic frequencies, ability to run MuTect and Varscan2 in parallel and the leveraging of actionable gene collections (e.g. COSMIC and TCGA).

Rapid Analysis

Shave days from once-tedious workflows. Our system allows immediate visualization of raw sequences for variant confirmation. Users may easily toggle between single case and large-scale clinical applications, generate provisional reports and review final reports - all from within our system.

Actionable and Customized Reports

Our system has proven power for identifying novel variants thanks to simple and powerful toggle filters for allelic frequencies, impact prediction and other critera, backed by global reference datasets. These features help pinpoint actionable variants for which custom reports may be created using integrated NofOne content. These reports match actionable cancer gene mutations with FDA-approved and/or investigational treatments for particular patients.

Immediately Visualize

Immediately Visualize

Raw Sequence Data

End-to-End Capabilities

We offer a full suite of other products and services from patient collection data management, sequencing and secondary analysis. When integrated with our CancerCODE system, we offer an unmatched comprehensive solution.

Integrate and Collaborate

Integrate with existing systems and use our ecosystem to collaborate with colleagues and institutions around the world. Leverage full-resolution data without moving big files.

Hardware is Optional

Our system may be run in the cloud, providing users with elastic scalability as well as compliant and best-in-class security (powered by DNAnexus). Pay only for the compute time and storage you need.

Features



  • Seamlessly compares tumor vs germline WGS and WES data
  • Runs the Mutect and Varscan2 algorithms and utilizes Icelandic and public domain allelic frequencies for improved sensitivity and specificity for tumor-specific mutation analysis
  • Identifies LOH, SNPs, lndels, rearrangements and CNVs in tumor and germline samples
  • Joins discoveries with COSMIC and TCGA data and interrogates actionable gene panels
  • Immediately accesses aligned sequences to confirm somatic mutations vs germline reads
  • Easily compare results with RNA-seq and arrayCGH data
  • Defines resistant driver mutations in recurrent cancers (pre- vs post-treatment tumor sequence analysis)
  • Identifies responders vs. non-responders
  • Compares tumor-specific vs survival variants
  • Reports gene and variant annotations relating to the sensitivity or resistance to drugs, immunotherapy, and chemotherapy