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Codified allows researchers to rapidly understand genetic variation in their samples. Researchers can quickly and accurately interpret genomic variants using data from a multitude of sources.

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Success Stories

Codified’s analysis tools give hope to family


The tools pioneered at Codified genomics allowed them to quickly prioritize the mutations in a young girl.  “The extra-ordinary thing is that this gene was not documented in any databases as being associated with human disease, but we were able to determine that the gene was so unlikely to contain one deleterious mutation, let alone two, that this gene bubbled up to the top of over 1,000 variants in the child's exome.” said Matthew Bainbridge, CEO at Codified Genomics who made the discovery.  

Read more about it at CNN and Stanford.

Tools from Codified Genomics are allowing us to realize the full potential of genome wide sequencing.
— Richard Gibbs (Director, Human Genome Sequencing Center)

Dopa-responsive dystonia

In 2009 we sequenced a pair of fraternal twins with dopa-responsive dystonia (Read about it in The Houston Chronicle and Nature). As they entered their teenage years the responsiveness of their symptoms to Dopa began to wane. Sequencing the children identified two variants in the SPR gene, a gene already known to cause DRD. Even more amazingly, the variants themselves were already known to be deleterious, but discovering that information involved laborious searches through multiple specialized databases as well as complicated and detailed literature review. Doing this for hundreds of samples at a commercial level is impossible, so we immediately began to collect variant data from many specialized databases in a centralized location so that we could quickly identify known mutations.

Read the paper and listen to the Beery's story here:

Severe psycho-motor retardation

In 2011 we sequenced a child with severe psycho-motor retardation and identified a de novomutation in the gene ASXL3.  Although no disease was associated with this gene, another gene from the same family, ASXL1, is associated with severe congenital disease.  We contacted our colleagues who had  discovered the association with ASXL1, to find that they had also been contacted by other researchers who had, in parallel, found de novo mutations in ASXL3.  Searching our internal database of previously sequenced patients we found 2 more individuals with mutations in this gene, which were subsequently found to be de novo too!  In a few short months we went from dealing with a previously undescribed disease to having identified 4 patients based not on phenotype, but on genotype alone.  This case demonstrates the importance of having access to all the variants that have ever been called in every patient and ready access to their phenotypic information.  Further, the association of genes with disease can be enhanced with an understanding of evolutionary biology, allowing us to connect related genes with related phenotypes.

Read about the impact of this discovery read the paper in GenomeMedicine

Codified Genomics’ automated analysis pipeline is critical for controlling costs as we make genomic diagnostic tests generally available to all subjects. The rapidly expanding set of clinical indications makes Codified’s approach essential to efficient use of genomics in today’s world.
— John W. Belmont MD,PhD (Professor, Molecular and Human Genetics, Associate Director, Cardiovascular Research Institute, Baylor College of Medicine)

The Codified Process


With over 24,000 exomes analyzed, the Codified Genomics process has experience at the heart of its development.  Our software has enabled hundreds of analyses of exomes, the discovery of dozens of new disease mutations and the description of entirely novel diseases.

The most expensive component of genome sequencing is the time that professionals spend pouring over data. The Codified Genomics process streamlines and standardizes tertiary analysis enabling the clinician to make the most of her time.

Codified Genomics provides data from a multitude of sources on the variant, gene, pathway and local genomic levels and helps hone in on causative variants quickly and accurately; Codified Genomics puts a world of knowledge at the clinician's fingertips. Automated processes enable the report to be fully ACMG compliant without requiring the reviewer to tediously classify every variant, freeing them to do what's most important: improving lives.

Codified Genomics enables intelligent filtering and prioritization by gathering all salient information for the genomic coordinate, variant, gene model, protein, function, expression, disease, population and system-interactions. This data is compiled together with assay metrics to allow automatic filtering and prioritization of variants for a patient. The data is displayed simply and cleanly to let the user make the final choice about which variants are and are not important.  Finally, this information is captured and used the next time a patient is reviewed to help make analysis faster and more accurate.


Data Analysis

Get results that are timely, accurate, complete.

  • Prioritized genomic variant data: See what matters first.
  • Fully Automated: Spend less time on routine classification.
  • Easy to use: Get your team up and running faster and consistently
  • Interact: Get your team talking, to each other, and the clinician.

Finding disease causing variants is difficult and time consuming.  Of the 100,000 variants typically discovered in an exome sequence, only a handful will have medical relevance.  Codified Genomics sifts through these variants, hiding those that are unlikely to cause disease, prioritizing those that are left, and giving the user a wide array of data to help find the cause of disease.

Codified Genomics facilitates the data needs of the user by keeping each and every variantdiscovered.  With access to over 15,000 exomes and genomes from diverse populations, however, our process can quickly eliminate those variants which are too common, or likely artifacts from consideration.  Using multiple models, Codified Genomics scores the deleteriousness of each variant, and combines that information with knowledge of the phenotype, gene, and disease alleles to score the variant.  The data for each variant is summarized and presented in an easily viewed interface with quick access to full information at the click of your mouse.


For more information, see Our Products.