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Codified Genomics Targets Clinical Testing Labs with Variant Interpretation Pipeline


Codified Genomics, a bioinformatics services vendor in Houston, Texas, that launched last year, is offering a variant interpretation service to clinical laboratories providing whole exome sequencing-based testing, that uses informatics capabilities developed at Baylor College of Medicine's Whole Genome Laboratory.

Matthew Bainbridge, Codified's president and CEO, said that the company charges under $500 per patient sample or trio for the use of its interpretation pipeline. Customers can upload VCF and BAM files and patient phenotype information into the web-based system where variants are annotated, categorized based on recommended ACMG guidelines, and those that are most likely responsible for the observed phenotype are prioritized and ranked first with results returned to the requesting lab in a matter of minutes. According to the company's website, Codified's system uses multiple information sources for its prioritization step including genomics coordinates, gene models, protein function, expression, and more.

"What we've really tried to focus on is making [the pipeline] … highly automated, very consistent, and less error prone" so that genetic testing labs, especially those that are just starting to offer exome sequencing services, don't have to deal with the more time- and resource-consuming steps of the variant interpretation process, Bainbridge told BioInform. For example, "we let the [web] interface echo the standard operating procedure" that labs have put in place to analyze variants and generate clinical reports.

"Depending on what you think the inheritance model is, you might use a different set of filters on your variants," he explained. "We can actually automatically set up those filters so that … each one of your hypotheses is set up into a tab and you click on it and it automatically filters what you need." This way, users in the lab have a standardized procedure for analyzing variant lists, thus ensuring more consistent results, he said.

On the automation side, a critical step is "making sure that we are looking at the phenotypes that are associated with the [patient] and the genes," he said. " One of the most time-consuming things in the testing that we've done with the WGL is …looking up what the gene does and how that matches what the [patients] do or [do not] have … because no one is an expert in every gene."

Codified's platform has a number of capabilities and customers in common with several products that are already on the market and a few others that are under development. Examples include CollabRX's Genetic Variant Annotation service, which provides variant interpretation to molecular diagnostics labs, and Omicia's Opal, which provides cloud-based variant annotation and interpretation to clinical researchers and CLIA labs.

Meanwhile, Qiagen Redwood City — formerly Ingenuity — is building a platform for scoring, classifying, and reporting the results of sequencing-based molecular diagnostic tests in collaboration with partners such as Emory Genetics Laboratory, GeneDx, and Partners Healthcare. And, Strand recently launched an early-access program to test a new variant interpretation pipeline in diagnostic testing labs prior to a full launch planned for spring 2014.

Bainbridge acknowledged that Codified does have a number of competitors, but he believes that the depth of the accumulated experience that the four-person firm has from analyzing exome sequences in clinical contexts at the WGL and also at BCM's Human Genome Sequencing Center will help the company make its mark. "We've processed … about 20,000 samples through our system, of which about half are associated with a severe phenotype, so we have lots of experience there," he said. Codified's founders have also established collaborative relationships with groups around the country through their work at BCM, which should be helpful in getting new customers to try out the service, he added.

Codified is primarily targeting clinical testing labs. It has a contract to provide interpretation services to BCM's WGL, but that does not mean that research labs can't use the pipeline as well, Bainbridge said. At BCM, for example, there are researchers that are using the Codified system to analyze data from patient cohorts with cardiac, renal, and neurological diseases among others, he said. "Our focus is [on] clinical single sample[s] and as it turns out, most of the time we are getting pediatric [cases] and that's where our strength is. But … we don't want to pigeonhole ourselves into one thing early on."