How to incorporate FACE2GENE phenotype data into WGS testing

phenotype data


When trying to solve a diagnostic odyssey case through whole exome (WES) or whole genome sequencing (WGS), access to complete and accurate phenotype data is one of the most important factors. In fact, if you read our earlier post on variant interpretation strategies for NGS data analysis, you’ll see that strategy #1 is filtering by phenotype. With so many potential variants to review, identifying those that best match the patient’s phenotypes is the quickest and most certain way to identifying the causal variant. To be successful, a number of criteria must be met. First, the phenotype data must be collected. Second, algorithms need to process the phenotype data against the called variants to identify the best matches. Lastly, the matched variants must be presented in a way that will be informative for the clinician reviewing the case.

To make it as easy as possible for clinicians to provide phenotype information when submitting cases for genetic testing, we partnered with FDNA (see August 2017 press release) to create a conduit between their widely used FACE2GENE phenotyping application and our genetic testing platform. A relationship that we most recently celebrated just last week at the European Society of Human Genetics (ESHG) annual meeting in Milan, Italy.

Working together, we’ve made it easy to directly submit phenotype data collected in FDNA’s FACE2GENE application to our lab when ordering Variantyx Unity™ whole genome testing. Through partnership with FDNA, entered phenotypes as well as syndromes suggested by their AI engine can be seamlessly passed on to Variantyx clinical coordinators using the “Send Phenotype for Lab Test” option in the FACE2GENE case record.


How does it work?

After creating a FACE2GENE case record with an uploaded patient photo, filling in the requested measurements and completing the phenotype profile, the process to submit the phenotype information is as easy as:

send phenotype data for lab test

  1. Click the “Send Phenotype for Lab Test” icon located in the top right-hand corner of the case record
  2. In the form that opens, set “Select Test” to “Whole Genome Sequencing”
  3. Then set “Select Lab” to “Variantyx”
  4. Click the “Continue” button

Our clinical coordinators are automatically notified of the submission and will ensure the accurate transfer of phenotype data to the test record in our platform. Not a user of FACE2GENE? Our clinical coordinators will use the information provided on the (TRF) and associated medical history files to directly enter the phenotype data into the test record. In both cases, the invaluable phenotype information is automatically put to use during downstream data analysis using our phenotype matching algorithm before being presented to the reviewing clinician.

Stay tuned for a more detailed discussion of the phenotype matching algorithm in a future post …


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