Whole Exome Sequencing Clinic Optional Rotation

As some of my fellow classmates have previously mentioned, we each have the opportunity to choose an optional clinical rotation in a specialty area that is of interest.  I elected to learn more about the targeted exome sequencing that is ordered at the Children’s Hospital of Pittsburgh (CHP) by working with Marianne McGuire, MS, CGC.  Targeted exome sequencing looks at the entire exome of a patient, but the laboratory then only reports the variants and pathological findings in genes associated with the phenotype (or physical symptoms) of that patient; this approach cuts down on incidental findings.

The majority of the time spent during this rotation was dedicated to researching the variants and pathological findings in the reports from the laboratory.  This requires the utilization of a variety of resources.  For starters, I performed a thorough review of the patient’s medical history and what testing had been performed  in order to know how relevant certain suspected syndromes were within the context of that individual’s medical history.  Next, I researched the altered genes and their associated syndromes. 

The resources I used most often were the Online Mendelian Inheritance in Man (OMIM) database, mutation-specific PubMed articles, and GeneReviews.  To learn more about the specific genetic change, in silico models such as MutationTaster were utilized.  Another commonly accessed resource was the ClinVar database, which is built by laboratory data to help clinicians research the changes found in their patients.  Using all of these resources and the patient’s history, I sorted the reported variants into those that were not likely causal and those that were likely causal for the patient’s condition.  After this process, all of the variants and research were presented to the ordering geneticist and he/she suggested additional testing and referrals that needed to be performed based on the findings.  All of this research and collaboration was made into an individualized presentation for each patient and their family for when they came in for a genetic counseling session to discuss their results.  To wrap up each case, a summary letter was created for the patient and their team of physicians detailing the variations seen and the diagnoses found.

Another unique experience I had during this rotation was to enter patient physical findings into an established research database for those patients who were diagnosed with a specific rare syndrome based on exome testing.  I also had the opportunity to reach out to some of the previously diagnosed families to see if they’d be willing to speak with a newly diagnosed family about their child’s experiences since diagnosis.

This was certainly an incredible opportunity to learn more about an amazing testing process, and some unique disorders.

-Erin Winchester, class of 2016