GeneDx Optional Rotation

Recently, I was honored to inaugurate the GeneDx optional rotation for the University of Pittsburgh Genetic Counseling program.  This rotation gave a tremendous amount of insight into the various roles a genetic counselor can play at a genetic testing company and how counseling skills can be used in alternative ways in the industry setting. 

The counselors organizing this rotation clearly put a lot of thought and care into providing a meaningful, hands-on, and varied experience.  The first week began with the Inherited Cancer group and an introduction to variant classification using the new ACMG guidelines.  

For the rest of the week, I was given a number of cancer gene variants to classify, which required an understanding of population databases, mutation databases, in silico models, functional studies and the ability to perform a thorough literature review.  The data gathered from these sources are then synthesized to determine a final classification for the variant.  

During the second week, I worked with counselors in Cardiology and Exome.  After being introduced to these programs, I continued to hone my ability to classify variants and also worked on crafting gene paragraphs as well as negative report writing.  

The third week was spent with Customer Service.  Over two days I observed the wide variety of tasks performed by Customer Service GCs such as fielding client questions by email and telephone, verifying that appropriate testing was ordered, flagging clients that may benefit from education services by the sales team, participation in the variant testing program, and opportunities for patient post-test counseling.

Throughout the rotation, I was also tasked with an independent gene vetting project.  I was asked to collect data that would aid in determining whether a new gene is ready for clinical testing or requires further research.  At the end of the rotation, I presented my findings to the members of the Inherited Cancer program.

Overall, this was an exciting and unique opportunity for an optional rotation that provided exposure to an area of genetic counseling that is experienced less often in the classroom and clinic-based rotations.

-Bess Wayburn, class of 2016  

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

2015 National Society of Genetic Counselors Annual Education Conference

Recently, the genetic counseling students attended the National Society of Genetic Counselors (NSGC) Annual Education Conference.  Here are some thoughts from our second year students about their first NSGC conference!

"Meeting so many successful and experienced counselors and being able to discuss varying aspects of the field with them, as colleagues, was very empowering.” - Erin

“I was amazed and inspired by Kristen Powers, and her documentary entitled “Twitch.” Kristen shared her journey to get tested for Huntington’s disease, and had very thoughtful answers to the questions posed by audience members about her experience.” – Amy D.

“I was surprised by how much fun I had! I met so many incredible genetic counselors ranging from new graduates to experienced pros, being surrounded by so many amazing and accomplished people was absolutely inspiring. I am so grateful and excited to be a part of this field” –Nikki

"I was very inspired by the lecture about Roe vs. Wade and Down Syndrome Information Acts. It was so intriguing to hear from a panel of experts that included a lawyer and English professor. As a student who is interested in law and ethics and how they interact with genetic counseling, the interdisciplinary lecture was a perfect fit! By the end, most of us in the audience had shed a few tears and felt a true call to action to advocate for our patients.” -Becca

“The conference in general was a great chance to meet GCs from around the country. Everyone was so friendly and excited to share advice with new grads as well as encourage us to apply for job opportunities.” 

–Amy B.

"The educational breakout sessions had a large variety of intriguing topics. It was an amazing experience to hear individuals at the top of their field explain revolutionary topics, debate ethical implications of technologies, and have general discussions regarding current and future practices. It is inspiring to see where our field has come from and what the future holds.”–Kerrianne

“I really enjoyed the session on CRISPR. The presenters raised many of the ethical debates and technical challenges of a new gene editing technology that may have a huge impact on the field. It’s important for GCs to be aware of these issues so they can be part of the conversation and help direct how this technology can be used responsibly.” 

-Bess

“The NSGC conference really made me feel encouraged by the growth of the field. It was so great to see that there are many genetic counseling jobs out there and that they WANT US! It is a nice reminder that we have worked hard, and all have a very bright future ahead with endless opportunities.” –Kelly

“I enjoyed having the opportunity to hear from and talk to so many genetic counselors in various specialties with a variety of backgrounds. Being in the environment itself, surrounded by people who are so interested in genetics and the advancement of genetic counseling was a unique and fun experience.” -Laura

“I really enjoyed the lecture on newborn and fetal exome/genome sequencing and the ethical implications that these useful technologies have in that setting. It applied to my thesis, but was also just generally interesting”. – Tricia

“I thought Dr. Austin’s address was up-lifting and powerful. It was inspiring to hear such a strong woman’s vision for the future of NSGC and the field of genetic counseling.” - Kristin

Prenatal Exome Sequencing – Are We Ready?

In recent years, exome sequencing has become an important diagnostic tool in genetics. Analyzing the protein-coding region of the genome, this test examines the majority of disease-causing genes to identify disorders that would otherwise be missed in individuals with multiple features not characteristic of one particular syndrome or condition. However, with the scope of such a complex test comes the possibility of genetic variants of uncertain clinical significance (VUS) and incidental findings unrelated to a patient’s clinical presentation. This complicates genetic counseling by adding more time, paperwork, and complexity to the consent and disclosure processes.

While not currently available in the prenatal setting, it is likely that exome sequencing will soon be available to prenatal genetic counselors. My thesis research focuses on how prenatal and laboratory counselors feel about the possible implementation of prenatal exome sequencing, and what factors influence those opinions. My goal is to assess in what situations they feel prenatal exome sequencing would be appropriate and to see if any discrepancies exist between the prenatal counselors, who are seeing patients in a clinical setting, and laboratory counselors, who are researching variants and writing reports that eventually go back to the clinic.

I developed my thesis project with assistance from my coworkers at the genetic testing laboratory where I worked prior to graduate school and my mentors at the University of Pittsburgh. Through developing my survey, I’ve learned important skills. Reviewing literature has helped to guide the survey creation process, and I’ve learned about specific ways in

which survey questions are coded to help ease the process of statistical analysis, such as creating questions that follow a “Likert scale”, e.g. Please rate how much you agree or disagree with the following (1=strongly disagree,  5=strongly agree).

In addition, my thesis has forced me to think about my own opinions regarding this testing, and to confront these opinions to help structure the questions in the best possible manner. I hope that the results of this survey will help to identify problem areas that should be addressed before prenatal exome sequencing is offered by labs, as well as to show any similarities or differences that develop from working in clinic versus working in the lab in regards to opinions of new testing implementation.

-Tricia Zion, class of 2016

A PhD in Human Genetics with a Focus in Genetic Counseling

The University of Pittsburgh Genetic Counseling Program is unique and sets itself apart from other programs in many ways, particularly through the opportunity to apply for the PhD program in Human Genetics with a focus in genetic counseling. The PhD provides a research supplement to a genetic counseling degree and broadens career opportunities.

Prior to entering the University of Pittsburgh Genetic Counseling Program Class of 2015, I enjoyed years of undergraduate research experience in basic science. Excited to learn about clinical research, I began my graduate work in the Division of Gastroenterology, Hepatology, and Nutrition with my mentor, Dr. David Whitcomb. My thesis work and clinical training encouraged and challenged me to consider the future of genetics in medicine and the genetic counseling profession in this ever-evolving field. My thesis focused on describing hereditary pancreatitis in the United States, but I was given the opportunity to also contemplate the role of genetic counselors in the management of complex disorders – diseases caused by multiple gene-gene and gene-environment interactions. While hereditary pancreatitis is inherited in a traditional Mendelian autosomal dominant fashion, the severity and complications of the disease vary widely and are influenced by numerous genetic and environmental factors. My experience fed my interest in complex disorders and personalized medicine, as well as my passion for research.

Although I am in the early stages of my PhD education, I am already enjoying the challenges and opportunity to learn more in-depth information of topics covered in the Genetic Counseling Program, whilst broadening my understanding of and contribution to the literature. These are proficiencies that will expand my career scope and better prepare me to make valuable contributions as the field forges onward. I am further inspired by the department’s mission and vision to prepare its graduates for the future of genetics in medicine, as well as take an active role in the development of these advances. Though the future is ever-changing, I am confident that whatever direction my career takes me–be it academic, research, clinical, or industry–I will be well prepared from my training here at the University of Pittsburgh.

Following my graduation from the Genetic Counseling program this past spring, I had the unique opportunity to take a job with Dr. Whitcomb to continue my research on hereditary pancreatitis and join a small team operationalizing a new innovative study focused on personalized medicine for complex disorders. Encouraged to pursue my interests in research through additional graduate training, I seized the opportunity to apply for the Human Genetics PhD program with a focus in genetic counseling. As a graduate of a genetic counseling program, I have already completed the majority of the required coursework and was drawn by the ability to focus on my research and take classes of particular interest to my work. 

-Celeste Shelton, class of 2015

Gastroenterology Clinic Optional Rotation

For one of our 3 or 4-week rotation blocks, second year students are able to pick a site that interests them.  I have an interest in cancer genetic counseling and wanted more exposure to GI cases.  For my optional rotation, I chose a rotation with Beth Dudley, MS, MPH, LCGC and Randall Brand, MD at the Cancer Genetics program at UPMC Shadyside in the Gastroenterology (GI) department.  In this rotation, I had the opportunity to counsel patients for polyposis, pancreatic cancer, and Lynch Syndrome.  I was also able to observe Dr. Brand perform colonoscopies, endoscopies, and pancreatic endoscopic ultrasounds (EUS).  Observing the procedures helped me to fully understand the screening procedures and have the confidence to discuss them with patients.  My favorite part of this rotation was the opportunity to see and participate in the full role of a genetic counselor starting from case prep and ending with the results disclosure and patient letter.  I prepped for cases by calling the patients and obtaining their medical and family history.  I then researched pertinent information based on the differential diagnosis and composed educational materials for the sessions.  I counseled the patients with Beth, and after the sessions, briefed Dr. Brand on the patient and then shadowed Dr. Brand during his discussion with the patient.  After the sessions I assisted Beth in sending the samples out to the testing labs and wrote up progress notes that summarized the counseling appointments and Dr. Brand’s appointments.  I loved that I was able to come in from time to time during my next rotation to call out the results to patients and then write results letters to patients.  This optional rotation was a great opportunity that allowed me to see more GI cancer cases and further develop my cancer genetic counseling skills.

-Laura Cross, class of 2016

Tips for first year students!

The class of 2016 shares some helpful hints for the incoming class as they begin the Program:

"Get to know your classmates and greater graduate student community by attending one of the awesome Welcome events hosted at the start of first semester." -Amy D.

“My advice would be, don’t wait until the last minute to study, especially for the most complex classes. Keeping up with the material will really pay off in the long run. Approach studying as ‘what do I need to know to be a good genetic counselor?’ rather than ‘what do I need to know to pass the test?’” –Tricia

“Use your classmates and instructors as the valuable resources that they are; everyone has unique views and embracing that can only improve your experience.”

 –Erin

“It can be really easy to become overwhelmed by the amount of work ahead of you. Don’t lose sight of your personal motivations for becoming a genetic counselor, those reasons can really help you to refocus if you start to worry about getting it all done. Also, keep tabs on your print allowance; you will use more than paper than you ever imagined.” –Nikki

“Don’t be afraid to make mistakes, but rather embrace them as learning experiences. You won’t be experts when you first start, but you will get there.” –Kristin

“You may have heard this before, but it’s true and it’s a big one: self-care is essential! Grad school is challenging and stressful, so find quick activities that will help you de-stress. Whether it’s hanging out with your classmates (or favorite second years!), going for a hike or run, watching a silly you-tube video, skyping a friend from home, popping bubble wrap, or taking a power nap. Find something that really works for you, and don’t feel guilty taking some time for yourself! You’ll be able to get so much more done if you’re relaxed.” -Becca

"Always keep an open mind. There are so many fields within genetic counseling and it’s easy to come into the program with a bias toward a certain specialty. You won’t know what you truly love until you’ve seen and experienced everything first hand. Unique experiences in your classes and rotations can impact your career path in ways you’ve never imagined.”-Kerrianne

"Keep a separate notebook or computer file of all the genetic syndromes you learn in classes, it'll really help you out in the second year as well as when you start studying for boards." -Laura

-Our second years, the class of 2015!

“Being in this program fosters a sense of comradery among your classmates and alumni. Take advantage of alumni as resources and keep your eyes on the end result: the rewarding work of being a genetic counselor!” –Amy B.

“Take advantage of all the free or reduced price perks that come with a Pitt ID. Walk over to the Carnegie Art and Natural History museums during a long break between classes or over to the Phipps Conservatory in Schenley park. Both are close to campus and free to students. Head downtown on the weekend to see a play or listen to the symphony for only $15. Whatever you chose, take some time to enjoy the city.” -Bess

"Two years goes by really quickly, relish in the little things, shenanigans with classmates, and the beautiful fact that you are entering into an amazing profession, passion, and community." -Kelly