Month: July 2019

Hip Hip (Micro)Array!

Hip Hip (Micro)Array!

This past weekend, LEDGE skimmed the surface of cancer genetics. We began by playing a round of true or false, posing options such as, “cancer can be passed from one person to another” and “all forms of cancer are heritable.” The answer to both of these is “false,” however these students know now more than ever that there are always exceptions to every rule. There are viruses, like human papilloma virus (HPV) and Epstein-Barr virus (EBV), that can manipulate the genome and cause cancer to occur. These are viruses that many people encounter during their lifetime that can be transmitted from person to person. Similarly, there are some forms of cancer that can be passed onto offspring; however, this is a very small percentage of the total number of cancer cases that occur. A point I also wanted to make clear to the students was that cancer is, in fact, a genetic disease. Although it may not always be heritable, the disease still alters parts of your genome to “make itself” happen. Therefore, things can be genetic, just not always heritable.

“…we all chatted about what the students want to be when they grow up and (equally as important) whether they think storming Area 51 is a good idea”

Students then learned about microarrays, a common technique used in clinical laboratories to study gene expression. In cancer patients, a microarray may be performed to look at their tumor gene expression profile versus their normal sample. Students used microarray cards to detect the gene expression of their own patients. If anything, LEDGE has taught students that there is a lot of “hurry up and wait” in science. In between incubation steps, we all chatted about what the students want to be when they grow up and (equally as important) whether they think storming Area 51 is a good idea. After all reagents were added, we visualized our microarray using UV light. Green indicated lower gene expression in the tumor sample than in normal cells, while red meant expression was higher. Yellow indicated that gene expression was the same in both samples, suggesting that this was a housekeeping gene. Students wrote down some of their observations in lab notebooks and we then moved on to our final portion of the workshop.

Some students had normal human karyotypes with no abnormalities, while others may have had trisomy 21 or Klinefelter’s syndrome. Other students were (un)fortunate enough to have to piece together a chimpanzee karyogram. The point of this exercise was not only to teach students about karyotyping, but to highlight the similarities between us and other primates.

“She described the need for more people in our career track and highlighted the benefit of becoming a bioinformatician: they are in such high demand that places will pay you anything to work there”

Dr. Elizabeth Ewen, a Ph.D. scientist who serves as the Genome Software Manager for Agilent Technologies, shared with students a bit about her background. Dr. Ewen is a Diagnostic Genetic Sciences graduate who started out into the workforce a bit unsure of where she would end up. She worked at Brigham and Women’s Hospital in Boston for three years as a cytogenetics technologist before she decided to attend graduate school for molecular and cell biology. With this degree, Dr. Ewen worked in various corporations as a Field Application Scientist before she settled, and got promoted to manager, at Agilent. She described to students the need for more people in our career track, and even highlighted the benefit of becoming a bioinformatician: they are in such high demand that places will pay you anything to work there. Dr. Ewen also talked about her ability to work from home, allowing her to raise a family while also being a manager. Her company also pays her to fly to places like Australia and Argentina for work, which she sees as a huge benefit to going into the field. Students seemed interested in Dr. Ewen’s talk, and hopefully they consider all the career options related to our field!

Published 7/24/2019 by Kathleen Renna

What is a chromosome’s favorite article of clothing?

A Pair of Genes!

Our second LEDGE workshop was very exciting! With thirteen kids in attendance, Maria Guyre, a genetic counselor, shared a bit about a day in her life. Maria explained why a family or person may seek out genetic counseling, whether it be due to a condition they don’t want to pass on to their child or they are displaying symptoms associated with a known genetic disorder. She then went on to discuss how someone can become a genetic counselor, starting with getting your undergraduate degree all the way to exploring and applying to master’s programs. Maria highlighted the high job satisfaction rate for genetic counselors and, with an increased need for more to enter the field, job prospects look promising. The key takeaway from our discussion was that genetic counseling is a diverse career with many fields and positions available, so you will never get bored!

genetic counselor

“The key takeaway from our discussion was that genetic counseling is a diverse career with many fields and positions available.”

 

We then went through some case studies that put the students in a genetic counselor’s shoes. We talked about things a doctor may see on an ultrasound that would prompt the need for a genetic counselor, such as an omphalocele, to what noninvasive prenatal screening (NIPS) is and who may be able to use it. Genetic counseling is not only for parents looking to conceive – you can seek genetic counseling for cancer, adult abnormalities, and even neurological conditions. We also went over some of the ways someone may be tested for a genetic condition, whether it be through sequencing, Southern blot, or, as we learned in this week’s dry lab session, karyotyping.

student karyotyping

Some students had normal human karyotypes with no abnormalities, while others may have had trisomy 21 or Klinefelter’s syndrome. Other students were (un)fortunate enough to have to piece together a chimpanzee karyogram. The point of this exercise was not only to teach students about karyotyping, but to highlight the similarities between us and other primates.

karyo queen

“Other students were (un)fortunate enough to have to piece together a chimpanzee karyogram.”

A chimp chromosome 5 looks a lot like a human chromosome 6, and their chromosome 1 looks just like ours except flipped upside down. The students agreed that the work was tedious, however it was definitely a good insight into a diagnostic genetics’ technique.

Published 7/24/2019 by Kathleen Renna

Diving Off the LEDGE into a World of Diagnostic Genetics!

Diving Off the LEDGE into a World of Diagnostic Genetics!

Our first LEDGE workshop was held this past Saturday and it went off without a hitch! We welcomed nine wonderful students to the Storrs campus to get an introduction to genetics and polygenic traits! We started off the session by talking about some frequent “genetic myths,” or traits that people think are genetic but really aren’t. Students learned that features such as dimples, cleft chin, and whether your ear lobes are free or attached to your head are not considered genetic. We also learned about something that I was taught in my very first DGS class at UConn in that many questions in genetics are answered by the simple phrase: it depends. Traits such as hitchhiker’s thumb and being able to roll your tongue may have some genetic components but environmental factors play a role as well. Students then got together to discuss traits that they believe to be polygenic, or have multiple genes involved. Ideas that they came up with were height, hair, and skin color. We also played around with the idea of multifactorial diseases and what this might mean for health issues such as hypertension or cardiovascular disease.

Scientist at work

“Students learned that features such as dimples, cleft chin, and whether your ear lobes are free or attached to your head are not considered genetic.”

We then moved into the laboratory exercise of DNA extraction. DNA extraction is the first step in many diagnostic technologies, such as PCR, next generation sequencing, and gel electrophoresis. Our young scientists were able to lyse (or break open) cells and precipitate the DNA in ethanol. As students learned, DNA is insoluble in a salt and alcohol mixture and therefore precipitated out as white stringy clumps in the center of the tube.

DNA test tube

Our session wrapped up with a talk from Dr. Jaclyn Beirne, a medical geneticist at UConn Health. She discussed with students the process of becoming a medical geneticist, which includes medical school, residency, and a fellowship program. She then went on to explain a day in the life of a geneticist by talking about a disorder she frequently sees. Phenylketonuria (PKU) is an inborn error of metabolism where a certain enzyme is functioning improperly leading to a build up of the amino acid phenylalanine. Dr. Beirne asked the students what some treatments may be for PKU, for which they had some very thoughtful and creative answers! One of the most common treatments is simply prescribing the patient a diet low in phenylalanine. In fact, Dr. Beirne encouraged students to check out the nutrition label on a bottle of Diet Coke. Diet sodas often contain sources of phenylalanine, so companies put it on their label as a warning to those with PKU.

Professor giving lecture

It was most definitely a productive session with great participation from all students! I want to thank Dr. Beirne and Sarah, a current DGS student, for taking time out of their busy schedules to spend the morning with us. Stay tuned for next week’s post after students learn about genetic testing!

Published 7/9/2019 by Kathleen Renna