Tuesday, November 3, 2020

Learning through osmosis – Training the next generation of genome scientists

When the first complete genetic blueprint for human beings was completed in 2003, the door opened to major advancesin the fields of medicine, biotechnology and the life sciences.

Students from the University of ݮƵ contributed to this ground-breaking projectand continue to make profoundscientificcontributions through co-op work terms atTheCentre for Applied Genomics (TGAC). TCAG, affiliated withtheHospital for Sick Children in Toronto,provides co-op students with training in relevant laboratory and analytical techniques.

“Thereare so many examples of significant impacts that ݮƵ students have had on our work,”saysRichardWintle, assistant director of TGAG.“We've had students work on new machine learning methods for understanding the human genome. We've had students verifying and validating findings in our autism genomic study. We've even had students stretching all the way back into the early years of the Human Genome Project, working on the annotation of human chromosome seven,and many of these have resulted in high impact publications and real advancements in the field.”

These exceptionalco-opwork experienceshaveledto TCAGbeing namedthe first-everwinner of theImpact in Researchaward. Thisaccoladeispart of the University of ݮƵCo-operativeand Experiential Education (CEE)Employer Impact Awards.

“As director of the Work-Learn Institute, I’m excited to see an employer like the Centre for Applied Genomics provide such rich and purposeful research programs for ݮƵ students– especially ones that include student contributions to research papers and academic journals,” says Judene Pretti. “Through these work experiences and opportunities, our students get to mobilize knowledge that will shape them into research professionals with global impact.”

“We’re very pleased to be able to contribute to improving and enhancing the number of genome scientists in Canada,”saysWintle.He says the skills they learn arecritical to success in the field of genomics in both the public and private sectors.

lab testing machine

TGAC,which consistently hires ݮƵ co-op students and alumni,encourages student involvement in academic journals and publications to share and highlight their work and discoveries.

“ݮƵ students help us to be more future-proof in that we can use the program to identify students who might be good employees later,”saysWintle. “Ofcourse, many of these students go on to have their own successful medical or research careers and some of them become long-term collaborators at ourCentre.”

Students are offered a vibrant, productive genome community with mentorship and support from highly experienced research experts, informatic teams, lab personnel, genomics analysts and PhD and co-op students from other institutions.

“We strongly believe that important work needs to be acknowledgedappropriately,”saysWintle. “One way we can do that is by making sure that our students are offered co-authorship on papers where they’ve contributed significantly to the work that’s being reported. It’s also very important for their own development, because co-authorship on an important paper is really a good way to demonstrate employers or future graduate supervisors that they’ve done some really good work.”

ThanujaSelvanayagam, a ݮƵBiochemistrygraduate,washappy to be able to contribute to a research publication and understand the process that goes into it.

“It’s pretty rare to get that experience as an undergraduate student,”saysSelvanayagam, who had twofour-month work termsand one eight-month work termwithTGAC.

LikeSelvanayagam, Charley Phillips,a BiomedicalEngineering graduate,says theopportunity to researchis a strong stepping-stone to future work and endeavours.

“It was really good learning experience for me to see just how much proof you need to bolster everything you write in a research paper, and addressing reviewer comments,”saysPhillips. “(It’s) a valuable skill that I was not aware I even needed to have until I worked through that process.”

Mentorship is key

Mentorship plays a big role inthe TGACco-op program,Wintleexplains, as students are paired with senior employees including postdoctoral fellows or technicians in the lab.

“Typically, the students are always surrounded by people with a lot of different skills,”Wintlesays. “One of the things I always tell students when they start here is that they should try and be a sponge and of course contribute to what we do, but also try and be a little bit selfish because there’s a lot of expertise around them, and they should try and take as much of that with them as they possibly can.”

“You can’t really avoid learning something by osmosis when you’re with us at TCAG.”

Q&A RichardWintle, assistant director of TGAC

How do ݮƵ co-op students make The Centre for Applied Genomics more innovative or future-proof?

Students really allow us to be more innovative by allowing us to be very flexible on how we approach our projects. It's very easy to ramp up work on a project by having a student or two joining us very quickly. ݮƵ students also help us to be more future proof in that we can use the program to identify students who might be good employees later. Many of these students go on to have their own very successful medical or research careers and some of them in fact become long term collaborators of our center.

What skills make a successful co-op candidate?

What we're looking for to make a successful co-op student in our organization is really enthusiasm. Lots of knowledge of the field and someone who's done a lot of background reading and already appreciates what we're trying to do, and just a willingness to try and learn to be a good scientist. They can learn technical skills, they can learn how to analyze data, but really, they need to learn as much as they can about being inquisitive about world around them, and really understand what it is that we're trying to accomplish when we talk about doing science.

How does TGAC enable co-op students to learn and develop their skills?

When we have students join us, we help them to learn their skills and develop their skills typically by pairing them with very experienced mentors. Sometimes that could be postdoctoral fellows or senior graduate students. If they're working in the lab, it could be very experienced laboratory personnel. Students are also always embedded in ongoing high impact projects. There are no make-work projects here. And really, by being involved in these projects, I think the students can understand what's going on (around) them. They can understand how they're contributing to something very large, in many cases, very big international collaborations. They can also take advantage of a lot of work that's already been done and a lot of experience of the personnel around them that can help them to learn how to contribute and how to become better scientists.

What do you hope co-op students take away from their work term with The Centre for Applied Genomics?

Ideally, what we'd like a co-op student to take away from a work term with us is really some enthusiasm to become a scientist and to learn more about what it really means to do science. We're a very enthusiastic bunch here. We love what we do. The primary reason for us to be here is for some of that to rub off on our students. Yes, they can learn great technical skills. Yes, they can learn to analyze data or design experiments and do all the nuts and bolts that are required for science. But really, we want them to learn to enjoy science and appreciate it.

What was something a ݮƵ student has done for TGAC that had a significant impact?

There are so many examples of significant impacts that ݮƵ students have had on our work. We've had students work on new machine learning methods for understanding the human genome. We've had students spend lots of time verifying and validating findings in our autism genomic study. We've even had students stretching all the way back into the early years of the Human Genome Project, working on the annotation of human chromosome seven and many of these have resulted in high impact publications and real advancements in the field.

One example of a publication that we're particularly proud of is one where three co-op students contributed to the work. It was a study that we did looking at the impact of different sources of DNA. On the quality of whole genome sequence data, we can get DNA from a blood sample or from a cheek swab or from saliva or really from any other tissue, those are the three sources that are most used. We want to know what's the impact on the quality of the sequence data that we can obtain from each of these different sample type. One of the (co-op students) worked in the lab a doing some bench work and wet lab work. Two of them were computational biologists who work on analyzing the data and developing methods to look at the quality of the genome sequence data that we obtained. It turned into a nice study and of course, all three of those students were co-authors on the resulting paper.

Why is it so important to TGAC to have co-op students contribute to research work?

It's very important for us to have co-op students here because Sick Kids Hospital which is of course where the Center for Genomics is located, is a teaching hospital. Part of what we do as the genome center within the hospital is really trying to train the next generation of genomes scientists in Canada. Without students without trainees, there's no point in having a teaching hospital. We’re very pleased to be able to contribute to improving and enhancing the number of genome scientists in Canada.

Why is involvement in research publications important for co-op student’s experience?

We strongly believe that important work needs to be acknowledged appropriately. One way that we can do that is by making sure that our students are offered co-authorship on papers where they've contributed significantly to the work that's being reported. It's also very important for their own development, because co-authorship on an important paper is really a good way to demonstrate to future employers or future graduate supervisors that they've really done some good work and had a big impact.

How does the team at TGAC support and mentor the students as they conduct research and analysis?

At TCAG, we support our students, mainly by making sure that they're mentored on a day to day basis by senior experienced people. Usually it's a postdoctoral fellow or a senior graduate student or one of the technicians in the lab, who's been at this for a very long time, but it really extends farther than that because we have a very large group here. Typically, the students are always surrounded by people with a lot of different skills. One of the things I always tell the students when they start here is that they should try and be a bit of a sponge and of course contribute to what we do but also try and be a little bit selfish, because there's a lot of expertise around them and they should try and take as much of that with them as they possibly can. It's a very collegial set of people, everybody talks to each other. There's really great opportunity to learn, not only from people that are engaged in the same kinds of work that the student is, but people are doing different things like our admin team or finance team, our laboratory staff or bioinformatics staff or the statistical analysts.

You really can't avoid learning something by osmosis when you're with us at TCAG.

How does TGAC train co-op students to work in laboratory environments?

At SickKids, there’s some formal training when students start, there's new employee onboarding. There are all kinds of policy training that's typically done online and in-person laboratory safety training.

Once students are starting to work in the genome center it is really all hands on, and it's really done on a one to one basis. We don't have any formalized training programs, the students start in and start doing things that are maybe a little bit simpler to begin with, and then slowly develop their skills. Typically, our students will spend a lot of time in the lab generating data and the first part of the work term and then as the word term progresses, they’ll probably transition to more data analysis, interpretation, and understanding the impact of the data they’re generating.

The short answer is we put them in the lab, and we get them going right away.

In 1990, an international research team set out to sequence and map all human genes (together known as genomes). Thirteen years later, this team produced the first complete genetic blueprint for human beings, opening the door to major advances in the fields of medicine, biotechnology and the life sciences.