Teaching Genomics and Genomic Technologies to Biomedical Engineers: Building Skills for the Genomics World

Karen R. Thickman

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Conference: 2018 ASEE Annual Conference & Exposition
Location: Salt Lake City, Utah
Publication Date: June 23, 2018
Start Date: June 23, 2018
End Date: July 27, 2018
Conference Session: Hands-On Skills in BME
Tagged Division: Biomedical Engineering
Page Count: 6
DOI: 10.18260/1-2--31052
Permanent URL: https://peer.asee.org/31052
Download Count: 558

Paper Authors

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Karen R. Thickman University of Washington

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Karen R. Thickman is a lecturer in the Department of Bioengineering at the University of Washington. She received an A.B. in biophysical chemistry from Dartmouth College, and a Ph.D. in molecular biophysics from the Johns Hopkins University School of Medicine. She was an assistant teaching professor at Carnegie Mellon University in the Computational Biology Department for five years before transitioning to the University of Washington. Thickman’s teaching interests include developing and teaching courses for an online professional masters program, courses in genomics and genomic technologies, and laboratory experiences. Thickman performs educational research and continuous improvement activities toward the goal of improving student outcomes. Thickman also engages in online education and research in this area to improve access to bioengineering education for students at various points in their careers.

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Abstract

During the last decade, the cost of sequencing DNA has plunged exponentially, primarily due to the development of new sequencing technologies. This change has impacted biomedical research, biotechnology, and pharmaceutical development. It is also beginning to change clinical practice. Students entering these fields need to have a basic understanding of the technologies that are used to explore the field of genomics and an understanding of the data they will encounter. Toward that end, I have developed and taught a genomics technologies and analysis course. Materials for replicating this course at other universities are available through github (http://bit.ly/GenAnal). An assessment of the effectiveness of this course is presented in this paper.

In this course, undergraduate students and graduate students learn about the technologies that are on the market or on the near horizon for sequencing DNA. Students learn to assess the benefits and drawbacks of each of these technologies and identify which technology is the best choice for different experimental tasks. Though guest speakers, they have the opportunity to interact with leading members of the sequencing and genomics community in our city.

Additionally, the course has a hands-on genomic data analysis component. In this computational lab section, the students are provided data from publicly available sites, and they perform analysis on this data. This includes genome assembly, gene expression analysis, and genome-wide association studies. In these labs, students use software that is currently used by researchers and professionals in the field.

Through a final project, students have the opportunity to explore and expand their interest in genomics. Students have chosen a variety of topics including: defining the criteria for a new type of sequencer, discussing the design of a genomics technology, and performing analysis on a novel data set. This project allows students to demonstrate mastery of a number of the learning objectives that are difficult to assess in exams.

This course successfully increased students' confidence in their understanding of genomics. In beginning- and end-of-course surveys, students reported their confidence increased by more than 23% in four different areas: the role of genomics in medicine, bioengineering, and biological research; and the role bioengineers play in genomics. Based on performance on the final exam, greater than 75% of the students exhibited mastery of more than half of the learning objectives. Planned improvements to increase mastery of the learning objectives are discussed.

This course has successfully introduced students to the world of DNA sequencing technologies and genomic analysis. As this is meant to be an introductory course, students are not equipped to take roles as genomics experts. However, I was pleased that in assessment of the course, students appear to be equipped to appraise uses of genomic technologies and data, understand how genomics may influence their careers, and explore more advanced training in this area.

Citation
Format

Thickman, K. R. (2018, June), Teaching Genomics and Genomic Technologies to Biomedical Engineers: Building Skills for the Genomics World Paper presented at 2018 ASEE Annual Conference & Exposition , Salt Lake City, Utah. 10.18260/1-2--31052

TY - CPAPER
AB - During the last decade, the cost of sequencing DNA has plunged exponentially, primarily due to the development of new sequencing technologies. This change has impacted biomedical research, biotechnology, and pharmaceutical development. It is also beginning to change clinical practice. Students entering these fields need to have a basic understanding of the technologies that are used to explore the field of genomics and an understanding of the data they will encounter. Toward that end, I have developed and taught a genomics technologies and analysis course. Materials for replicating this course at other universities are available through github (http://bit.ly/GenAnal). An assessment of the effectiveness of this course is presented in this paper.

In this course, undergraduate students and graduate students learn about the technologies that are on the market or on the near horizon for sequencing DNA. Students learn to assess the benefits and drawbacks of each of these technologies and identify which technology is the best choice for different experimental tasks. Though guest speakers, they have the opportunity to interact with leading members of the sequencing and genomics community in our city.

Additionally, the course has a hands-on genomic data analysis component. In this computational lab section, the students are provided data from publicly available sites, and they perform analysis on this data. This includes genome assembly, gene expression analysis, and genome-wide association studies. In these labs, students use software that is currently used by researchers and professionals in the field.

Through a final project, students have the opportunity to explore and expand their interest in genomics. Students have chosen a variety of topics including: defining the criteria for a new type of sequencer, discussing the design of a genomics technology, and performing analysis on a novel data set. This project allows students to demonstrate mastery of a number of the learning objectives that are difficult to assess in exams.

This course successfully increased students&#39; confidence in their understanding of genomics. In beginning- and end-of-course surveys, students reported their confidence increased by more than 23% in four different areas: the role of genomics in medicine, bioengineering, and biological research; and the role bioengineers play in genomics. Based on performance on the final exam, greater than 75% of the students exhibited mastery of more than half of the learning objectives. Planned improvements to increase mastery of the learning objectives are discussed.

This course has successfully introduced students to the world of DNA sequencing technologies and genomic analysis. As this is meant to be an introductory course, students are not equipped to take roles as genomics experts. However, I was pleased that in assessment of the course, students appear to be equipped to appraise uses of genomic technologies and data, understand how genomics may influence their careers, and explore more advanced training in this area.

AU - Karen R. Thickman
CY - Salt Lake City, Utah
DA - 2018/06/23
PB - ASEE Conferences
TI - Teaching Genomics and Genomic Technologies to Biomedical Engineers: Building Skills for the Genomics World
UR - https://peer.asee.org/31052
DO - 10.18260/1-2--31052
ER -