Board # 15 :Building Engineering Skills for the Genomics Revolution, a Genomics Technologies and Analysis Course for Biomedical Engineers

Karen R. Thickman

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Conference: 2017 ASEE Annual Conference & Exposition
Location: Columbus, Ohio
Publication Date: June 24, 2017
Start Date: June 24, 2017
End Date: June 28, 2017
Conference Session: Biomedical Division Poster Session
Tagged Division: Biomedical
Page Count: 5
DOI: 10.18260/1-2--27773
Permanent URL: https://sftp.asee.org/27773
Download Count: 407

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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. Previously, she was an assistant teaching professor at Carnegie Mellon University in the Computational Biology Department for five years. She received a Ph.D. in molecular biophysics from the Johns Hopkins University School of Medicine and an A.B. in biophysical chemistry from Dartmouth College. Thickman develops and teaches courses for an online professional masters program, courses in genomics and genomic technologies, and creates laboratory experiences. She also performs educational research and aimed at continually improving student learning and outcomes, and conducts research in online education to improve access to bioengineering education for students at various times in their careers.

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Abstract

Work in progress: Building engineering skills for the genomics revolution, a Genomics Technologies and Analysis Course for Biomedical Engineers

Over the past decade, the development of next-generation sequencing technologies has led to dramatic changes in how genetic information is gathered and analyzed. These changes have led to substantial improvements in biomedical research and medical practices. Biomedical and bioengineering students are entering a world where understanding how to obtain and analyze large-scale genetic data is a valuable skill. Though there are large challenges in the genomics field that bioengineers are uniquely positioned to address, it is still an area many degree programs do not emphasize. This course offers a template for teaching bioengineers to enter and lead in this area. To provide our students with an opportunity to develop the skills necessary to advance genomics and its applications, I have developed a genomics technology and analysis course for advanced undergraduate students and graduate students.

This course explores the technological developments that enabled the development of next-generation technologies, including the constraints and criteria for developing these technologies. Students acquire the skills to assess the pros and cons of each technology in isolation and in comparison to each other. Students learn to identify the needs of a particular question or experiment and to choose and defend which technology would be most useful. They learn to define the kinds of questions that are answerable with current technologies, and to identify the questions that are hard or impossible to address. Looking to the future, they also discuss specific technological advances that could allow one to obtain data to answer these challenging questions.

Additionally, the course provides an opportunity to gain analytical skills by performing hands-on analysis of large-scale genomic data. The statistical theories that underlie the analysis programs are discussed and demonstrated with in-class activities. In weekly computational lab sessions, students use state-of-the-art analytical tools for genomic analysis. These tools include R, HapMap, Sleuth, and Sailfish. These labs build familiarity with commonly used genomics software and skills to analyze complex data.

Students perform a final project for the course that focuses on synthesizing the material they learned in the class and exploring their interests in the area more fully. These projects include defining the design criteria and constraints of current or proposed genetic sequencing technologies, or analysis of a chosen data set. These projects demonstrate the skills gained by the students during the course.

In addition to homeworks and projects, student exams will be used to evaluate how well the students have mastered the learning goals of the course. Preliminary analysis from the first course offering indicates most students met the learning goals of the course. In the following offering, student progress will be evaluated systematically through the use of quizzes as well as the final exam. Additionally, changes in student perceptions of interest and importance of genomics technologies will be assessed through surveys.

All course materials will be made available to instructors interested in developing a similar course at their college or university.

Citation
Format

Thickman, K. R. (2017, June), Board # 15 :Building Engineering Skills for the Genomics Revolution, a Genomics Technologies and Analysis Course for Biomedical Engineers Paper presented at 2017 ASEE Annual Conference & Exposition, Columbus, Ohio. 10.18260/1-2--27773

TY - CPAPER
AB - Work in progress: Building engineering skills for the genomics revolution, a Genomics Technologies and Analysis Course for Biomedical Engineers

Over the past decade, the development of next-generation sequencing technologies has led to dramatic changes in how genetic information is gathered and analyzed. These changes have led to substantial improvements in biomedical research and medical practices. Biomedical and bioengineering students are entering a world where understanding how to obtain and analyze large-scale genetic data is a valuable skill. Though there are large challenges in the genomics field that bioengineers are uniquely positioned to address, it is still an area many degree programs do not emphasize. This course offers a template for teaching bioengineers to enter and lead in this area. To provide our students with an opportunity to develop the skills necessary to advance genomics and its applications, I have developed a genomics technology and analysis course for advanced undergraduate students and graduate students.

This course explores the technological developments that enabled the development of next-generation technologies, including the constraints and criteria for developing these technologies. Students acquire the skills to assess the pros and cons of each technology in isolation and in comparison to each other. Students learn to identify the needs of a particular question or experiment and to choose and defend which technology would be most useful. They learn to define the kinds of questions that are answerable with current technologies, and to identify the questions that are hard or impossible to address. Looking to the future, they also discuss specific technological advances that could allow one to obtain data to answer these challenging questions.

Additionally, the course provides an opportunity to gain analytical skills by performing hands-on analysis of large-scale genomic data. The statistical theories that underlie the analysis programs are discussed and demonstrated with in-class activities. In weekly computational lab sessions, students use state-of-the-art analytical tools for genomic analysis. These tools include R, HapMap, Sleuth, and Sailfish. These labs build familiarity with commonly used genomics software and skills to analyze complex data.

Students perform a final project for the course that focuses on synthesizing the material they learned in the class and exploring their interests in the area more fully. These projects include defining the design criteria and constraints of current or proposed genetic sequencing technologies, or analysis of a chosen data set. These projects demonstrate the skills gained by the students during the course.

In addition to homeworks and projects, student exams will be used to evaluate how well the students have mastered the learning goals of the course. Preliminary analysis from the first course offering indicates most students met the learning goals of the course. In the following offering, student progress will be evaluated systematically through the use of quizzes as well as the final exam. Additionally, changes in student perceptions of interest and importance of genomics technologies will be assessed through surveys.

All course materials will be made available to instructors interested in developing a similar course at their college or university.

AU - Karen R. Thickman
CY - Columbus, Ohio
DA - 2017/06/24
PB - ASEE Conferences
TI - Board # 15 :Building Engineering Skills for the Genomics Revolution, a Genomics Technologies and Analysis Course for Biomedical Engineers
UR - https://sftp.asee.org/27773
DO - 10.18260/1-2--27773
ER -