DNA

Instructor: Jennifer Doll, Ph.D.

Department, School/College: Department of Biomedical Sciences, College of Heath Sciences

 

Intervention Overview
The purpose of this intervention was to develop more engaging content and associated activities for the online section of the BMS 560, Molecular and Genetic Diagnostics course. This 500 level Biomedical Sciences course is a very factually based course in which the methodology for molecular-based clinical laboratory tests is taught. For the project, two of the seven modules (modules 5 and 6) were targeted. In development of these modules, I focused on gathering engaging web-based content and developed associated activities that went beyond the factual information of the testing procedures, asking students to provide their opinion on various topics. Students were also asked to interact with one another in their activities.

Title: BMS560, Molecular and Genetic Diagnostics

Level: Undergraduate/Graduate

Mode: Online

Session type: 16-week semester

Enrollment: 19 students

This intervention was selected to enhance the student learning experience by collecting dynamic web-based content and integrating that content into activities that engaged students in critical thinking beyond reciting the factual information. Through these activities, it was also hoped that the students would feel more involved in the learning process.

A modular redesign of two modules was selected as an approach to solving this pedagogical challenge:

 

Traditional Module

Converted Module

Content

PowerPoint presentations with written explanations in the notes section

 

Web-based content

Activities

Muddiest Points discussion forums

 

Question-based discussion forum

For traditional modules, the primary formats utilized were PowerPoint presentations with written explanations in the notes section along with ‘Muddiest Points’ discussion forums. For the converted modules (i.e., modules 5 and 6), web-based content was the primary source of information coupled with a question-based discussion forum. In this discussion forum, I posted 18 different questions, with each student having to answer a different question. These questions were based on the web-based content and also went beyond the factual information of the testing procedures, asking students to provide their opinion on various topics. The last step of this was for students to agree or disagree with another student on a separate question.

Converting two modules instead of the whole course was chosen as an intervention because it allowed me to:

  • Gather feedback from my students to know that converting the modules created a better learning experience for them.
  • Manage my workload (e.g., converting two modules takes much less time than doing them all, which is especially important given the need to evaluate the impact of the intervention).

Finally, these modules were chosen because they provided some level of controversy, focusing on the Human Genome Project and Human Identification and Genetic Testing and Molecular Oncology.

The components of this modular redesign took place in three different facets: pre-intervention, during intervention, and post-intervention.

Pre-Intervention

I conducted web searches using the key terms in the module titles. The following table lists the website resources identified by module and includes the web link to these resources:

Module 5:

 

Text-based web resources

 

PBS Learning Media

http://www.pbslearningmedia.org/resource/tdc02.sci.life.gen.hgp/human-genome-project/

Genetics Home Reference – Human Genome Project

http://ghr.nlm.nih.gov/handbook/hgp (Human Genome Project)

http://ghr.nlm.nih.gov/handbook/genomicresearch?show=all (Genomics)

National Human Genome Research Institute

https://www.genome.gov/20019523 (Genome-Wide Association Studies

https://www.genome.gov/11006943 (frequently asked questions)

Stanford Encyclopedia of Philosophy

http://plato.stanford.edu/entries/human-genome/

23andMe (direct to customer genome analysis company)

https://www.23andme.com/

Animations and videos

 

DNA Learning Center

http://www.dnalc.org/view/16812-Animation-39-A-genome-is-an-entire-set-of-genes-.html (Genome & sequencing methods)

http://www.dnalc.org/resources/animations/sangerseq.html (Sanger sequencing)

http://www.dnalc.org/view/15923-Cycle-sequencing.html (Cycle sequencing

NOVA – Sequence DNA yourself

http://www.pbs.org/wgbh/nova/body/sequence-DNA-for-yourself.html

Module 6:

 

Text-based web resources

 

National Human Genome Research Institute

http://www.genome.gov/19516567

National Cancer Institute

http://www.cancer.gov/about-cancer/causes-prevention/genetics/risk-assessment-pdq#section/all

(note: this is a multiple page in-depth site)

Reuters (genetic Testing in the news)

http://www.reuters.com/article/2015/04/12/us-usa-healthcare-cancer-insight-idUSKBN0N30EM20150412

While the websites were chosen for the accuracy and appropriateness of information to the course and module educational goals, websites that mentioned issues involving areas of controversy within the topics were particularly sought. This was done to allow students to become involved with the material on a more personal level, rather than just in understanding factual information on assays and assay development.

To directly engage them in the material, a question-based discussion forum was included in the modules. For this discussion forum, I constructed specific questions, based on the web resources, for the students to answer. Table 2 lists the questions that were generated for module 5.

1. Why did the FDA ban 23andMe from providing genome wide health-related information directly to consumers?

2. Identify key similarities and differences between hierarchical shotgun and whole genome shotgun sequencing. (i.e. compare and contrast)

3. Over the years, the estimated number of genes has varied up and down.  At one time, it was estimated to be close to 100,000. More recent estimates from the HGP are ~20,000, which is 1% of the genome.  Provide an explanation for why the estimated number of genes has varied over the years.

4. Through the HGP, sequencing technologies rapidly advanced, leading to 2nd and 3rd generation sequencing technologies and finally to next generation (NextGen) sequencing technology. Describe key similarities and differences between these three methods. 

5. The human haplotype (HapMap) project began in October of 2002. Explain what the goals of this project were and why its goals are important to genomic research.

6. Explain what genome wide association studies are and what they are used for.  Include in this answer what other genomic resources are used in such studies.

7 & 8. 23andMe is a private biotech company offering personal genomic information directly to consumer.  As discussed in question number 1, the FDA banned 23andMe from providing genome wide health-related information. However, now it has approved one specific test for Bloom syndrome.  Do you agree or disagree with the FDA's regulation of what information 23andMe can provide directly to consumers?  Support your position.

9 & 10. What is meant by 'clinically actionable' data?  Do you think we are there yet and should be sequencing patients’ genomes as part of their health program?   For this question, one student can take a pro sequencing and one student can take a con sequencing position; however, both students must address the question of what is considered clinically actionable data.

11. The HGP included the Ethical, Legal and Social Implications (ELSI) program.   Why was this included as part of the project? What are some of the ethical concerns associated with the project? In your opinion, are these valid concerns?   Support your opinion.

12. Craig Ventor’s company, Celera, began their genomic sequencing endeavors by focusing on expressed sequence tags (ESTs). What are ESTs and why is it important to also sequence these in addition to the genomic DNA? What information can be gained from such sequences?

13. Why are centromere regions so difficult to sequence? Is it possible that we will never have confirmed sequences from these regions? Does this apply to other regions of the genome? If so, what regions?

14. What are single nucleotide polymorphisms (SNPs)?   Why have they become so important in genomic research? What genomic research projects are they being utilized in and why?

15. What is pharmacogenomics? How is it related to the HGP and other genomic research projects? Specifically, what project(s) is it tied to? Are there currently any drugs being prescribed or not prescribed based on pharmacogenomics? How do you see this field affecting clinical laboratories?

16. How does the cost of the first genome sequenced compare to the cost now? What has influenced this cost? Describe what has contributed to the cost of sequencing decreasing taking into account both methodologies, technologies and reagent costs.

17. Compare and contrast Maxam-Gilbert and Sanger dideoxy sequencing methods.   What are the advantages and disadvantages of each? Which is more commonly used now? Support your answer.

18 & 19. The price tag of the HGP was quite hefty at almost $3 billion dollars, and the price tag of the HapMap project was over $100 million. Some view the cost as a waste of money as few immediate returns on the investment have come to fruition. Others view it as a long term investment. Choose one of these positions (i.e. the projects are not providing the return on investment or the project will provide returns, it is just in the long term) and defend your position.

The second part of this question-based discussion forum was that the students had to respond to a post, agreeing or disagreeing with it and/or adding information. This type of discussion forum was not used in other modules.

During the Intervention

The intervention was implemented in Modules 5 and 6 which corresponded to weeks 9-12 of the course, with module 5 being weeks 9-10 and module 6 being weeks 11-12. Students were introduced to the new strategy in several ways. First, the module schedule included the timeline for the web-based content and question-based discussion content information. In addition, content links were posted under the module content area, and the question-based discussion forums were also included under the content area like this:

<a href="http://virtualteachingcommons.org/wp-content/uploads/2015/09/doll-screenshot.png"><img class="alignnone size-full wp-image-572" src="http://virtualteachingcommons.org/wp-content/uploads/2015/09/doll-screenshot.png" alt="doll-screenshot" width="905" height="1421" /></a> 

Post-Intervention

For modules 5 and 6, student participation was gaged via the question-based discussion posts.   I reviewed and graded each discussion post of the discussion forum on a point-based system. The initial answer to a posted question and the response / follow up to another student’s question were graded separately, with the two grades combined for the final discussion post grade. Within the grading function, I provided written feedback to the students on their posts in the feedback text box. With all posts, I felt that it was important to explain why points were deducted and to provide direction for improvement. Along with this, I also provided general thoughts and insights on the post as well as kudos to students with great responses. Lastly, I added comments to discussion posts, to both the original post and to the response post, on the open forum website.

Method

Students provided anonymous feedback on the intervention through an instrument that provided closed and open-ended questions. These questions focused on measuring student satisfaction regarding the intervention and understanding key course concepts. Students were also asked to reflect on things that worked well and convey constructive feedback for future changes to the intervention to benefit future students.

Results

There were 19 students enrolled in the online section of this course. Of the 19, 18 completed the semester. One student did not complete most of the course work for the semester, including modules 5 and 6, and thus, this student was not included in the strategy analysis.

Of the 18 remaining students, six students (33%) responded to a survey that was constructed to measure satisfaction with and perceived learning in the converted modules. Of the 6 respondents, 5 (83%) rated the converted modules on the neutral to positive side of the scale in regards to helping them understand the course concepts and deepening their understanding of polymorphisms and genetic disease. All the survey participants reported that the new content helped them to think more critically about the course concepts.

In addition, most comments were favorable with respect to the format of the modules. In particular, the students particularly liked the question-based discussion forums. One student commented:

“I liked this new format of answering discussion questions much more than the muddiest points questions. I don’t feel I’m learning anything with the muddiest points questions. The discussion questions help me to learn the content better and I think this type of format is a much better way to learn.”

Another student commented on the overall effectiveness of using the format of modules 5 and 6 in the course:

“I believe I learned the material in these modules much better than in previous modules and I would recommend for future classes, all modules be held this way.”

Based on these comments as well as the survey results, it seems that the project for these modules was successful in engaging the students in the learning process. Lastly, the mean quiz scores between the modules were compared, and the mean quiz score for modules 5 and 6 was higher than that of modules 1-4 and 7. For modules 1-4 and 7, the mean quiz score was 15.16 out of 20 with a range of 14.28-16.61 (n=5; standard deviation ±0.897). For modules 5 and 6, the mean quiz score was 16.42 with a range of 15.89-16.64 (n=2; standard deviation ±0. 0.746). Although difference did not achieve statistical significance (P=0.95), likely due to the small test size, it is encouraging, particularly taken with the survey results.

One last comparison was made for this online class as a part of this project. During the course of the semester, I was teaching this online version of the class as well as a face-to-face version of the class. While this is not a module-by-module comparison, it is of interest for online teaching in general to compare the course grades between students in each section. The mean final grade for the online class (n=18) was 81.33% ± 8.582. The mean final grade for the face-to -face section (n=26) was 81.45% ± 8.40. These data suggest that the online course is as effective in conveying course content as a face-to-face approach.

My overall conclusion for this project is that the strategy employed in modules 5 and 6 was successful in engaging the students more. As this is a class I will now teach an online version of each spring semester, I will expand this strategy into other modules, with the goal of eventually having some web-based content and/or question-based discussion forums in all models. One goal for the upcoming year, as the discussion forums are graded, is to develop specific rubrics for student responses in the question-based forums. This will aid in both guiding students in their answers as well as provide clear grading criteria. Another future goal within this would be to directly link the web-based content to assessment activities, i.e. such as completing an interactive website-based task.

There are a few caveats with the question-based discussion forums and responses, as well as the muddiest points discussion forum. One caveat surrounds the issue of plagiarism. Plagiarism was clearly addressed in the syllabus; however, throughout the semester, issues emerged with students simply coping and pasting information, sometimes even using my PowerPoint text, without using quotes or referencing the source of the material. I had to remind students several times, via news posts and class emails, that plagiarism would not be tolerated and that discussion posts must be in their own words, and after several modules, included statements to this effect in the instructions of each module discussion forum.

A second caveat with the question-based discussion forums, as well as the muddiest points discussion forum, is the time required to review all comments. Even with the current class size (n=18), it took a significant amount of time to review these forums. Review was absolutely necessary to ensure that students were posting accurate information so that other students were not misdirected. For this class, the online enrollment is capped at 25. While my experience suggests that it is well worth the time to review the posts in detail, it would be very challenging with many more students, and in larger classes, next to impossible without the help of teaching assistants for the course. I think that in a larger class, without a teaching assistant, it would be necessary to use an alternative approach. Overall, however, with a class size of less than 25 students, using web-based content with the question-based discussion forums is an engaging and productive approach.