Course Syllabus

Genomics in Clinical Practice

Semester & Location:	Fall 2024 - DIS Copenhagen
Type & Credits:	Elective course - 3 credits
Major Disciplines:	Biology, Biomedicine / Biotechnology, Pre-medicine / Health Science
Prerequisites:	One year of biology, one chemistry course, and one course in either molecular biology or genetics, all at university level.
Faculty Member:	Ulrik Stoltze, Anna Byrjalsen and Matthias Nybro Smith  Current students please use the canvas inbox to contact
Program contact:	Science and Health Department shsupport@dis.dk
Program Director:	Susana Dietrich
Time & Place:	Mondays and Thursdays, 16:25 - 17:45 Location: N7-C25

Instructors

Ulrik Kristoffer Stoltze M.D. (University of Copenhagen, 2017), Phd-student at The Pediatrics Oncology Lab (Bonkolab, 2019-21). Former Clinical Genetics resident (Rigshospitalet, 2018-19), General Practice resident (Søborg, 2018), Surgery resident (Herlev Hospital, 2017). POST-fellow at St. Jude Children’s Research Hospital (Memphis, 2016). Active in Genomics research since 2015 with several publications in genetics and bioethics with a focus on childhood cancer. He is conducting one of Denmark’s largest genomics studies offering whole-genome sequencing to any cancer patient under 18 years old. Teaching at DIS since 2017.

 

Course Description

‘Lifecode’ is the word. In the first half of the 20th century, many would argue, the word was ‘atom’, and by the second half it was ‘silicon’, but in the 21st century the word is ‘lifecode’. In the past 50 years, scientific advances have sparked a revolution - and while few realize it - that revolution is taking place all around us today. The back-end code of our lives is being read, but how do we understand what we are reading, how do we interpret it, and perhaps most importantly, how do we act on it?

This course explores the genomic revolution’s impact on medical science, clinical diagnoses and cutting-edge treatments, illustrating both where the genomic ideology has triumphed and where it has failed. We will dive into diagnostic sequencing technologies, pre-implantation, prenatal and preventive medicine, and explore current gene therapies including the promise of genome editing, as well as, debate the multifaceted ethical implications of clinical genomics.

 

Expected Learning Outcomes

After the successful completion of this course, students will be able to:

• Understand, explain and discuss the science, biology, and history of genetics and genomics
• Recognize and characterize genetic syndromes and discuss their impact on an individual and societal level
• Relate and debate bioethical implications of clinical genomics and prenatal/preimplantation diagnosis
• Understand the technologies of modern genomics and apply them to hypothetical case/situations

 

Approach to teaching

This course applies several types of teaching modalities, including lectures, reflective group-work, theoretical cases, student-to-student presentation,s and in-class discussions. The course also includes graded and ungraded tests/quizzes, a journal club, and e-based exercises.

 

Required readings

• Relevant pages from the textbook Oxford Desk Reference Clinical Genetics And Genomics.
• Relevant chapters from the book The Gene - An Intimate History.
• Scientific review articles and papers
• Educational videos from Cognito etc.

(please refer to the canvas pages, also attached to each lecture)

 

Evaluation and Grading

To be eligible for a passing grade in this class all of the assigned work must be completed.

The factors influencing the final grade and their weights are reported in the following table:

Component	Weight
Participation (individual)	20%
Molecular patient presentation (group)	5%
Molecular patient report (group)	5%
Midterm test (individual)	20%
Journal club (group)	20%
Final paper (pairs)	30%
Total	100%

Participation

Participation grade is based on attendance and academic activity during class, including engagement in the student’s own learning, as well as that of others.

Molecular patient presentation and report (group)

Due to covid  in-class patient case will likely not be feasible. As a substitute each group (of 3 students) will present and do short wirte-up of a molecular patient case.

Test (individual)

The midterm test will be based on the content of the classes up until the time of the test. The test will include a combination of multiple-choice and short essay questions.

Journal club (group)

For one session of two lectures student-groups will prepare a presentation on a study of either a genomics technology or a genetic diagnosis. At the end of the class they will present their paper’s main results and discussion-points to the other groups.

Final paper (nucleic groups)

For the final paper, the students will write a paper about a self-chosen subject. There are three models

• Gene Detective. The group is assigned a shortlist of variants and a brief phenotype. The group must independently (with reasonable help from the instructor) work out the diagnosis and give a brief description of their methods and a short scientific description of their proposed diagnosis.
• Genomics Futurist. The group may write on any subject related to the future of genetics/genomic medicine. Potential topics include:
• Gene therapy
• Cloning
• Cancer prevention
• Large-scale genomics projects
• Personalized medicine
• Bioethicist. The group may write on any subject related to the ethical implications of genetics/genomic medicine. Potential topics include:
• Gene therapy
• Prenatal/pre implantation medicine
• Genetic privacy
• Genetic testing of children
• Direct-to-consumer genetics

This paper (1000 words max, not including references, 12-point). Students are asked to lock in their final topic of choice and writing partner shortly after the midterm. All papers must include a min. of 5 and max. of 10 scientic references. Up to 2 figures/tables (can be composites).

 

Field Studies

Two field studies are planned for this course The first is to a commercial sequencing facility in Copenhagen (most likely Beijing Genomics Institute CPH), where students will have the opportunity to see a sequencing facility and learn about the commercial applications and implications of genomics. 

The second is with the government-driven National Genome Center. Here the student will learn about the public strategies currently being explored, that are aimed at improving diagnosis and personalized medicine and debate about the many prospects and challenges in such a project.

 

Lecture topics (subject to change up to 2 weeks prior to class):

Academic Regulations:

Please make sure to read the Academic Regulations on the DIS website. There you will find regulations on: 

• Course Enrollment and Grading  
• Academic Expectations and Honor Code 

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