Course Syllabus

 

Genomics in Clinical Practice

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Draft syllabus

Semester & Location:

 Fall 2020 - 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

Program Director: Susana LS Dietrich
Time & Place:

Mondays and Thursdays, 14:50 - 16:10, V23-201


Faculty

ulrik.png

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 the Human Health and Disease core course 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, live in-class cases, student-to-student presentation and in-class discussion. The course also include graded and ungraded tests/quizzes, a journal club and e-based exercises.

 

Required readings

  • Relevant chapters from the anthology textbook “Genomic and Precision Medicine”.
  • Scientific review articles
  • Scientific papers for journal club
  • Educational videos from Osmosis

 

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 20%
Patient case 10%
Test 1 10%
Test 2 10%
Journal club 10%
Theoretical case 10%
Final paper 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.

 

Patient case

The in-class patient case will include a clinical patient either with a diagnosed genetic disease or suspected of one. The students will lead the patient and family health history taking and individually write a 2-page patient chart write-up about the findings and their testing/management plan.

 

Tests

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

 

Journal club

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.

 

Theoretical case

For one session the students will apply their learning in tiered cases. Each group of students will be given a theoretical patient and will have to make clinical decisions based on the information provided. Based on their decision the cases will develop. At the end of the class each group presents their case.

 

Final paper

For the final paper the students will write a paper about a genetic disease, a genomic technology or a bioethical issue related to genetics in the format of a scientific review paper. This 3-4 page paper will be done in groups of 2-4 students.

 

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):

 

Lectures (23) Focus
The clinical geneticist’s organ: Chromosomes and DNA Understanding of the principles genetics will be brushed up. We will focus on the structure/organisation of the genome and the chromosomes, as well as the meiotic and mitotic cell divisions and their implications in genetic health and disease.
The recipe for life: Protein synthesis Refresher lecture on protein synthesis with special focus on the implications of genetic aberrations. 
Reading the code of life: DNA-sequencing This course will focus on 3 types of sequencing, each representing an era of genetics, namely the past (60s-00s), the present(00s-10s) and (perhaps) the future (20s and on):
  1. Sanger sequencing (60s-00s), the slow, expensive, but tried and tested, modality used historically to make several advances in the field, and still used today to verify findings.
  2. Next-Generation Sequencing (00s-10s), which in this course will focus mainly on Illumina’s set-up of fluorescence-based sequencing, that holds more than 90% of the current sequencing market.
  3. Nanopore (20s and on), or Third-gen Sequencing, is a developing technology, that is part hype, part very real, ultra-small DNA-sequencers that hold a promise of a second genomic revolution, that will bring DNA-testing to the bedside.
Understanding the code of life: DNA analysis This includes a fundamental understanding variants, i.e. of single nucleotide polymorphism (SNPs), single nucleotide variations (SNVs), smaller insertions or deletions (indels), trinucleotide repeat disorders (TRDs), copy number variations (CNVs) and chromosomal aberrations, including how they occur. Students will be given assignments using real-life research tools (PeCan, ExAC databases), that allows exploration of assigned variants.
Genetics in the clinic: Counseling and family history Focuses on the the clinical tools used by geneticist’s: how to take a patient/family history, and how to subsequently add to this using registries and EMRs. Also explains modes of inheritance.
Chromosomal aberrations: The “big” syndromes Four chromosomal aberration syndromes are described, along with their implications on the family and society.
Cardiogenetics: Hereditary diseases of the heart Four cardiac syndromes are described, along with their implications on the family and society.
Mitochondrial disease: When the other genome is sick Four mitochondrial syndromes are described, along with their implications on the family and society.
Oncogenetics: Predicting cancer Four cancer predisposition syndromes are described, along with their implications on the family and society.

Metabolic disease: When proteins kill

Four metabolic syndromes are described, along with their implications on the family and society.
Neurogenetics: Early and late syndromes of the brain Four neurological/muscular syndromes are described, along with their implications on the family and society.
Preventing genetic disease: Family planning Prenatal and preimplantation genetics. The concepts and their applications are described along with the ethical consideration.
Theoretical pt. case As described in "Evaluation and Grading"
Treating genetic disease: Targeting the problem How precision medicine is changing certain diseases - including ones where no treatment was previously available.
Curing genetic disease: Removing the problem Here the prospects of gene therapy and gene editing is discussed. While most of the applications are still in research or theoretical we investigate how this will impact clinical care and its ethical implications
Neonatal and population screening: Early diagnosis  This lecture is dedicated to population wide screening. When and why should it be considered. We also investigate direct-to-consumer genetics and its implications.
Journal club As described in "Evaluation and Grading"

Going deeper: The future of genomic medicine 

In this lecture we take a closer look at next-steps in genomics. The field is advances rapidly and students may find themselves working with vastly different concepts if they advance into a career in genetics. 
Genetic syndromes and where to find them Final lecture. Evaluation and recapitulation of major themes including preparation for the final paper. We also take a non-curricular tour around the world and explore certain syndromes highly endemic to specific geographical locations.

 

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Course Summary:

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