Curriculum

MMG 3001Y, Session 1 (Fall, year 1) and Session 2 (Winter, year 1); 78 hours / session, 2 credits

Course Content and Organization 

 This two-term course brings all students to a common knowledge base and introduces advanced concepts including, but not limited to:

·       Major aspects of Mendelian inheritance and single-gene disorders

·       Quantitative trait genetics

·       Complex and polygenic disorders

·       Epigenetics

·       Pharmacogenomics and personalized medicine

·       Cancer genetics

Students learn human genetics from the perspective of phenotype / clinical presentation toward genotype in addition to a focus on molecular genetics and underlying mechanisms of human disease. Class time includes working through clinical and diagnostic case studies, and students will have ample opportunities to engage with world leaders in research and clinical work in each of the major topic nodes. MMG 3001Y will include an assessment of both individual and group work. This fundamental course provides a knowledge framework for the entire program and introduces key concepts that will be examined in detail in subsequent courses.

Students in Advanced Human Genetics will contribute some of their assigned writing pieces to the course blog, which can be found at The MedGen Project. 

Learning Outcomes

By the end of this course, students will be able to

1. Read and interpret academic and medical genetics literature, and explain that interpretation in both writing and orally

2. Effectively and concisely describe your own performance and your experience of coursework in writing via basic metacognition exercises

3. Describe in writing and orally the molecular and genetic mechanisms of fundamental aspects of human disease

Prerequisites 

Formally, this course has no prerequisites, although the content assumes that incoming students have a basic understanding of molecular biology and undergraduate genetics.

INSTRUCTOR

Dr. Erin Styles, Dr. Kinjal Desai

MMG 3002Y, Session 1 (Fall, year 1), 78 hours, one credit

Course Content and Organization

The ability to effectively analyze genomic data requires a strong foundation in both bioinformatics and statistics. This course begins with an introduction to major computer programing concepts using the R coding language and the UNIX shell. Students are taught statistical theory and perform statistical tests using R to analyze biological datasets. This course focuses on practical knowledge, with interspersed discussions of how genomics integrates into the larger fields of statistics, computer science and applied math.

Students are required to bring a computer to class a Wi-Fi internet connection to participate in the labs for tutorials and labs. 

Learning Outcomes 

By the end of this course, students will be able to:

1)    Use the UNIX shell (command line) and associated concepts and tools.

2)    Understand major computer programming concepts.

3)    Select and perform appropriate statistical analyses on biological datasets in R.

Instructors and Coordinator 

Drs. Gary Bader, Philipp Kim, Hannes Röst, Lincoln Stein, Johanna Carroll

MMG 3003Y, Session 2 (Winter, year 1) and Session 3 (Summer, year 1) 2x78 hours, two credits

Course Content and Organization 

This course teaches the theory and practice of molecular biology relevant to genetic and genomic testing. This two-session course will cover classic, modern and emerging genetic methods. The course focuses on computational techniques to analyze genomic data. Students who complete this course will understand the scientific principles underlying genomic tests, be able to examine the limitations and applications of current tests, and have the necessary background to understand new assays.

Students are required to bring a computer to class with a Wi-Fi internet connection to participate in tutorials and computational labs. The course does not include a wet-lab component.

Learning Outcomes 

By the end of this course, students will be able to:

1. Effectively and concisely describe the individual aspects of both classical and next-generation genomics methodologies, with attention to concept, applications, prospects and limitations, and risks inherent within each method

2. Select appropriate methodologies to address case study and exercise problems, and describe in writing and orally the logic behind selecting particular methods

3. Perform various fundamental bioinformatics tasks using command-line coding, the R coding language, and several additional free software tools.

4. Select appropriate methodologies to address a scientific question (clinical or research).

5. Analyze sequencing data and link a sequence variant to a particular disease

6. Read and interpret academic and medical genetics literature, and explain that interpretation in both writing and orally.

Instructors 

Drs. Johanna Carroll and Martina Steiner

MMG3201H, continuous, 0.25 credits

This course is required learning unless you are able to demonstrate excellence in this area

Course Content and Organization

This graduate professional development module is an integral component of the MMG 3006Y umbrella course. It’s organized as a continuous series of workshops and events that span the duration of the program, geared towards helping each student navigate their professional future in the field of Medical Genomics, including but not limited to:

·       The generation of an Individual Development Plan (IDP)

·       Resume/CV building and optimizing

·       Constructing a personal narrative and the importance of storytelling in the job interview process

·       Value propositions

This module is comprised of a combination of lecture, discussion, and project-based learning, and will include primarily the assessment of individual work.

Learning Outcomes 

By the end of this course, students will be able to

1.     Refer to a fully-formed and realized IDP to organize their movement from the academic world at the University of Toronto towards a professional role

2.     Participate in informational and behavioural/fit interviews confidently, with a clear narrative around their own skills, competencies, and values

3.     Generate and rework their resumes/CVs and cover letters in an organization/position-dependent manner

Instructors

Sun Ooi and Zoya Retiwalla

MMG3202H, Spring in Year 1, 0.25 credits

This course is required learning unless you are able to demonstrate excellence in this area

This course aims to generate next-generation sequencing data.

In partnership with Illumina, we will perform WGS on trios to demonstrate the full complexity of the human genome.

Students will learn how to do wet-lab work for whole-genome sequencing.

Learning Outcomes 

After the course, the students will be able to:

1. Consider ethical aspects around planning an experiment involving human subjects.

2. Adhere to laboratory safety practices.

3. Prepare libraries for next-generation sequencing

4. Perform quality control on DNA samples and libraries

5. Determine the quality of the whole genome sequencing experiments

6. Learn laboratory best practices on working with genomic DNA.

7. Learn the power and limitation of current whole-genome sequencing technology

Instructors

Dr. Martina Steiner

MMG3203H, Summer in Year 1, 0.25 credits

This course is required learning unless you are able to demonstrate excellence in this area

This course aims to analyze next-generation sequencing data.

In partnership with Illumina, we will analyze WGS data to demonstrate the full complexity of the human genome.

Students will learn how to use whole-genome sequencing technology to identify disease-causing mutations in complex human disorders.

Learning Outcomes

After the course, the students will be able to:

1. Process the sequencing data to obtain genetic variant calls

2. Find out the ethnicity and family relationship of the subjects involved

3. Use available bioinformatics tools to facilitate interpretation of function and effects of the variants

4. Confirm the accuracy of the variant calls from the reads and alignments

5. Identify potential disease-relevant and pathogenic mutation(s)

6. Understand and be aware of secondary genetic findings

7. Learn the power and limitation of current whole-genome sequencing technology

Instructors 

Dr. Ryan Yuen

Coordinator: Dr. Martina Steiner

MMG 3004Y, Session 4 (Fall, year 2), 78 hours, one credit

Course Content and Organization 

This course teaches students the terminology and jargon relevant to genomic research to enable access to medical and scientific literature, and how to translate it for specific contexts and audiences. In addition, students are trained to effectively and bi-directionally translate clinical information into accessible language. 

Concepts include but not limited to:

·       Effective science communication

·       Visual communication

·       Writing of genetic test reports

·       Direct-to-consumer genetic testing and communication

·       Communication in a professional environment

·       Journalism and entrepreneurship

Students will work on different individual and group assignments, creating pieces of writing tailored to a specific target audience, generating clinical test reports, and planning and recording a webinar.

Learning Outcomes 

By the end of this course, students will be able to

1.     Use written, oral and visual communication efficiently to target a specific audience

2.     Compose a comprehensive and targeted genetic test report

3.     Critically evaluate academic and non-academic writing and speaking

4.    Effectively communicate the benefits and limitations of genetic testing and genomics

Instructor 

Dr. Martina Steiner

Sample Student Work 

Webinars about a topic and for a target audience of the students’ choice:

• Making, Modifying, and Improving Volcano Plot and Heatmap (grad students and anyone who wants to learn these skills)

• Gene Editing (lay audience)

• Direct-to-consumer genetic testing (lay audience)

• Familial hypercholesterolemia (for physicians (GPs)

• Methods for triplet repeat disorders (part 1 and part 2) (for students of genomics and genomics specialists)

• Treating Genetic Disorders: Spinraza for Spinal Muscular Atrophy

MMG 3005Y, Session 4 (Fall, year 2); 78 hours, one credit

Course Content and Organization 

This course explores the current ethical, legal and social landscape of human genetic analysis, focusing on the application of genome science to patient care. Students explore the manifold legal and ethical implications of genomic science, including but not limited to:

·       The ethics of care

·       Disclosure and privacy, obtaining patient consent, ethical implications and protocols for the use of patients in research studies, and emerging issues reporting of incidental findings

·       Data protection

·       Ethical and legal tensions in healthcare, with a focus on the communication of genetic findings in the paediatric setting, and for patients with religious beliefs or value systems that affect clinical care

·       Health policy and legislature, and public health ethics

MMG 3005Y is comprised of a combination of lecture, student-directed seminar, and project-based learning and will include assessment of both individual and group work. 

Learning Outcomes 

By the end of this course, students will be able to

1.     Read and interpret medical and governing agency policy documentation pertaining to genetic testing, and explain that interpretation in both writing and orally

2.     Clearly articulate the mandatory steps involved in obtaining patient consent to genetic testing and including patients in clinical research studies

3.     Describe current policies surrounding the reporting of incidental findings, and apply these policies to make concise decisions about how and what to report in in-class case studies

Prerequisites 

This course has no prerequisites.

Instructors 

Drs. Michael Szego and Dave Langlois

See details here

MMG3204, Fall in Year 2, 0.25 credits

This course is an elective - you are welcome to choose between this course and MMG3205H to fulfil your fourth short course

Background

Variant interpretation is at the core of clinical genome analysis. Assessing whether a variant is involved in a disease phenotype informs clinical decision-making. Genome analysts require a deep understanding of genetics and of genomic methods, of the available databases and literature resources. It takes practice to consolidate this information efficiently and effectively, and this experience comes from working through many cases, and from learning with experts in the field. This module offers opportunities to engage with industry experts on technical aspects of variant interpretation and learning from genome analysts who are experts in a range of disease areas.

Course structure

We invite experts from industry, clinical and research labs to demonstrate their products and their work-flow. Students will get insights into the thought-process of genome analysts, expand their knowledge of field-specific literature on variant interpretation, perform variant analysis at an advanced level, and will learn about new and emerging methods that can provide critical information for variant interpretation.

Learning Outcomes

Students will gain insights into up and coming technologies at the edge of current clinical practice. Furthermore, students will expand their variant interpretation skills by working through case studies for different diseases and with experts from various specialties.
After the course, the students will be able to:

1. Access and apply appropriate resources for advanced variant interpretation
2. Efficiently and effectively interpret variants in various disease areas at an advanced level
3.  Review the ACMG/AMP standards and guidelines for the interpretation of sequencing variants, including gene and classification specific papers from ClinGen 
4. Identify and handle challenges encountered in clinical variant interpretation
5. Critically evaluate new and emerging methods for their suitability in variant interpretation
6. Engage with company representatives to obtain meaningful information

Coordinator

Dr. Martina Steiner

MMG3205H, Fall in Year 2, 0.25 credits

This course is an elective - you are welcome to choose between this course and MMG3204H to fulfill your fourth short course

Course Content and Organization

This module is a component of the MMG 3006Y umbrella course. It’s organized as a short course of lectures, discussion, and student-led seminars designed to be highly engaging, dynamic, and likely different each time it runs. This is where students can expect to be exposed to the bleeding edge of the field of genomic medicine and where they will position themselves at the vanguard of the field. They will learn about cutting-edge technologies that may or may not yet have reached the clinic directly from the experts researching, developing, and using them. This seminar class will provide a survey of topics and is rooted in a journal-club style of discursive learning. It will include primarily the assessment of individual work.

Instructors

Dr. Evgueni (Zhenya) Ivakine, Dr. Ashish Deshwar