All Lectures are Friday 2:00-3:20 pm in York Hall 3010 (YH 3010) (Map). Clicking on the class topics below will take you to corresponding lecture notes, homework assignments, and required reading material.

1 Fri, 01/12/18 Course introduction & genome fundamentals
Introduction to the course, Overview of major learning objectives and topic areas. Human genome review: What is DNA? What is a genome? What does the genome do? How do genomes differ between individuals? How is the genome decoded? Exploring what genetic errors are and what causes them.
Slides, Homework
2 Fri, 01/19/18 Genomics and cancer treatment
What is cancer and how does it arise? Example genes implicated in cancer. What has been learned from genome sequencing of cancer? How can sequencing advance cancer treatment? Why do some anticancer drugs fail and how might genomic approaches help address the issue? Can genomic approaches help detect early cancer and monitor treatment effectiveness? What is immunotherapy? Can genomics be used to harness a patient’s own immune system to fight cancer?
Slides, Readings, Notes
3 Fri, 01/26/18 Recent advances in genomic technologies and their clinical applications
How are genomic technologies currently impacting the practice of medicine? What recent and future advances in genomic technologies have the potential for major clinical impact? What other ‘omes’ are useful for medicine? Can the transcriptome, proteome and metabolome be useful? How deeply can a person be analyzed? The promise and hype of personalized medicine. Open discussion of how genomics can inform on disease risks and some of the challenges associated with the use and management of genomic and related health information. We will also learn about the 100,000 Genome project and where genomic medicine could take us next.
Slides, Reading
4 Fri, 02/02/18 How to read a scientific paper & Introduction to student presentation assignments
A guide for selecting, reading and understanding peer-reviewed primary research articles, How to obtain a basic understanding of a published science paper and decide whether or not it is a reputable study? How does the described work contribute to advancing the scientific knowledge base or our technical capabilities? Introduction to student presentation assignments.
A 12 step guide to reading primary research articles,
Topics for student presentation
Student group assignment and presentation dates
5 Fri, 02/09/18 Student group literature presentations
Group 2 & Group 3
Each week 2 student groups of 3 students each will present selected primary literature on recent genomic advances of relevance to biomedical science and health care. Topics may be selected from any of the primary articles noted in our blog posts to date or the following topic list. Presentations should be 25-30 minutes in length with all group members contributing. Your groups PPT or PDF slides should be emailed to me by 9am on the Friday of your presentation.

Group 2 Paper: Neopepsee: accurate genome-level prediction of neoantigens by harnessing sequence and amino acid immunogenicity information
Group 2 Presentation: Google Slides link

Group 3 Paper: Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer’s disease
Group 3 Presentation: Google Slides link
6 Fri, 02/16/18 Student group literature presentations
Group 4 Paper: De novo mutations revealed by whole-exome sequencing are strongly associated with autism
Group 4 Presentation: Google Slides link

Group 1 Paper: ‘Is this knowledge mine and nobody else’s? I don’t feel that.’ Patient views about consent, confidentiality and information-sharing in genetic medicine
Group 1 Presentation: Google Slides link
7 Fri, 02/23/18 Student group literature presentations

Group 5 Paper: ACTN3 genotype and modulation of skeletal muscle response to exercise in human subjects
Group 5 Presentation: Google Slides link

Group 6 Paper: Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
Group 6 Presentation: Google Slides link
8 Fri, 03/02/18 Student group literature presentations
Group 7 Paper: Association of oral microbiome with risk for incident head and neck squamous cell cancer
Group 7 Presentation: Google Slides link

Group 8 Paper: Alterations of oral microbiota distinguish children with autism spectrum disorders from healthy controls
Group 8 Presentation: Google Slides link
9 Fri, 03/09/18 Student group literature presentations
Group 9 Paper: Genetic susceptibility to cardiovascular disease and risk of dementia
Group 9 Presentation: Google Slides link

Group 10 Paper Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine
Group 10 Presentation: Google Slides link
10 Fri, 03/16/18 Ethics and the communication of genomic and related health information
Key ethical and communication principles relating to genomics, Can your genetic information be used against you? Who controls your genomic and other health information? What is the role of the physician and what are the implications of direct-to-consumer genomic testing? What are the major risks that must be considered when using genomic data? We also consider the issues surrounding the use of genetic information prenatally (e.g. in sperm banks).
Open discussion; Course review; Course wrap up and course evaluation completion.