BIOL 338: Introduction to Genomics: W2017 draft syllabus

Prerequisite: BIOL 233 or 234, or FRST 302

Instructors:

Keith Adams                                                             Jae-Hyeok Lee

321 Biodiversity Research Centre             2327 Biological Sciences Building

 

Meeting times:

- Lectures: 10:00 – 10:50 on Monday, Wednesday, and Friday

- Tutorial:  Tutorials are required (not optional help sessions) and contain new material related to the lecture topics.

T03: 12:30 – 2:00 Wednesdays in Woodward G41

T01: 11:00 – 12:30 Thursdays in Woodward B75

T02: 12:30 – 2:00 Thursdays in Woodward B75

 

Course overview:

This course will provide students with an introduction to the relatively new and cutting‐edge discipline of genomics. It will be organized into five sections: Contents, organization, and dynamics of genomes; genome sequencing and annotation; genomics approaches to studying gene expression; genome analysis and comparative genomics; research in genomics. Applications of genomics to human health and disease, crop plant improvement, and other applied situations will be included. Tutorials will consist of computer labs to introduce students to web resources in genomics, along with group discussions of genomics research papers and timely topics in genomics.

Course learning outcomes:

Ÿ  Achieve a working knowledge of concepts and recent discoveries in genomics

Ÿ  Explain how technological advances have led to conceptual advances in genomics

Ÿ Relate concepts and discoveries in genomics to human disease, crop plant improvement, and    

     other applied situations

Ÿ  Utilize major web resources in genomics

Ÿ Identify the main results from a genomics research study and interpret figures from a   

     primary research paper

 

 

Evaluation:

Midterm exam 1 - 18%

Midterm exam 2 - 18%

Final exam – cumulative - 35%

Tutorial exercises – 18% (1.5% per tutorial)

Pre-reading quizzes – 6%

Clicker questions/attendance – 5%

 

Reading:

No textbook. Readings will consist of literature review articles from journals and other materials to give an introduction to the lecture topics. Readings for tutorials will consist of primary research papers and other materials. Readings will be posted on the course Connect site. There will be a pre-reading quiz approximately once per week.

Required materials:

A laptop computer or tablet is needed for computer exercises in certain tutorials. Clickers are needed for all lectures.

 

Lecture schedule

 

Section 1: Contents, organization, and dynamics of genomes (Adams)

 

Jan. 4 – Course introduction, introduction to genomics

 

Jan. 6, 9 - Chromatin structure and methylation 

 

Jan. 9, 11 - Transposable elements: types and their abundance in genomes

 

Jan. 13, 16 - Repetitive DNA: satellites and microsatellites

 

Jan.  18, 20 - Centromeres and telomeres

 

 

Jan. 23 - 27 – Sex chromosomes

 

Jan. 30 – midterm exam #1

 

Section 2: Resource building - Genome sequencing and annotation (Lee)

 

Feb. 1 - Promises and advances in genomics

 

Feb. 3 - Research questions in genomics

 

Feb. 6 – Next generation sequencing-enabled research applications

 

Feb. 8 -10 - Basics and practice of genome assembly (focused on Human genome assembly by CVI)

 

Feb. 13 - Family day, no class

 

Feb. 15-17 - Genome annotation: Chromosome mapping, gene structure, and gene content

 

Section 3: Genomics approaches to studying gene expression (Adams)

 

Feb. 27 – March 1 – Transcriptomics

 

March 3 - 6 – Proteomics

 

March 8 - Uses of NGS in evolution studies

 

March 10 - Midterm exam #2

 

Section 4: Genomics-enabled biology: mutation profiling and comparative genomics (Lee)

 

March 13 - System genomics as an integrated research tool

 

March 15-17 - Targeted sequencing: Exome sequencing for mutational profiling and functional genomics approaches

 

March 20-22 - Population-level genomics: 1000 genome projects and genome wide association studies (GWAS)

 

March 24 - Personalized genomics: survey, introduction, and discussion

 

March 27-29 - Comparative genomes (focused on Human Evolution and Macroevolution)

 

Section 5: Research in genomics (Adams and Lee)

 

Mar-31 - Current topics in genomics: CRISPR system, genomics to combat infectious diseases

 

April 3 - Research presentation (Adams Lab)

 

April 5 - Research presentation (Lee Lab)

 

 

Tutorials, indicated by weeks

 

[Jan. 9] 1. Research paper discussion: transposable elements

 

[Jan. 16] 2. Computer exercise: GenBank gene and chromosome records, BLAST searching

 

[Jan. 23] 3. Research paper discussion: sex chromosomes

 

[Jan. 30] 4. Peer teaching and discussion: pros and cons of various NGS platforms (interactive)

 

[Feb. 6] 5. Research paper discussion: NGS-based genome assembly (Klebsormidium genome, as a review of the key concepts in genome assembly) - The need for long-reads?

 

[Feb. 13] 6. Computer exercise: Annotation of a protein-encoding gene (Computer algorithms and public databases)

 

[Feb. 27] 7. Computer exercise: Gene expression and human genomics databases

 

[March 6] 8. Research paper discussion: Proteomics

 

[March 13] 9. Research paper discussion: exome sequencing (Mendelian genetic disorder, as a review of the key concepts in the exome study) - The statistical power of exome-reads?

 

[March 20] 10. Survey on public views about personalized medicine (Briefing of their homework in class -no tutorial sessions per se)

 

[March 27] 11. Research paper discussion: comparative genomics study (Human specific traits, focused on comparative techniques)

 

[April 3] 12. Paper discussion: CRISPR system