INTERNATIONAL BURCH UNIVERSITY
Faculty of Engineering and Natural Sciences
Department of Genetics and Bioengineering
2016-2017

SYLLABUS
Code Name Level Year Semester
GBE 336 Genomics Undergraduate 3 Spring
Status Number of ECTS Credits Class Hours Per Week Total Hours Per Semester Language
Area Elective 5 2 + 2 121 English

Instructor Assistant Coordinator
Şenol Doğan, Assist. Prof. Dr. Senol Dogan Senol Dogan, Assist. Prof. Dr.
[email protected] [email protected] no email

This course is organized as an integrated presentation of genome organization, genome sequencing and characterization, comparative genomics, and introductory genomic data analysis. It covers the basic terms, such as genome, transcriptome, and proteome, as well as more advanced concepts, for example, genome sequencing, gene activity regulation, evolution and phylogeny, epigenomics, and organelle genomics. This course is taken concurrently with a lab course which teaches students how to analyze genomes in silico using various bioinformatics tools.

COURSE OBJECTIVE
The cognitive, affective and behavioral objectives of this course are following:
• Introduction to the structure, organization, function and evolution of the genome.
• Familiarizing students with the functioning of the genome
• Explaining the analysis of the evolution of higher structural organisms.
• Explaining gene and cDNA libraries, microchips, and statistical processes of gene expression as well as gene and genome databases.

COURSE CONTENT
Week
Topic
  1. Introduction to Genomics
  2. DNA Sequencing
  3. Next Generation Sequencing
  4. Single Nucleotide Polymorphisms
  5. Copy Number Variations
  6. Genomic Variations and Anthropology
  7. Genome-wide Association Studies
  8. MIDTERM EXAM
  9. Chronic Myelogenous Leukemia
  10. Genomics and Drug Therapy
  11. Genetic Variation in Somatic Human Tissues
  12. Genomic Studies and Bioinformatic Tools
  13. Whole Genome Sequencing as Genetic Diagnostic Tool
  14. Student Presentations
  15. FINAL EXAM

LABORATORY/PRACTICE PLAN
Week
Topic
  1. Pubmed- Scientific Paper Search
  2. DNA Sequencing Discussion
  3. Next Generation Sequencing Use in Genomics Discussion
  4. Single Nucleotide Polymorphisms and Disease
  5. UCSC and Ensembl Genome Browsers and CNV Search
  6. Use of Genomics in Population Studies Discussion
  7. Genome-wide Association Studies

  1. MIDTERM EXAM
  2. CML Associated Gene Mutations Search and Analyisis
  3. Mutations in genes; Ensembl and UCSC Search
  4. Ensembl and UCSC Search for SLC35A2 Gene Variations
  5. Bioinformatic Tools Used in Genome-wide Association Studies
  6. UCSC Search for Gene Mutations
  7. Discussion
  8. FINAL EXAM

TEACHING/ASSESSMENT
Description
  • Interactive Lectures
  • Practical Sessions
  • Presentation
  • Discussions and group work
  • Assignments
Description (%)
Method Quantity Percentage (%)
Midterm Exam(s)130
Presentation
Laboratory120
Final Exam140
Total: 90
Learning outcomes
  • Describe the structure, organization and function of the genome
  • Connect the fundamental and applied biological, biomedical and biotechnological areas of focus
  • Use this knowledge in future analysis of processes of the genome
  • Recognize gene and cDNA libraries and microchips
  • Statistically interpret processes of gene expression
TEXTBOOK(S)
  • Brown, T. A. (2002). Genomes. 2nd ed. Oxford, UK: BIOS Scientific Publishers Ltd

ECTS (Allocated based on student) WORKLOAD
Activities Quantity Duration (Hour) Total Work Load
Lecture (14 weeks x Lecture hours per week)14228
Laboratory / Practice (14 weeks x Laboratory/Practice hours per week)14228
Midterm Examination (1 week)122
Final Examination(1 week)122
Preparation for Midterm Examination11414
Preparation for Final Examination11515
Assignment / Homework/ Project11414
Seminar / Presentation11818
Total Workload: 121
ECTS Credit (Total workload/25): 5