MEB713 - STRUCTURE and FORMATION MECHANISMS of GENOME VARIATIONS

Course Name Code Semester Theory
(hours/week)
Application
(hours/week)
Credit ECTS
STRUCTURE and FORMATION MECHANISMS of GENOME VARIATIONS MEB713 2nd Semester 3 0 3 7
PrequisitesLimited to a quota of 10 students
Course languageTurkish
Course typeElective 
Mode of DeliveryFace-to-Face 
Learning and teaching strategiesLecture
Discussion
Team/Group Work
Other: Project Design, Presentation  
Instructor (s)Prof. Pervin DİNÇER 
Course objectiveAfter completing this course, students will learn the effects of genome variation in molecular pathology and they will gain knowledge about the mechanisms of genome variations. 
Learning outcomes
  1. Students will; Describe genome variation.
  2. Classify genome variations and learn the differences between types of genome variations.
  3. Understand SNVs and their mechanisms.
  4. Understand CNVs and their mechanisms.
  5. Understand the insertion / deletion variations and their mechanisms.
  6. Understand de novo mutations and their mechanisms.
  7. Learn nomenclature of the genome variations.
  8. Gain knowledge about the databases and consortia related to genome variations.
Course ContentIn this course, the lectures will be given on classification of genome variations such as small or large, rare or common, pathogenic or nonpathogenic, somatic or germ line, inherited or de novo; SNV, indel, CNV, de novo and other different genome variations and their mechanisms, nomenclature of the genome variations and databases related to genome variation, consortia (HapMap, 2000 genome, ENCODE, etc.), Within the scope of this course, students will discuss five review or research articles. In addition, a project will be designed by the students as a group work related to the processes needed to show the effects of different types of DNA variations. 
References1. Cooper DN, Krawczak M, Human Gene Mutation, Bios Scientific Publishers, 1993.
2. Brown TA Genomes, Bios Scientific Publishers, 1999.
3. Strachan T, Tead AP, Human Molecular Genetics, Garland Science, Taylor and Francis Group, 2011. 

Course outline weekly

WeeksTopics
Week 1Description/definition and classification of genomic variations/SNV (single nucleotide variation), CNV (copy number variations) and indels (insertions deletions variations)
Week 2SNVs and formation mechanisms
Week 3Paper discussion (Presentation)
Week 4CNVs, and formation mechanisms
Week 5Paper discussion (Presentation)
Week 6Paper discussion (Presentation)
Week 7Indel variation and formation mechanisms
Week 8Paper discussion (Presentation)
Week 9De novo mutations
Week 10Paper discussion (Presentation)
Week 11Naming properties of the genome variations in the literature and related databases
Week 12Genome Consortia (OMIM, HUGO, DbSNP, HapMap, 2000 genome, GWAS, ENCODE, etc.)
Week 13Genome Consortia (OMIM, HUGO, DbSNP, HapMap, 2000 genome, GWAS, ENCODE, etc.)
Week 14Project presentations
Week 15Preparation for the final exam
Week 16Final exam

Assesment methods

Course activitiesNumberPercentage
Attendance00
Laboratory00
Application00
Field activities00
Specific practical training00
Assignments00
Presentation520
Project130
Seminar00
Midterms00
Final exam150
Total100
Percentage of semester activities contributing grade succes650
Percentage of final exam contributing grade succes150
Total100

WORKLOAD AND ECTS CALCULATION

Activities Number Duration (hour) Total Work Load
Course Duration (x14) 14 3 42
Laboratory 0 0 0
Application000
Specific practical training000
Field activities000
Study Hours Out of Class (Preliminary work, reinforcement, ect)148112
Presentation / Seminar Preparation5525
Project11212
Homework assignment000
Midterms (Study duration)000
Final Exam (Study duration) 11515
Total Workload3543206

Matrix Of The Course Learning Outcomes Versus Program Outcomes

D.9. Key Learning OutcomesContrubition level*
12345
1. To gain knowledge about general features, development and pathogenesis of allergic diseases.      
2. To conceive the interaction between innate and adaptive immunities in allergic inflammation and to evaluate their contribution to disease pathogenesis.     
3. To learn cell types and their characteristics and roles in allergic diseases.      
4. To have information concerning genetic basis of allergic diseases and gen-enviroment interactions.    X 
5. To obtain knowledge on the legal regulations and ethical approaches directed towards clinical studies, and to comply with these ethical principles, being aware of their importance at an individual level and for society     
6. To follow new developments and Technologies in the field of allergic inflammation, to know the equipment and material used in this field and to be able to use basic molecular and cell biology techniques.      
7. To be able to use information technology effectively in life for professional use.     
8. To discuss at a national and international level, topics related to allergic diseases, to possess the knowledge and the capability to solve problems and to master a foreign language, in such a way that this knowledge will serve as principles of life long learning.      
9. To present individually or as a team opinions in a scientific environment on theoretical and practical topics, to discuss systematically with specialists, to defend and question norms, to assess the results in the framework of quality processing.     
10. To analyse research data obtained in allergic diseases using statistic methods, to report according to evidence or present in a national/international scientific field.     
11. To know the working standards of an allergic research laboratory, to implement the rules of data acquisition and scientific reporting, ethics and biosafety.     

*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest