Department of Biomedical Engineering

BME 420 | Course Introduction and Application Information

Course Name

PCR-based Molecular Diagnosis

Code	Semester	Theory (hour/week)	Application/Lab (hour/week)	Local Credits	ECTS
BME 420	SPRING	2	2	3	6

Prerequisites	None
Course Language	English
Course Type	ELECTIVE_COURSE
Course Level	First Cycle
Mode of Delivery	Face-To-Face
Teaching Methods and Techniques of the Course	Presentation/Discussion Laboratory Question&Answer Problem solving
National Occupational Classification Code	-
Course Coordinator	Doç. Dr. Osman Doluca
Course Lecturer(s)	Doç. Dr. Osman Doluca
Assistant(s)	Araş. Gör. Hüseyin Saygın Portakal

Course Objectives

The objective of this course to introduce the basics of polymerase chain reaction. Throughout the course students learn how to prepare samples and set up PCR instruments and evaluation of the results of PCR technique in diagnosis of genetical or communicable diseases.

Learning Outcomes

The students who succeeded in this course;

Name	Description	PC Sub	* Contribution Level
Name	Description	PC Sub	1	2	3	4	5
LO1	Will be able to describe the principles of Polymerase Chain Reaction (PCR)	1.5		X
LO2	Will be able to prepare components of PCR	4		X
LO3	Will be able to design primer and probe for PCR	3.2				X
LO4	Will be able to write PCR protocol	3.2			X
LO5	Will be able to evaluate the results obtained from the PCR device.	5.3				X

Course Description

The course covers the definition and history of polymerase chain reaction (PCR) method and how this method evolved through the years. The course covers principles of modern PCR methods and basic application of a PCR protocol starting from sample preparation to evaluation of the results obtained from PCR instruments. The course covers the introduction to common genetic and communicable diseases and PCR applications for their diagnosis in modern medicine.

Related Sustainable Development Goals

Course Category	Core Courses
	Major Area Courses	X
	Supportive Courses
	Media and Managment Skills Courses
	Transferable Skill Courses

WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES

Week	Subjects	Required Materials	Learning Outcome
1	Introduction to Molecular Diagnosis	Lecture Notes	LO1
2	Principles of Polymerase Chain Reaction (PCR)	Chapter 2, Viljoen, G. J., Nel, L. H., & Crowther, J. R. (2005). Molecular Diagnostic PCR handbook. Springer Science & Business Media. ISBN 978-1402034046	LO1
3	Reverse Transcriptase PCR	Chapter 5, Viljoen, G. J., Nel, L. H., & Crowther, J. R. (2005). Molecular Diagnostic PCR handbook. Springer Science & Business Media. ISBN 978-1402034046	LO1
4	Quantitative PCR	Chapter 5, Viljoen, G. J., Nel, L. H., & Crowther, J. R. (2005). Molecular Diagnostic PCR handbook. Springer Science & Business Media. ISBN 978-1402034046	LO1
5	Biological Samples and Isolation Methods	Lecture notes	LO2
6	PCR optimization	Lecture notes	LO2
7	Template design	Chapter 3, Viljoen, G. J., Nel, L. H., & Crowther, J. R. (2005). Molecular Diagnostic PCR handbook. Springer Science & Business Media. ISBN 978-1402034046	LO3
8	Homework		-
9	Primer design	Chapter 3, Viljoen, G. J., Nel, L. H., & Crowther, J. R. (2005). Molecular Diagnostic PCR handbook. Springer Science & Business Media. ISBN 978-1402034046	LO3
10	Prob design	Chapter 3, Viljoen, G. J., Nel, L. H., & Crowther, J. R. (2005). Molecular Diagnostic PCR handbook. Springer Science & Business Media. ISBN 978-1402034046	LO2
11	Setting Up PCR Protocol	Chapter 3, Viljoen, G. J., Nel, L. H., & Crowther, J. R. (2005). Molecular Diagnostic PCR handbook. Springer Science & Business Media. ISBN 978-1402034046	LO4
12	Post-PCR Melting Analysis	Lecture notes	LO4
13	Normalization Methods and Reporting	Chapter 3, Viljoen, G. J., Nel, L. H., & Crowther, J. R. (2005). Molecular Diagnostic PCR handbook. Springer Science & Business Media. ISBN 978-1402034046	LO5
14	PCR-based diagnosis of Genetic and Communicable Diseases	Chapter 7, Viljoen, G. J., Nel, L. H., & Crowther, J. R. (2005). Molecular Diagnostic PCR handbook. Springer Science & Business Media. ISBN 978-1402034046	LO5
15	Review and Lab Design for PCR		-
16	Final Exam		-

Course Notes/Textbooks	Viljoen G. J. Nel L. H. & Crowther J. R. (Eds.). (2005). Molecular diagnostic PCR handbook. Springer science & business media. ISBN 978-1402034046
Suggested Readings/Materials	-

EVALUATION SYSTEM

Semester Activities	Number	Weighting	LO1	LO2	LO3	LO4	LO5
Laboratory / Application	1	30	X	X	X	X	X
Homework / Assignments	1	30			X		X
Final Exam	1	40	X	X	X	X	X
Total	3	100

ECTS / WORKLOAD TABLE

Semester Activities	Number	Duration (Hours)	Workload
Participation	-	-	-
Theoretical Course Hours	16	2	32
Laboratory / Application Hours	16	2	32
Study Hours Out of Class	14	3	42
Field Work	-	-	-
Quizzes / Studio Critiques	-	-	-
Portfolio	-	-	-
Homework / Assignments	2	16	32
Presentation / Jury	-	-	-
Project	-	-	-
Seminar / Workshop	-	-	-
Oral Exams	-	-	-
Midterms	-	-	-
Final Exam	1	42	42
		Total	180

COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP

#	PC Sub	Program Competencies/Outcomes	* Contribution Level
#	PC Sub	Program Competencies/Outcomes	1	2	3	4	5
1	Engineering Knowledge: Knowledge of mathematics, science, basic engineering, computation, and related engineering discipline-specific topics; the ability to apply this knowledge to solve complex engineering problems.
	1	Mathematics
	2	Science
	3	Basic Engineering
	4	Computation
	5	Related engineering discipline-specific topics		LO1
	6	The ability to apply this knowledge to solve complex engineering problems
2	Problem Analysis: Ability to identify, formulate and analyze complex engineering problems using basic knowledge of science, mathematics and engineering, and considering the UN Sustainable Development Goals relevant to the problem being addressed.
3	Engineering Design: The ability to devise creative solutions to complex engineering problems; the ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions.
	1	Ability to design creative solutions to complex engineering problems
	2	Ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions			LO4	LO3
4	Use of Techniques and Tools: Ability to select and use appropriate techniques, resources, and modern engineering and computing tools, including estimation and modeling, for the analysis and solution of complex engineering problems, while recognizing their limitations.			LO2
5	Research and Investigation: Ability to use research methods to investigate complex engineering problems, including literature research, designing and conducting experiments, collecting data, and analyzing and interpreting results.
	1	Literature research for the study of complex engineering problems
	2	Designing experiments
	3	Ability to use research methods, including conducting experiments, collecting data. analyzing and interpreting results				LO5
6	Global Impact of Engineering Practices: Knowledge of the impacts of engineering practices on society, health and safety, economy, sustainability, and the environment, within the context of the UN Sustainable Development Goals; awareness of the legal implications of engineering solutions.
	1	Knowledge of the impacts of engineering practices on society, health and safety, economy, sustainability, and the environment, within the context of the UN Sustainable Development Goals
	2	Awareness of the legal implications of engineering solutions
7	Ethical Behavior: Acting in accordance with the principles of the engineering profession, knowledge about ethical responsibility; awareness of being impartial, without discrimination, and being inclusive of diversity.
	1	Acting in accordance with the principles of the engineering profession, knowledge about ethical responsibility ethical responsibility
	2	Awareness of being impartial and inclusive of diversity, without discriminating on any subject
8	Individual and Teamwork: Ability to work effectively, individually and as a team member or leader on interdisciplinary and multidisciplinary teams (face-to-face, remote or hybrid).
	1	Ability to work individually and within the discipline
	2	Ability to work effectively as a team member or leader in multidisciplinary teams (face-to-face, remote or hybrid)
9	Verbal and Written Communication: Taking into account the various differences of the target audience (such as education, language, profession) on technical issues.
	1	Ability to communicate verbally
	2	Ability to communicate effectively in writing
10	Project Management: Knowledge of business practices such as project management and economic feasibility analysis; awareness of entrepreneurship and innovation.
	1	Knowledge of business practices such as project management and economic feasibility analysis
	2	Awareness of entrepreneurship and innovation
11	Lifelong Learning: Lifelong learning skills that include being able to learn independently and continuously, adapting to new and developing technologies, and thinking questioningly about technological changes.