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| TBB6022 | Next Generation Sequencing | 2+2+0 | ECTS:7.5 | | Year / Semester | Fall Semester | | Level of Course | Third Cycle | | Status | Elective | | Department | DEPARTMENT of BIOSTATISTICS and MEDICAL INFORMATICS | | Prerequisites and co-requisites | None | | Mode of Delivery | Face to face | | Contact Hours | 14 weeks - 2 hours of lectures and 2 hours of practicals per week | | Lecturer | -- | | Co-Lecturer | | | Language of instruction | | | Professional practise ( internship ) | None | | | | The aim of the course: | | The aim of this course is to understand the basic principles of the next generation sequencing technology. These principles include biological applications, basics in data processing, statistical and informatics theories in data analysis, advantages, limitations, and assumptions of different methodologies, and biological interpretation of the results. |
| Programme Outcomes | CTPO | TOA | | Upon successful completion of the course, the students will be able to : | | | | PO - 1 : | Understand the basics of biological questions | | | | PO - 2 : | Implement different analysis tools (such as alignment, alternative splicing, variant call) | | | | PO - 3 : | Fully understand the standard data structure; capable of retrieve relevant information through basic programming | | | | PO - 4 : | Understand statistical/computational models to solve different biological questions | | | | CTPO : Contribution to programme outcomes, TOA :Type of assessment (1: written exam, 2: Oral exam, 3: Homework assignment, 4: Laboratory exercise/exam, 5: Seminar / presentation, 6: Term paper), PO : Learning Outcome | | |
| In this course, new generation sequencing technology, data processing processes, DNA sequencing, RNA sequencing and ChIP sequencing will be dealt with in detail. The current publications will be followed to examine the experimental environments where the new generation sequencing technologies are used. |
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| Course Syllabus | | Week | Subject | Related Notes / Files | | Week 1 | Overview of next generation sequencing technology | | | Week 2 | Data processing (Analysis workflow, sequence quality evaluation, alignment theories, data formats, data visualization) | | | Week 3 | DNA-seq I
- What is genetic variations?
- What is the importance of sequencing in complex diseases and what are the investigations?
- Next Generation Sequencing (NGS) and genetics of complex disease (etiology)
- NGS and personal genome sequencing
- Whole genome sequencing
| | | Week 4 | DNA-seq II: Bioinformatics topics for DNA-seq data analysis | | | Week 5 | Basics of library preparation protocols for SOLiD platform
(Tour to the Center for Medical Genomics sequencing facility)
| | | Week 6 | Exome sequencing in FIA and PD
DNA-seq III
- Prioritizing genetic variants
- Non-synonymous variants (SIFT, PolyPhen)
- Synonymous variants
- Regulatory variants
- Statistical methods on rare variants
| | | Week 7 | RNA-seq I
- Biological theories on RNA-seq experiments
- Alignment
- Gene expression analysis
| | | Week 8 | Midterm exam | | | Week 9 | RNA-seq II
- Differential expression analysis
- Alternative splicing
| | | Week 10 | RNA-seq III
- Transcript variation
- Allele-specific expression
- RNA editing
- smRNA
| | | Week 11 | ChIP-seq I: Biological theories on ChIP-seq analysis | | | Week 12 | ChIP-seq II: Experimental and Bioinformatics Considerations
- DNA frament evaluation
- Peak identification
- Two condition comparison
- Saturation analysis
- Motif finding and related theories
| | | Week 13 | ChIP-seq III - Bioinformatics topics in ChIP-seq analysis
- DNA methylation
- Statistical considerations
- Bioinformatics tools
- Histone modification
- Experimental approaches
- Statistical considerations
- Hidden Markov model annotating histone marks
| | | Week 14 | General review | | | Week 15 | Student presentations | | | Week 16 | Final exam | | | |
| 1 | Algorithms for Next-Generation Sequencing Sung W.K.CRC Press 2017 | | | 2 | Bioinformatics: A Practical Handbook Of Next Generation Sequencing and Its Applications Spector P. 2016 | | | |
| Method of Assessment | | Type of assessment | Week No | Date | Duration (hours) | Weight (%) | | Mid-term exam | 8 | | 1 | 40 | | Homework/Assignment/Term-paper | 15 | | 1 | 10 | | End-of-term exam | 16 | | 2 | 50 | | |
| Student Work Load and its Distribution | | Type of work | Duration (hours pw) | No of weeks / Number of activity | Hours in total per term | | Yüz yüze eğitim | 4 | 13 | 52 | | Sınıf dışı çalışma | 2 | 14 | 28 | | Arasınav için hazırlık | 2 | 7 | 14 | | Arasınav | 2 | 1 | 2 | | Ödev | 4 | 5 | 20 | | Dönem sonu sınavı için hazırlık | 2 | 16 | 32 | | Dönem sonu sınavı | 2 | 1 | 2 | | Total work load | | | 150 |
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