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課程名稱 |
次世代定序分析
Next Generation Sequencing Analysis |
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開課學期 |
110-2 |
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授課對象 |
生命科學院 基因體與系統生物學學位學程 |
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授課教師 |
林友瑜 |
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課號 |
GenSys5024 |
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課程識別碼 |
B48EU0390 |
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班次 |
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學分 |
3.0 |
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全/半年 |
半年 |
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必/選修 |
選修 |
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上課時間 |
星期五2,3,4(9:10~12:10) |
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上課地點 |
生科4B |
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備註 |
本課程以英語授課。地點:生科院4B教室
總人數上限：30人
外系人數限制：15人 |
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課程簡介影片 |
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核心能力關聯 |
核心能力與課程規劃關聯圖 |
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課程大綱
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課程概述 |
This course will put equal emphasis towards lecture and hands-on experience. Most weeks will include classroom lecture followed by computer lab time. There will be several homework projects assigned throughout the course. Office hours and additional lab time will be available for students who have questions regarding the lecture or lab portion of the course. Server accounts will be provided at the beginning of the course and rescinded upon completion of the course. |
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課程目標 |
During the past decade, large sequence data sets generated by next generation sequencing (NGS) has become the mainstream method to obtain and study genomic information. This course will cover the concept, methodology, algorithms, and current advances and tools for handling NGS generated
data sets. Upon completion of the course, students should gain a more comprehensive understanding of the overall process of next generation sequencing starting from sample preparation to data analysis.
Students should also become capable of processing and analyzing NGS data. |
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課程要求 |
Grades will be based on attendance and discussion in class (15%), homework project (30%), midterm exam (25%), and final exam (30%).
Some background in biology and genetics is preferred but not required. No computer science prerequisites for this course. |
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預期每週課後學習時數 |
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Office Hours |
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指定閱讀 |
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參考書目 |
Main textbook：
Next-Generation DNA Sequencing Informatics. Brown. 1st edition.
Supplementary textbook：
1. Next-Generation Sequencing Data Analysis. Wang. 1st edition.
2. Microarray Analysis. Schena. 1st edition.
3. Introduction to Bioinformatics. Lesk. 4th edition.
4. Statistics and Data Analysis for Microarrays Using R and Bioconductor. Dr?ghici. 2nd edition. |
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評量方式
(僅供參考) |
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週次 |
日期 |
單元主題 |
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第1週 |
2/18 |
Introduction |
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第2週 |
2/25 |
Principles of next generation sequencing |
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第3週 |
3/4 |
NGS archives, quality control and normalization |
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第4週 |
3/11 |
Data assembly, alignment, and annotation |
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第5週 |
3/18 |
Detection and comparison of mutational profiles |
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第6週 |
3/25 |
Comparison of expression profiles |
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第7週 |
4/1 |
Liquid biopsy |
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第8週 |
4/8 |
Midterm exam |
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第9週 |
4/15 |
Single cell sequencing |
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第10週 |
4/22 |
Genome wide association studies |
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第11週 |
4/29 |
Epigenetic modification analyses |
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第12週 |
5/6 |
Splicing, viral integrations and genomic structural variations |
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第13週 |
5/13 |
Bioinformatic tools for NGS analyses |
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第14週 |
5/20 |
Incorporation and development of analytic pipelines |
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第15週 |
5/27 |
Current research focus of iconic NGS studies |
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第16週 |
6/3 |
6/3 Dragon Boat Festival |
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第17週 |
6/10 |
Final Examination |
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