NEXT GENERATION SEQUENCING TECHNOLOGIES: Principles, Applications & Data Analysis (2 credits)

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1 of 5 COURSE TITLE:

NEXT GENERATION SEQUENCING TECHNOLOGIES:

Principles, Applications & Data Analysis (2 credits)

Course number: BIOC6240

Pre-requisites: NONE

Instructor: Anelia Horvath, PhD, [email protected] Course Background

The demand for low-cost, high-throughput genome investigative studies has triggered the development of Next Generation Sequencing (NGS) technologies. Improved performance and decreasing costs have facilitated the development of a growing number of diverse NGS applications. The - $3-billion price tag for the first human genome in the 1990’s can now pay for a million human genome sequences, each completed within a few weeks. As a result, personal genome sequencing is becoming routine research and exome sequencing is being explored for diagnostic and therapeutic needs. NGS is expected to benefit many areas, ranging from molecular medicine, diagnostics, therapy design and response prediction, to basic sciences such as evolutionary biology, energy production, agriculture, anthropology and forensics.

To master this continuously expanding field requires novel educational approaches, and several efforts have been recently initiated by a number of leading University and Research centers such as the Broad Institute, Baylor College of Medicine, and the University of Washington. Next Generation Sequencing Technologies: Principles and Applications has been developed to provide our graduate students theoretical basis as well as practical applications on NGS-based data generation, management and analysis.

Justification for the course

NGS applications are achieving a growing role in the diagnostics, prevention and treatment of human diseases, requiring groundbreaking knowledge and expertise. This course is designed to provide students with theoretical and practical knowledge of NGS technologies and applications related to human health. The ultimate purpose of a comprehensive NGS educational program is a response to the field’s quickly expanding employment opportunities, for well-prepared scientists and physicians with vision on the NGS clinical and research applications.

Course Description

BIOC6240 “Next Generation Sequencing Technologies: Principles and Applications” will consist of two major modules. The first module will introduce students to the molecular principles underlying NGS technologies and will provide them with an understanding of possible research and clinical applications. It will also educate them about the major steps in the NGS process line - from the wet lab (library preparations), through “on instrument” processing (the actual sequencing process), to analysis and management of the raw and processed data.

The second module is focused on the NGS analytical pipelines and data interpretation. It is designed to supply theoretical and practical knowledge about analysis of NGS generated datasets. Combined, the two modules will

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2 of 5 provide students with the ability to interpret results from NGS and to prioritize findings based on quality, statistical considerations, and biological meaningfulness. Students will be oriented into designing their own projects targeting specific scientific questions or clinical needs.

A course project will include an NGS based proposal designed to address a particular scientific or clinical question. The course closely follows the progress in the NGS field; every lecture will end with a 10-min presentation of the most significant recent discoveries or developments in the field. A separate lecture at the end of the course will address specific NGS-based interests expressed by the students during the semester. The course-line will include lectures and demonstrations. All lectures will have take-home assignments/quizzes to familiarize students with the NGS concepts, methods, analytical approaches as well as web resources.

Course Objectives

By the end of the course, students will be able to • Understand the molecular basis of NGS

• Have a detailed vision on NGS Applications and Opportunities in Science and Medicine • Apply practical skills on NGS data analysis

• Transform the outputs from the NGS platforms into biologically meaningful datasets • Interpret NGS data

• Identify in silico genomics and bioinformatics’ tools for post-analytical data interpretation

• Extract, score, sort and filter NGS findings based on a) Technical quality b) Biological priority c) Potential Pathogenicity d) Statistical considerations

• Design NGS based approaches for clinical and research applications

Grading

Grades for the course will be based on take-home assignments (10%), exam (30%), term project (40%), project presentation (10%), and participation in class (10%).

Expected background

Students should have general knowledge of how to use a computer, common software such as Microsoft Office, and a web browser.

Use of computers

Computer workstations are provided; bring your own wireless laptop if you wish. The GWU Blackboard system will be used.

Course materials

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Course Syllabus (tentative)

Lecture Date Topics Lecturer

Module 1 Introduction to Next Generation Sequencing Technologies

1 01/14/2021

Introduction to the 3 generations of sequencing: First

(Sanger) and Second (Massively Parallel) Generations of Sequencing. Examples. Comparative overview of the

available platforms: Illumina, Roche, Applied Biosystems,

Principles, Advantages and Challenges.

Anelia Horvath Online, 4pm

2 01/21/2021

Introduction to the 3 generations of sequencing II: Third

(Single Molecule Real Time) Generation of Sequencing. Examples. Comparative overview of the available

platforms: Helicos Biosciences, Oxford (Nanopore), Pacific

BioSciences - Principles, Advantages and Challenges. Overview of the three generations of sequencing.

3 01/28/2021

Applications of NGS: Enrichment libraries II: ChIP and ATAC

sequencing, Hi-C Sequencing – Molecular Principles and Approaches for Enrichment (capture, immunoprecipitation, DNA-crosslinking).

Single Cell Sequencing

Technical notes: Single and paired-end sequencing.

Short paper presentations and discussion (students).

4 02/04/2021 Microbiome – sequencing, analysis, data mining

Marcos Perez-Losada, SPH, GWU Online, 4pm 5 02/11/2021 Basics of Script-writing and programming for NGS data _analysis.

Nathan Edwards Georgetown University Online 4pm 6 02/18/2021

Intro to data analysis - Bulk and Single cell RNA sequencing analysis: Part1

Alignment, Assembly, Abundance estimation, Splice Isoforms Assessment

Short paper presentations and discussions (students).

Anelia Horvath Online 4pm

7 02/25/2021

Intro to data analysis - Bulk and Single cell RNA sequencing analysis: Part1

Variation calls, Variation Annotation

Anelia Horvath Online 4pm

8 03/04/2021 Midterm EXAM & _{Assignment of Individual Projects} Anelia Horvath Online 4pm

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4 of 5 Module 2 Data Analysis

9 03/11/2021

Analytical Pipelines (Hands-on): Transcriptome Sequencing: Team Projects on RNA sequencing. Script running Step-by-step

Part I

Anelia Horvath, TAs Online

4pm

03/18/2021 SPRING BREAK

10 03/25/2021

Part II

4pm

11 04/01/2021

Part II

4pm

Module 3 Results Interpretation and Downstream analysis

12 04/08/2021

Example of RNA-seq application – Cancer Analysis Hands on – individual and team projects.

Integration of OMICS datasets

4pm

13 04/15/2021

Results Integration, Interpretation and Downstream analysis

Pathway Analysis, Gene Ontology Analysis Visualization: Volcano plots, Heat Map

4pm

14 04/22/2021 Students NGS project presentation I (10-15 min, _{graded). Discussion.} Anelia Horvath Online 4pm

15 04/29/2021 Final Exam & Online Party Anelia Horvath Online

4pm

Dynamic sub-modules:

- 10-min presentation of major most recent discoveries or developments in the field of NGS at the end of each lecture.

- Starting from the first lecture, the students will be asked to submit subjects of their interests; the requests will be collected and discussed during lecture 14.

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5 of 5 Additional details

Missed Exam policy

To be eligible to schedule a make-up exam, you must have e-mailed or talked to the instructor prior to missing an exam or given timely notification that you were sick on the day of an exam.

Attendance and Professionalism

Students are required to attend classes. Attendance will be taken at the beginning of class. A 50% or more than 50% absence will result in a deduction of 5 points in the final grade. If a student arrives after roll has been called, it is incumbent on the student to inform the instructor, at the end of class, that he/she is late. Statements such as, “I was late for class last Tuesday but forgot to tell you” will not change the absence. All students are expected to conduct themselves in a professional manner. Unprofessional behavior such as, but not limited to, repeated disruption of class (including habitually walking in after class has started), sleeping in class, doing other course work in class, reading a newspaper in class, a ringing cell phone, frequent side conversations with other students and/or rudeness toward any person will be considered a serious violation of this standard and will lower your grade accordingly.

Academic Integrity

Students must maintain academic integrity and be free from fraud and deception. Please review the University’s policy on academic integrity at www.gwu.edu/~ntegrity/code.html. Examples of academic dishonesty include, but not limited to, cheating, plagiarism, enabling someone else to cheat. The usual punishment for academic dishonesty is an “F” for the course or a lesser penalty for infractions of a more minor nature.

Students with Disabilities

Students who require disability-related accommodations should contact the instructor privately in the first week of the course. They should also contact Disability Support Office at 202-994-8250, Suite 242, Marvin Center to establish eligibility and to coordinate reasonable accommodations.

Adverse Weather/Class cancellation

The instructor will follow recommendations of the GWU in the event of severe weather or other threat. Students should call the university hotline at 202-994-5050 or check online at www.gwumc.edu. The instructor will adjust the class schedule in the event of cancelled classes.