Postgraduate Course: Analysis and Reporting of Next Generation Sequencing (MCLM11058)
Course Outline
| School | Deanery of Molecular, Genetic and Population Health Sciences |
College | College of Medicine and Veterinary Medicine |
| Credit level (Normal year taken) | SCQF Level 11 (Postgraduate) |
Availability | Not available to visiting students |
| SCQF Credits | 20 |
ECTS Credits | 10 |
| Summary | This course aims to provide students with a detailed understanding of the technology behind next generation sequencing, the requirements for sample handling and the parameters that determine quality of sequence generated. The course will cover the analysis of data for mutation detection, somatic and germline, using a range of bioinformatics approaches. 50% of this module will involve development of a real next generation sequencing clinical service.
Aims of the course
1. To provide a detailed explanation of the techniques used for next generation sequencing analysis and the bioinformatic interpretation of clinical NGS data.
2. To enable students to develop the skills required to implement NGS pipelines into NHS clinical laboratory practice in both germ line genetics and somatic analysis of cancer.
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| Course description |
The first half of the course will be taught by lectures and interviews that will be made available online as the course progresses, introducing students to the new topics in order. Furthermore, discussion boards and other online activities such as quizzes will be used to keep students engaged and to reiterate the key learning outcomes for specific material. Therefore students would have a weekly block of material consisting of ~1 hour of lectures (material dependent) alongside ongoing discussion boards and reading students should be studying and researching independently and continuously. In addition there will be two in-person tutorials, that provide students with an opportunity to critically engage with the material and apply the content they have learned. Tutorials will be led by experienced academics, clinical scientists and clinicians. For the second half of the course students will undertake an NGS development project, supervised by an appropriate local supervisor. The specific nature of projects will vary, depending on local service needs and background of the student.
Course Structure:
The course is divided into four conceptual blocks and two practical data analysis tutorials:
4A. Next generation sequencing technologies
4B. Bioinformatics approaches to analysing NGS data
Tutorial 4.1: Data management exercise I: VCF Generation
Tutorial 4.2: Data management exercise II: VCF Analysis
4C. Variant interpretation: mechanisms of mutation action and the de-novo paradigm for rare disease causation
4D. Practical implementation of NGS.
Assessments:
Assessments are designed to be directly relevant to individuals working in the National Health Service, as such they are often modelled on content-specific standardised reports and relevant clinical practice. Assessments utilised to monitor students' progression will include:
a) Ongoing assessment of individual student's interactions with discussion boards throughout the course
b) Weekly formative quizzes in the first half of the course only
c) A written assignment - Students will complete a Variant Analysis Report based on the sequence data analysis performed during the course tutorials.
d) Written lab report - Students will write a laboratory report on the student-specific next generation sequencing implementation project.
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Entry Requirements (not applicable to Visiting Students)
| Pre-requisites |
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Co-requisites | |
| Prohibited Combinations | |
Other requirements | None |
| Additional Costs | Purchasing of books, personal computers if not using university facilities |
Course Delivery Information
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| Academic year 2017/18, Not available to visiting students (SS1)
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Quota: None |
| Course Start |
Flexible |
Timetable |
Timetable |
| Learning and Teaching activities (Further Info) |
Total Hours:
200
(
Lecture Hours 5,
Seminar/Tutorial Hours 4,
Supervised Practical/Workshop/Studio Hours 84,
Online Activities 8,
Feedback/Feedforward Hours 4,
Formative Assessment Hours 8,
Summative Assessment Hours 18,
Programme Level Learning and Teaching Hours 4,
Directed Learning and Independent Learning Hours
65 )
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| Assessment (Further Info) |
Written Exam
0 %,
Coursework
100 %,
Practical Exam
0 %
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| Additional Information (Assessment) |
Written Exam - 0%
Coursework - 100%
Practical Exam - 0%
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| Feedback |
Students will receive formative or summative feedback on all assessed pieces of work. |
| No Exam Information |
Learning Outcomes
On completion of this course, the student will be able to:
- Explain and compare different next generation sequencing technologies
- Analyse NGS data and VCF files using the Galaxy data analysis platform
- Evaluate the role of exome and whole genome sequencing in a diagnostic setting
- Develop original and creative approaches to establishing a new NGS assay as part of a clinical service
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Reading List
| Primary research articles and authoritative reviews will be provided to students during the course. |
Additional Information
| Graduate Attributes and Skills |
Not entered |
| Keywords | Molecular Pathology,Genetics,Genomic Medicine,Genomics,Cancer,Next Generation Sequencing |
Contacts
| Course organiser | Dr Amy Hansen
Tel: (0131 6)51 8757
Email: |
Course secretary | Mrs Alison Kyte
Tel: (0131 6)51 1041
Email: |
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