NWI-BB086
Genomics for Health and Environment
Course infoSchedule
Course moduleNWI-BB086
Credits (ECTS)12
CategoryBA (Bachelor)
Language of instructionEnglish
Offered byRadboud University; Faculty of Science; BioWetenschappen;
Lecturer(s)
PreviousNext 5
Lecturer
ing. T.A. van Alen
Other course modules lecturer
Lecturer
dr. A.B. Brinkman
Other course modules lecturer
Lecturer
dr. A.P.M. de Brouwer
Other course modules lecturer
Lecturer
prof. dr. H.J.M. op den Camp
Other course modules lecturer
Lecturer
dr. S.J. van Heeringen
Other course modules lecturer
Academic year2019
Period
KW1  (02/09/2019 to 03/11/2019)
Starting block
KW1
Course mode
full-time
Remarks-
Registration using OSIRISYes
Course open to students from other facultiesYes
Pre-registrationYes
Pre-registration openfrom - up to and including -
Waiting listYes
Placement procedureDone manually by Back Office
ExplanationDone manually by Back Office
Aims
Learning outcomes: At the end of the course you can:
  • conduct nucleic acid isolation and library preparation for the major next-generation DNA sequencing machines in a small team 
  • use the Bash shell to navigate directory structures, manipulate files and execute commands in an automated manner
  • identify functionally relevant genetic variation in genes
  • define the human microbiome and explain the role metagenomics plays in its investigation
  • define the transcriptome and explore its features
  • define human genetic variation
  • explore metabolic and signal transduction pathways
  • report on your next generation sequencing research findings in a public talk
  • reflect on ethical questions and implications pertaining to next generation sequencing applications in medicine and ecology.
Content
The general objective is to provide students with theoretical background and hands-on experience in microbial (meta)genomics, medical genomics and transcriptomics.  Bioinformatic aspects of genome complexity, read mapping, next generation DNA sequencing (NGS) signal quantification and functional interpretation are taught.
There is a 3 week long department-specific full time practical component to this course, split across the Microbiology (FNWI), Human  Genetics (UMCN) and Molecular Biology (FNWI) departments. During this practical you will perform research in groups of 3 students together with researchers from one of the departments, working with them on their ongoing research topic. Hence GHE students are exposed to state-of-the-art research practice. Students from each practical group report their findings during a two-day symposium which also hosts international speakers.
Level

Presumed foreknowledge

Test information
The final mark is determined for 55% by the Final exam, 15% Essay, 10% Practical report, 10% Practical work and 10% for Final symposium presentation.
Specifics
Participation is limited to 45 students who must register personally through the course coordinator (clogie@science.ru.nl) in May and June. If more than 45 applications are received by mid-June, a stratified random drawing proportional to the number of applications emanating from Biologists/MLS/HLO student cohorts is held and supernumerary students are put on a waiting list. After June 17th, the course is filled-up on a first-come-first-served basis and supernumerary students are put on a waiting list.
Additional comments
Participation is limited to 45 students who must register personally through the course coordinator (clogie@science.ru.nl) in May and June. If more than 45 applications are received by mid-June, a stratified random drawing proportional to the number of applications emanating from Biologists/MLS/HLO student cohorts is held and supernumerary students are put on a waiting list. After June 17th, the course is filled-up on a first-come-first-served basis and supernumerary students are put on a waiting list.

Topics
• Metagenomics
• Human genomics
• Transcriptomics

Test information
The final mark is determined for 55% by the Final exam, 15% Essay, 10% Practical report, 10% Practical work and 10% for Final symposium presentation.

Required materials
Learning Management System (Brigthspace)
Learning materials are made available through Brightspace, including lecture power points, working group hand-outs and practical protocols.

Recommended materials
Book
Useful but not obligatory books include Lehninger Principles of Biochemistry, Lodish Molecular Cell Biology and Brock Biology of Microorganisms

Instructional modes
Course/Lectures
Attendance MandatoryYes

Guided computational exercises
Attendance MandatoryYes

Lab course
Attendance MandatoryYes

Response course

Self study

General
Self-study in the first four weeks should be mostly dedicated to essay writing and keeping up with lectures and computational classes. During the second half of the course, self-study time should enable presenting data and analyses during the student symposium and prepare for the written test.

Student presentations
Attendance MandatoryYes

Theoretical and applied tutorials
Attendance MandatoryYes

Writing and peer reviewing
Attendance MandatoryYes

Tests
Essay
Test weight3
Test typeEssay
OpportunitiesBlock KW1, Block KW2

Practical
Test weight6
Test typeLab course
OpportunitiesBlock KW1

Exam
Test weight11
Test typeExam
OpportunitiesBlock KW1, Block KW2