NWI-BB086
Genomics for Health and Environment
Course infoSchedule
Course moduleNWI-BB086
Credits (ECTS)12
Category03 (Advanced)
Language of instructionEnglish
Offered byRadboud University; Faculty of Science; BioWetenschappen;
Lecturer(s)
PreviousNext 1
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. C. Logie
Other course modules lecturer
Examiner
dr. C. Logie
Other course modules lecturer
Coordinator
dr. C. Logie
Other course modules lecturer
Academic year2022
Period
KW1  (05/09/2022 to 06/11/2022)
Starting block
KW1
Course mode
full-time
RemarksMaximum capacity: 45. Course coordinator controls enrolment
Registration using OSIRISYes
Course open to students from other facultiesNo
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.

Instructional Modes
  • Tutorial
  • Response course
  • Presentation
  • Self-study
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. Minimum grade for all parts is 5.5. 
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.

In the case of not being able to attend one or more practical courses/lab days due to corona measures, the course coordinator will decide if the student is obligated to re-take the missed meeting and how this will take place.
 
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

Sustainability certificate
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