HIV-1 full genome analysis (HIV-FGA)
Germany (bvmd) - Universitaet zu Koeln, Cologne
Infectious Diseases
Institute of Virology
Prof. Dr. Herbert Pfister
Dr. Rolf Kaiser, Finja Schweitzer
Fluent English, German
4 weeks
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Type of Research Project
- Clinical Project with Laboratory work
What is the background of the project?
Background information: HIV-1 causes the acquired immune deficiency syndrome (AIDS) if no antiretroviral treatment is performed. Today a large variety of drugs is available to successfully treat the disease, but HIV is able to develop resistance to any of the antiretroviral drugs. The mechanisms, namely the responsible mutations causing resistance are known in most of the cases of treatment failure, but still a remarkable number of cases occur that do not display resistance mutation. It is therefore necessary to analyze a larger genomic region than only the target gene of HIV. We have preliminary laboratory protocols that shall allow us to analyze (sequence) the whole HIV-genome and analyze it.
What is the aim of the project?
Aim of the project:
We will develop a technique to routinely analyze the whole HIV genome in order to investigate the achieved information together with the bioinformaticians in our cooperation.
The data will be used to upgrade the geno2pheno HIV resistance interpretation system.
What techniques and methods are used?
Techniques and methods: Preparation of HIV from blood and from cell culture. The techniques that shall be used are PCR-Amplification, Sanger Sequencing and preparation for next generation with Illumina-Technique. The evaluation will be performed with tools like Lasergene-Navigator, BLAST, geno2pheno, HIV-GRADE and others.
What is the role of the student?
What are the tasks expected to be accomplished by the student?
Individual training will be provided on the specific project.Participation in the seminars and lectures of the Institute and the University clinics is also recommended. The student will be able to perform sample preparation and molecular biology techniques. This includes handling of infectious material, contamination-free work in the laboratory and analysis of results with different computer based tools. We expect the student the student to learn diagnostic and clinical aspects of HIV-, HBV- and HCV-infections. We enable clinical contacts with infectious disease specialists, gastroenterologists. From this we expect the student to take the information home to his country and hopefully apply knowledge and keep contact to us for future projects
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
Skills required: The student should be able to read and understand English manuscripts, namely specific medical literature and laboratory manuals in English. For the use of students considering participating in the project, further information can be found from the following articles: The geno2pheno and genafor homepage as well as articles from our group can be found in the internet, but these are not mandatory for the work in our lab.
Are there any legal limitations in the student’s involvement
Type of students accepted
This project accepts:
- Medical students
- Pre-Medical students from the American-British system
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