Projects
Name
(Bucharest) Molecular Techniques in the Diagnosis of Male Infertility
University
Romania (FASMR) - University of Medicine and Pharmacy "Carol Davila", Bucharest
Domain
Genetics
Departement
Medical Genetics Chair, University Of Medicine and Pharmacy, Bucharest, Romania
Head
PhD, Relu Cocos
Tutor
PhD, Relu Cocos
Languages
English
Duration
4 weeks
Availability
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
No No No No No No No No Yes Yes No No
Type of Research Project
- Basic science
What is the background of the project?
Male infertility has increased up to 50% since 1955 in the world and 10-15% of couples are already suffering from it. Even if there are some advances in assisted reproductive technologies infertility is considered a major health issue. Human societies have dramatically changed the human life style which led gradually to the increase of environmental pollutants. The presence of variable phenotypes in infertile patients showing apparently identical microdeletions suggests the presence of other modifier genes able to produce different genetic backgrounds, which in turn could balance or enhance the molecular defect produced by the loss of genes mapped within AZF loci. The spermatogenic mechanisms are not just related to the Y chromosome but also to several hundred genes located on different autosomes that are believed to be involved in spermatogenesis and its regulation. Given the growing number of candidate genes we propose to develop a 135 gene targeted sequencing (Next Generation Sequencing) diagnosis protocol of the interesting genomic regions associated to this condition in order to further increase our knowledge on the molecular base of male infertility.
What is the aim of the project?
This project aims to develop a targeted sequencing protocol of genomic regions in order to identify novel gene mutations, to facilitate the clinical diagnosis process and to reduce considerably the price of multiple Sanger sequencing tests.
What techniques and methods are used?
1. Amplification of small segments for small isolated pieces of DNA (Deoxyribonuclic acid) using Multiplex PCR (Polymerase chain reaction). 2. Library preparation to generate collections of DNA (Deoxyribonuclic acid) using the Ion AmpliSeq Library Kit v2.0. 3. Next Generation Sequencing using the Ion PGM (Personal Genome Machine) sequencing Kit. 4. Data Analysis using genome analysis scripts and softwares, by comparing obtained results with an existing data-set.
What is the role of the student?
- The student will mainly observe
- The student will observe the practical experiments but will be highly involved in the analysis of the results
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
1. Perform Multiplex PCR using a set of 6 primers to identifiy the microdeletions on the Y chromosme. 2. Prepare libraries for the NGS sequencing using the Ion AmpliSeq DNA and RNA library kit. 3. Conduct bioinformatics data analysis using a customized pipline consisting of Burrowse Wheeler Aligner (BWA), the SAMtools software and Picard utilities for indexing, sorting, RG line and duplicate removal. Single Nucleotide Variants (SNV) and Deletions (INDELs) will be filtered against diffrent databases and annotated using ANNOVAR tool. The above techniques will be shown to the students at the beginning of the project. They will have to perform on their own a part of these techniques, but the presence of the tutor is mandatory.
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
No
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- No specific outcome is expected
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
Previous experience with: PCR techniques
Are there any legal limitations in the student’s involvement
No
Hours
4
Type of students accepted
This project accepts:
- Medical students
- Students in biomedical fields
Articles
- Human male infertility and its genetic causes. Toshinobu Miyamoto et al. Reprod Med Biol. April 2017 Volume 16; Issue 2; Pages 81-88; DOI: 10.1002/rmb2.12017
- The nucleus: An international journal of cytology and allied topics: A bibliometric study Adithya Kumari; Shivaram Rao SRELS Journal of Information Management Vol. 37 No. 1 March 2000. Paper F. p59-74.