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Postdoctoral position: Rare Disease Genomics
Host/Location: Division of Molecular Biology and Human Genetics, Rare Disease Genomics Group, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Medical Campus
Value of Award: Competitive tax-free fellowship
Duration: Tenable for 2 years with the possibility of a further extension, depending on available funding. Please note that postdoctoral fellows are not appointed as employees at SU and are therefore not eligible for employee benefits. Postdoctoral fellowships are also awarded tax free.
A rare disease (RD) is defined as one that affects fewer than 1 in 2000 people. Although individually “rare”, collectively there are over 7000 different RDs, which affect a significant proportion of the population and impact the lives of millions of South Africans. Over 80% of RDs are genetic in origin and most have their onset in childhood. However, to date, people with RDs have been disproportionately underrepresented in terms of research, diagnosis and treatment, especially in Africa. Using conventional testing, patients remain on their “diagnostic odysseys” indefinitely. Next generation sequencing (NGS) technology has revolutionized diagnosis in RDs. The Rare Disease Genomics group has recently established an undiagnosed disease programme (UDP) at SU, to use state of-the-art NGS technologies to end the diagnostic odyssey for South African patients with RDs.
We are seeking an enthusiastic postdoctoral fellow to join our multidisciplinary team, to oversee and develop the bioinformatics arm of the UDP. The successful candidate will benefit from working in a young, dynamic and diverse research group with national and international collaborations and numerous opportunities for further training.
- Analysis of NGS datasets (whole exome and genome)
- Analytical method development specifically suited to NGS technologies
- Data mining, analysis and interpretation
- Construction and curation of databases and specific computational tools
- Hypothesis generation for new scientific questions and research studies
- Manuscript and grant writing
- Oversee the bioinformatics arm of the Rare Disease Genomics in South Africa: UDP project
- Contribute to study design and implementation – including student projects
- Development of key documents such as protocols, SOPs, etc
- Training of students and other scientists
- Oversee reporting and interpretation of data
- PhD in Human Genetics, Bioinformatics or a related field
- Experience with analysis of NGS datasets (exome and genome sequencing)
- Experience in working in Linux environments
- Proficiency in common scripting languages (Python, R, other)
- Sequencing analysis and pipeline design
- Experience in computational and statistical analysis of high-dimensional and multivariate data
- Comprehensive use of computational clusters and cloud-based computing
- Excellent organisational, planning and interpersonal skills
- High level of accountability, integrity and a good understanding of confidentiality
How to apply
Please send the following to Professor Shahida Moosa at firstname.lastname@example.org
- Motivation for applying for this position
- Updated CV including publication list
- Proof of PhD qualification and copy of academic transcript
- Names and email addresses of two referees, who can be contacted immediately upon shortlisting
Closing date: 30 September 2021
Commencement of duties: January 2022 - negotiable
Early applications are encouraged. We will stop looking when we find a suitable candidate.
MSc and PhD positions: TB Genomics Research Group
The TB Genomics Group has applied for project funding and is looking for students to do parts of the work as Masters, or PhD projects.
Full disclosure: Please note that the project does not have attached bursary funding. As such, any potential students would need to find personal funding. The purpose of this call is to find interested students who we can assist with bursary- and Harry Crossley project funding applications.
For more information related to the project please see below.
Identification and characterization of non-tuberculosis mycobacteria (NTM) in South Africa, and their role in modulating the macrophage immune response to other lung pathogens”
Little is known about nontuberculous mycobacteria (NTM) that cause pulmonary diseases (NTM-PD), which is a rising global health concern. NTM species are naturally resistant to most common antibiotics. Diagnosis of NTM-PD is technically challenging, expensive, and sometimes inaccurate. Despite the frequent isolation of various NTM species from patients with NTM-PD, data on pathogenic NTM species and their genetic characteristics is still incomplete. Several studies have reported the isolation of NTM in patients with pulmonary infection, often concurrently, or after a previous infection with Mycobacterium. tuberculosis(MTB). Interaction between these two mycobacterial species and how they modulate the immune system in the presence of other mycobacterial species is still an unexplored topic.
NTM-PD samples identified by National Health Laboratory Service, Greenpoint during routine diagnosis, as well as non-pathogenic species from our NTM sample bank will be genetically characterized by whole genome sequencing and compared by phylogenetic analysis of the genomic diversity. To elucidate the immune response to NTM and MTB coinfection, THP-1 macrophages will be infected with both NTM species and MTB H37Rv sequentially and simultaneously. Macrophage cytokine and chemokine secretions in response to coinfection will be measured using qRT-PCR and Luminex, and metabolic pathways will be determined using RNA-sequencing. Mass spectrometry will be used to identify secreted proteins from pathogenic and non-pathogenic NTM strains.
Characterization of the NTM-PD pathogenic species and identification the immune response to these species may assist in determining the clinical significance of these pathogens and lead to identifying biomarkers of various NTM species' infectivity. Comparison of the genomic and immune determinants of pathogenic and non-pathogenic species will contribute to knowledge on the fundamental determinants of virulence in mycobacteria. This will have important implications for the diagnosis and the management of this condition.
If you are interested, please contact email@example.com and firstname.lastname@example.org