PhD Student (2x) | AD-REPEAT

Are you a bioinformatician interested in learning more about the genetics that enable individuals to live past 100 years old? What makes others vulnerable to Alzheimer's Disease? Do you want to work with long-read sequencing technologies and use computational expertise to unravel rich datasets?

As Ph.D. researcher, you will help unravel a unique long-read genomics dataset of Centenarians (cognitively healthy individuals older than 100 years of age) and Alzheimer’s disease patients.
It is clear that genetic elements are involved with both the increased risk of Alzheimer’s Disease and with the escape of Alzheimer’s Disease, but it is not yet clear which elements are involved. In the AD-REPEAT project, you will investigate the role of large structural genomic variations using Pacbio SMRT long-read sequencing data from hundreds of genomes from well-phenotyped Alzheimer’s Disease patients and cognitively healthy centenarians from the 100-plus Study cohort. This is a unique dataset that represents the extreme ends of the cognitive spectrum, enabling you to maximize the effect size of your analysis. Further, you will also investigate the somatic differences between centenarian blood and brain samples.
We are looking for a PhD for four years to analyze these novel, exciting and rich datasets. You will employ both reference-based and de-novo assembly approaches in order to quantify and analyze the variability of structural variants in the human genome. Our research aim is to:

What will be your responsibilities?

• Monitoring the generation of PacBio SMRT long-read sequencing data;
• Development of approaches and algorithms to call structural variations from long-read sequencing data (i.e. variable nucleotide tandem repeats, VNTRs, but also other structural variants);
• Analysis and interpretation of structural variations in the context of Alzheimer’s disease and longevity;
• Validation of structural variations using GWAS data (developing imputation approaches) and WGS short-read data.