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:

1. Study which structural changes affect the risk to develop Alzheimer’s disease
2. Identify structural variations vulnerable for somatic mutations
3. Identify and investigate structural variations that modify across generations.

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.

• You have a recent M.Sc. degree in Bioinformatics, Genetics or related studies, with a solid computer science background;
• Experience with sequencing data and methods development is required. Experience with PacBio long-read sequencing data is preferred;
• Experience with programming, data visualization and data handling in Python, R, or related languages;
• Proficient in Unix/Linux-based command line and cluster environments; Experience with programming and high-performance computing.

The research area of interest is rapidly growing, and there is no standard analysis pipeline or method, so your creativity will be essential. Within this project most communication will be in English, so fluency in English and excellent communication and organizational skills are essential.

Fixed-term contract: 12 months, to be extended for another 36 months upon evaluation.

We offer a four year PhD contract (starting for 12 months, to be extended for another 36 months upon evaluation). The salary scale starts according to PhD guidelines at € 2495,- in the first year, growing to € 3196,- in the last year (based on a 36 hour contract).

• In addition to a good salary, we offer, among other things, 8.3% end-of-year bonus and 8% holiday allowance.
• Free and unlimited access to the training offer of our online learning environment GoodHabitz.
• Your pension is accrued at ABP. Amsterdam UMC contributes 70% of this premium.
• We reimburse 75% of your public transport travel costs and also offer a bicycle arrangement.

For more information about our employment conditions, please visit our website.
A reference check can be part of the selection procedure. In addition, applying for a VOG (Certificate of Good Conduct) is mandatory for every new employee. The application for a VOG is started from Amsterdam UMC as soon as the new employee has been appointed.

Amsterdam UMC

The Academic Medical Center (AMC) and the VU University Medical Center (VUmc) today joined forces in an administrative merger. The chairmen of both Boards of Directors signed the merger into force this afternoon. The signing ceremony took place in downtown Amsterdam, in a fitting location overflowing with Dutch medical history: the 17th century Anatomy Theater in a traditional weighing house called De Waag.
Following an intensive multi-year planning process, the two Amsterdam academic hospitals are working together as of this moment under a collective name: Amsterdam UMC. This enables both Amsterdam university medical centers to further develop their core business together: complex patient care, scientific research, and education & training. Amsterdam UMC kickstarts a gradual process of continuous integration. Initially, this will be most visible in two sectors: patient care and scientific research.

Human Genetics and the Alzheimer Center

Our lab is based at the department of Human Genetics and the Alzheimer Center at the Amsterdam University Medical Center. This projec is a collaboration with PacBio and with the Delft Bioinformatics Lab at the Technical University in Delft. See also: www.holstegelab.eu.