Jobs

Postdoc Researcher in Identification of Genetic Repeat Sequences associated with Alzheimer’s Disease

Employer

Amsterdam UMC

Location

Amsterdam , The Netherlands

Principal Investigator

Henne Holstege

Contact

h.holstege@amsterdamumc.nl

Description

The Holstege lab is interested in the genetics associated with the increased risk of cognitive decline and the genetics associated with the escape of cognitive decline until extreme ages. In the current project the postdoc will compare large structural genomic variations in large sample of genomes from well-phenotyped Alzheimer Disease patients with genomes from a large sample of well-phenotyped cognitively healthy centenarians (www.100plus.nl). Further, the lab will investigate the somatic differences between centenarian blood and brain samples, using Pacbio SMRT sequencing to generate long-read sequencing data. The lab is looking for a postdoc for at least three years to analyze these novel, exciting and rich data.

The postdoc researcher 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. The research aims are:

(i) to study which structural changes affect the risk to develop Alzheimer’s disease,
(ii) to identify structural variations vulnerable for somatic mutations,
(iii) to identify and investigate structural variations that modify across generations.

The postdoc's main responsibilities are:

  • 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.

The lab has a central position in studying WGS/WES data in the Alzheimer’s field and this data is available.

Salary Scale 10: 2911 tot 4615 euro gross when employed full-time (depending on qualifications and experience), and an 8.3 percent 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 percent of this premium.

The lab reimburses 75 percent of your public transport travel costs and also offers a bicycle arrangement.

For more information about our employment conditions, please visit the lab's 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.

Additional information

The preferred starting date for this position is February/March 2021 but this is negotiable.

If you’re interested about this position, contact Henne Holstege, via telephone number 020 444 8704. If you need more information about the application procedure, contact Brend de Jong, corporate recruiter at 020 444 8704.

You can apply till 21 January 2021 by using the apply button.

Acquisition based on this vacancy is not appreciated.

Requirements

  • A recent Ph.D. 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.
  • Proficiency in Unix/Linux-based command line and cluster environments.
  • Experience with programming and high-performance computing.
  • You are communicative, well organized, independent and willing to supervise.

The lab looking for a candidate who has experience with sequencing data and methods development. The research area of interest is rapidly growing, and there is no standard analysis pipeline or method. Programming skills in different languages (python, bash, R) and experience in cluster computing systems is essential. You are highly motivated, creative and willing to supervise. Within this project most communication will be in English, so fluency in English and excellent communication and organizational skills are essential.