PhD position, Biological Psychology, Amsterdam
Project: Imputation of rare genetic variants in the Dutch population based on GoNL
(Genome of the Netherlands)
Background
The department of Biological Psychology of the Faculty of Psychology and Education of the VU University studies individual differences in health, behavior and lifestyle in relation to genetic and environmental factors with the use of (twin)family data. Within the context of a large collaborative bionbank project in the Netherlands (http://www.bbmri.nl/) we aim to contribute to the analysis of rare genetic variants and their influence on complex phenotypes.
Within BBRMI-NL (Biobanking and Biomolecular Resources Research Infrastructure, the Netherlands) a high-profile €2M project was initiated to establish a nation-wide genetic map of (rare) variants in the Netherlands. The overall aim of the project is two-fold: (1) to gain insight in the population structure of the Dutch and (2) to improve genetic research of health and disorder by providing a better characterization of (rare) genetic variants in the Dutch population. To this end, whole genome sequence data on approximately 750 samples (250 trios) will be integrated with existing GWAS data. Hence, you will have the opportunity to work on a unique data set obtained with state-of-the-art technology and of unprecedented scale. As a geneticist / bioinformatician you will create a database that contains the integrated data.
Job description
The current project involves genome-wide imputation of all known genetic variants in the Dutch population in samples that have GWA data available for a more limited number of variants. As a reference map for imputation, whole genome sequence data have been collected in 250 Dutch trios (2 parents and 1 offspring). Currently this reference dataset is being phased and quality control steps are performed. The imputed data will be roughly 100.000 samples for which GWAS data are available in the Netherlands BBRMI effort. In order to successfully impute data, the data quality needs to be carefully checked and aligned. Imputation faces some demanding challenges from an IT perspective and several issues need to be resolved. The project will involve carrying out and improving the imputation from both an IT and a genetic perspective. Next, imputed data can be used for GWAS on (longitudinal) phenotypes that are present within the Dutch biobanks.
Qualifications and skills
You have an MA-degree and interest in IT and genetics.
You have experience with Linux and scripting code, cluster computer batching, statistical genetic analyses, R and large text files data manipulation.
Salary: The PhD student will receive a salary starting at € 2.042,- per month, and increasing to € 2.612,- gross per month in year four (full-time).
Additional information: The position is for 1 year initially with extension into 3 or 4.
Information on a comprehensive range of benefits can be found at this website
Information: For more information please contact dr Jouke Jan Hottenga (j.j.hottenga@vu.nl), dr Morris Swertz (m.a.swertz@gmail.com) or prof Dorret Boomsma (di.boomsma@vu.nl ).
More information on our department can be found on this website.
Application: please write a letter accompanied by a curriculum vitae. Applications should be sent to VU University Amsterdam, dept. of Biological Psychology, attn. Natascha Stroo, project manager, Van der Boechorststraat 1, 1081 BT Amsterdam. It is also possible to apply by email to: natascha.stroo@vu.nl