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PhD project

Effects of Germline Structural Variation on the Biology and Pathology of the Large Intestine

Call for applications for a fully financed PhD.

Project description 

The human reference genome contains many “gaps” which cannot be characterized using standard short-read whole genome sequencing (SR-WGS). Recently, long-read WGS (LR-WGS) studies show that such gaps vary in DNA sequence structure and copy numbers between individuals. This newly identified genome structural variation (SV) expectedly contributes to inter-individual differences in health and disease, however, this is still largely unexplored. 

This PhD project will study the mechanisms by which germline SV affects the molecular biology and pathology of the large intestine in patients with colorectal cancer (CRC). We will combine LR- and SR-WGS to map SV genome-wide, establish a novel reference genome encompassing SV diversity and use this to evaluate the impact of SV on gene regulation (enhancer/silencer usage), disease pathways and outcome in a large patient cohort. Concurrently, the impact of SVs on genome folding will be studied by chromosome conformation capture techniques. Hereby, the project will provide new insight into how SV affects CRC, which may, ultimately, help to personalize disease treatment based on a person´s inheritance.

Your work will focus on producing and analyzing SR- and LR-WGS data using germline DNA from CRC patients. You will be the driving force in both “wet lab” activities (e.g. establishment of pipelines for LR-WGS, orchestration of SR-WGS activities, cell culture work) and “dry lab” activities (e.g. contribution to development of methods for analysis of SV using WGS data and integration of multiomics datasets). As a PhD student your position is primarily research-based but may also involve teaching assignments.

You will be working under supervision of Assoc. Prof. Jesper Bramsen in the CRC Research Group, headed by Prof. Claus L Andersen, at the Department of Molecular Medicine (MOMA), Faculty of Health, Aarhus University (AU). The group consists of ~15 employees incl. Assoc. Professors, Postdoc´s, PhD-, master- and bachelor-students. Research focus is both on developing new methods for CRC detection based on circulating tumor DNA and on identification of new genomic biomarkers for personized medicine by multiomics characterization of tumors. This PhD project will expand this latter research activity to include SV analysis of patient germline DNA.

Department of Molecular Medicine (MOMA)

MOMA offers a unique interdisciplinary research environment focusing on translational cancer research powered by genomics. The department houses state-of-the-art next-generation sequencing and laboratory facilities, cancer biobanks and an extensive genomics data infrastructure. MOMA has close ties to the clinic, to the Bioinformatics Research Centre, (AU) and participates in the Danish National Genome Center. 

Your place of work will be the Department of Molecular Medicine (MOMA), Science Center Skejby, Brendstrupgårdsvej 21A, 8200 Aarhus N, Denmark.     

Qualification

In order to be assessed as qualified for a PhD study, you hold - or soon will - a Master’s degree within molecular biology, molecular medicine, biology, medicine or equivalent.

Preferentially, you should have the following skills:

  • Experience in experimental lab work including e.g. next generation sequencing, cell culture work, PCR etc.
  • Experience in bioinformatics data analysis, preferably using R or Python
  • Fluency in written and spoken English
  • As a person, you are ambitious, take ownership, have a collaborative attitude, and possess good communication and interpersonal skills.    

How to apply

Please submit your application via this link. Application deadline is 14 June 2021 23:59 CET.

Shortlisting will be used. Preferred starting date is 1 September 2021. Interviews are expected to be conducted during June-July 2021.   

For information about application requirements and mandatory attachments, please see our application guide 

Further information

If you have any questions about the position, please contact:

Associate Professor Jesper Bertram Bramsen (project supervisor; email: Bramsen@clin.au.dk) and

Professor Claus Lindbjerg Andersen (group leader; email: cla@clin.au.dk)     

 

All interested candidates are encouraged to apply, regardless of their personal background. Salary and terms of employment are in accordance with applicable collective agreement.