Postdoc with Clinical Translational Focus

Do you want to contribute to top quality medical research?

A Clinical Postdoc position in Translational Cancer Genomics funded by Karolinska Institutet (KI) and Science for Life Laboratory (SciLifeLab) is immediately available. The position is shared between the Foukakis Laboratory at KI BioClinicum (lead lab) and the Crosetto Laboratory for Quantitative Genome Biology at SciLifeLab.

You will bridge the expertise of the Foukakis lab in clinical oncology with the expertise of the Crosetto lab in genomics, overseeing the application of methods for profiling genomic copy number and structural alterations to breast cancer specimens collected in the frame of two clinical trials (PREDIX Luminal B and PHASIPHAE) led by Karolinska University Hospital.

Your main goal will be to investigate how spatio-temporal intratumor heterogeneity at the genomic level correlates with response to chemotherapy vs. endocrine and targeted therapy in luminal breast cancer patients.

You will work both in a clinically focused (Foukakis lab) and in a technology oriented (Crosetto lab) environment, benefitting from cross-disciplinary interactions and acting as a bridge between clinicians, technologists and bioinformaticians in both labs.

Your mission

As a Postdoc with strong translational focus, you will initially learn the CUTseq method that was previously developed in the Crosetto lab (Zhang et al, Nature Communications 2019) and recently applied for immuno-genomic profiling of breast cancer samples in a joint effort between the Foukakis and Crosetto labs (Zerdes et al, npj Breast Cancer 2021).

You will then apply CUTseq as well as a single-cell version of it (scCUTseq) recently developed in the Crosetto lab, to profile somatic copy number alterations (SCNAs) and structural variants (SVs) in luminal B breast cancer specimens that have been collected in the PREDIX Lum B (trial no. NCT02603679) and PASIPHAE (trial no. NCT03322215) clinical trials.

Samples include biopsies before and after neoadjuvant therapy as well as surgical biopsies, which will allow investigating how SCNAs and SVs evolve under selective pressures during therapy.

Furthermore, you will work towards implementing CUTseq on circulating tumor DNA (ctDNA), assessing the sensitivity of the method for detecting SCNAs and SVs in ctDNA during patient follow-up.

In all these efforts, you will work alongside experts in breast cancer treatment, cancer genomics, and bioinformatics, and actively participate in the analysis of the sequencing data that will be generated.

Your profile

Do you have a strong affinity for translational medicine and a strong background in molecular biology and genomic techniques? Do you enjoy fast-paced collaborative science and working with people from different cultures and backgrounds? Are you genuinely interested in contributing to helping patients by conducting rigorous experiments and data analyses? Are you meticulous, attentive to detail and self-critical? Then you are the right person!

Prior experience with various NGS techniques (e.g., RNA-seq, whole-exome sequencing, targeted sequencing) and familiarity with the bioinformatics tools required to analyze their data, as demonstrated by leading authorship(s) on papers published in authoritative, peer-reviewed journals is a pre-requisite. Prior work in the field of cancer genomics is desirable but not indispensable.

The successful candidate must hold a master’s degree in medicine, biomedicine, biotechnology or equivalent and a PhD in the field of genomic technologies (incl. single-cell genomics) and/or cancer genomics.

Qualified to be employed as a postdoctor is one who has obtained a doctorate or has equivalent scientific competence. It is considered as an advantage if you have completed your doctoral degree within the last three years, if there are special reasons, your degree may have been completed earlier. Applicants who have not completed a doctorate at the end of the application period may also apply, provided that all requirements for a completed degree are met before the (intended) date of employment. This must be substantiated by the applicant's main supervisor, director or equivalent.

What do we offer?

Karolinska Institutet is one of the world's leading medical universities. Our vision is to pursue the development of knowledge about life and to promote better health for all. At Karolinska Institutet, we conduct innovative medical research and provide the largest range of biomedical education in Sweden. Karolinska Institutet is a state university, which entitles employees to several benefits such as extended holiday and a generous occupational pension. Employees also have free access to our modern gym and receive reimbursements for medical care.

Application

An employment application must contain the following documents in English or Swedish:

A complete curriculum vitae, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
A complete list of publications
A summary of current work (no more than one page)
Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances
Verification from the thesis defence committee or the equivalent (only if the thesis defence is scheduled within three months after the application deadline)

Welcome to apply at the latest March 15th.

The application is to be submitted through the Varbi recruitment system.

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