10/10/2019

PhD Student (in Cancer Genetics)

This job offer has expired


  • ORGANISATION/COMPANY
    Medical Univeristy of Gdańsk
  • RESEARCH FIELD
    Biological sciencesBiology
    Medical sciences
  • RESEARCHER PROFILE
    Established Researcher (R3)
  • APPLICATION DEADLINE
    12/01/2020 23:00 - Europe/Brussels
  • LOCATION
    Poland › Gdańsk
  • TYPE OF CONTRACT
    Temporary
  • JOB STATUS
    Full-time
  • HOURS PER WEEK
    40
  • OFFER STARTING DATE
    01/03/2020
  • EU RESEARCH FRAMEWORK PROGRAMME
    H2020
  • REFERENCE NUMBER
    PhD/MAB/1/2019

We are now seeking two graduate students (one for each research group) to conduct research program in the area of human genetics. The prospective candidates will receive support and mentoring from senior colleagues in the fields of genetics, cell and molecular biology. We will also provide access to state-of-the-art equipment and computing resources.

Research group:

1. Loss of chromosome Y and human disease (PI: Prof. Jan Dumanski)

2. Mosaicism for autosomal post-zygotic mutations (PI: Arkadiusz Piotrowski, Ph.D., assoc. prof.)

Project title/Context:

Mutations acquired during lifetime that lead to increased risk for human disease, with focus on cancer

The centre is funded within the International Research Agendas Programme of the Foundation for Polish Science. The 3P-Medicine Lab (Preventive, Personalized, Precision) International Research Agenda is joint unit of Medical University of Gdansk in Poland and Uppsala University in Sweden.

More about the center:

https://ira3p.mug.edu.pl/

https://www.fnp.org.pl/en/3p-medicine-preventive-personalized-precision/

More about participating universities:

https://www.uu.se/en

https://mug.edu.pl/

Project description:

The 3P-Medicine Laboratory (personalized, preventive, precision) is a new science center specializing in research on acquired genetic mutations as risk factors for cancer and other diseases. Our center is focused on somatic mutations that occur early in life in seemingly normal cells that eventually contribute to malignant transformation. Primary interest is in common malignancies that are etiologically related to environmental stimuli: breast cancer, colorectal cancer, urinary bladder cancer and prostate cancer. Our unique collection of clinical samples includes not only primary and metastatic tumors, but also multiple biopsies of macroscopically normal tissue including frozen sections, peripheral blood, viable skin and stromal fibroblasts as well as cryopreserved primary cell cultures. A part of the centre is working on Loss Of chromosome Y (LOY) in men, mainly in connection with cancer and Alzheimer’s disease (AD).

More about research group:

Loss of chromosome Y and human disease

The group is devoted to the research on association between LOY in peripheral blood and higher risk of cancer and AD in aging men. Our ultimate goal is to develop LOY-based screening approach for the assessment of non-hereditary cancer and neurodegeneration risk, years before first clinical symptoms become apparent. We are aiming to unravel the functional mechanisms of LOY in the process of disease development. We will analyze selected populations of peripheral blood leukocytes, tumor infiltrating and brain immune cells as well as cell culture models. We will use state-of-the-art methodology including cell sorting, high dimensional flow cytometry, laser microdissection, genotyping microarrays, massively parallel sequencing of DNA, bulk RNA- and single cell RNA-seq, spatial transcriptomics. The resulting wet-lab data will be subjected to advanced bioinformatic and biostatistical analysis.

Mosaicism for autosomal post-zygotic mutations

Our primary interest is in common malignancies that are etiologically related to environmental stimuli: breast cancer, colorectal cancer, urinary bladder cancer and prostate cancer. Over the past 15 years we have established a vast collection of clinical samples and long term follow-up data in collaboration with the major oncological centers in Poland. Currently, we continue collecting prospective cases with aim of >85K samples by the end of 2023. This unique cohort includes peripheral blood, primary and metastatic tumors, viable skin and stromal fibroblasts, multiple biopsies of normal tissue including frozen sections as well as cryopreserved primary cell cultures.

In order to achieve the main goal of the program we genotype samples for somatic point mutations, copy number alterations, as well as copy number neutral genomic structural rearrangements. The genomics is further combined with bulk and single cell expression analysis as well as biochemical and functional tests on patient-derived primary cell cultures. For this we utilize genotyping microarrays, targeted/whole-exome/whole-genome massively parallel resequencing of DNA, nanopore based long read sequencing or linked-reads DNA sequencing, laser microdissection combined with padlock probes for analysis of spatial mutation distribution in tissues, bulk RNA- and miRNA-seq, single cell RNA-seq as well as spatial transcriptomics. The resulting wet-lab data along with clinical characteristics and follow-up is subjected to downstream analysis by the bioinformatics team.

 

Key responsibilities include:

Our program is highly collaborative and so will require extensive interactions with clinical partners, biobanking and bioinformatics teams. Also, short term visits to foreign partner (Uppsala University) are inherent part of the program.

Group: Loss of chromosome Y and human disease

1. Sorting of selected populations of leukocytes.

2. Performing downstream experiments on sorted cells (involving genotyping microarrays, ddPCR, laser microdissection, massively parallel sequencing techniques in genetic and transcriptomic context and single cell analysis).

3. Participation in high throughput data analysis.

4. Interactions with clinical partners, biobanking and bioinformatics teams.

Group: Mosaicism for autosomal post-zygotic mutations:

The Ph.D. candidate will have the opportunity to gain and broaden expertise in the aspects of human genetics related to somatic origin of cancer with emphasis on single cell genomics and transcriptomics.

The Ph.D. student will be responsible for establishing and maintaining primary cell cultures and tissue specimens from clinical samples, performing downstream experiments in vitro on cell cultures and in situ on tissue samples.

The experiments will involve heavy utilization of massively parallel sequencing techniques in genetic and transcriptomic context, including methods for single cell analysis.

Participation in high throughput data analysis will be also required.

 

Benefits

We offer:

1. Opportunity to gain and broaden expertise in the aspects of human genetics related to somatic origin of cancer with emphasis on single cell genomics and transcriptomics.

2. Mentoring and support from senior colleagues in the fields of genetics, cell and molecular biology, bioinformatics and biostatistics.

3. Opportunity for motivated PhD students to work in an international multidisciplinary training environment.

4. International collaboration opportunities including short term visits to foreign partner (Uppsala University).

5. Access to state-of-the-art equipment and computing resources.

Selection process

1. CV;

2. Motivation letter;

3. References to at least two mentors with phone and email adress.

Please submit all above documents in a single pdf file.

Due to the entry into force of Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016, we also require that your job advertisements include a clause requesting the candidate’s consent to the processing of his or her personal data by the institution which carries out the recruitment process: “I agree to the processing of personal data provided in this document for realizing the recruitment process pursuant to the Personal Data Protection Act of 10 May 2018 (Journal of Laws 2018, item 1000) and in agreement with Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (General Data Protection Regulation)”.

Additional comments

Stipend (non-taxable income), net 3500 PLN per month (1 EUR = 4.3 PLN, 1 USD = 3.9 PLN) corresponding with average net salary rate in Poland, health and social insurance

Offer Requirements

  • REQUIRED EDUCATION LEVEL
    Biological sciences: Master Degree or equivalent
  • REQUIRED LANGUAGES
    ENGLISH: Excellent

Skills/Qualifications

1. B.Sc. or M.Sc. in biology, biotechnology, molecular biology or equivalent.

2. Background in cancer research, cell culture, massively parallel sequencing techniques, bioinformatics or biostatistics is desired, although not absolutely required.

3. Prior participation in foreign scholarships or trainings and scientific achievements is welcome.

4. Interest in writing research manuscripts is highly encouraged.

5. Good knowledge of written and spoken English.

6. Strong motivation for research work, flexibility and self-driven interest to learn new techniques.

7. Good communication and work organization skills.

8. Ability to work in a team.

Work location(s)
2 position(s) available at
Medical Univeristy of Gdańsk
Poland
Gdańsk
80-211
Dębinki 7

EURAXESS offer ID: 453447

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