Job title: Laboratory Research Scientist – Sequencing & Cancer Dynamics
Location: The Francis Crick Institute, Midland Road, London
Contract: Fixed-term (3 years), Full time
Closing date: 24th May 2021 23:59
The research group and role
This is a post within the Advanced Sequencing Facility (ASF), based at the Francis Crick Institute, London. The ASF is a core-funded laboratory which provides Next Generation Sequencing (NGS) services to the one hundred or so research groups that work there. Based in the heart of London and hosting the latest cutting-edge sequencing platforms, the team carries out all aspects of NGS from project design through to delivery of the sequence data for analysis. Next generation sequencing has revolutionised our approach to biology making this a key technology for a large proportion of the pioneering research groups based at the Crick. The post holder will work specifically with the Cancer Dynamics Research Laboratory, led by Dr Samra Turajlic, and provide sequencing support for a range of translational studies, including Renal and Melanoma TRACERx (Tracking Cancer Evolution through therapy (Rx)), PEACE and HOLST-F (http://tracerx.co.uk/; https://clinicaltrials.gov/ct2/show/NCT03004755; https://clinicaltrials.gov/ct2/show/NCT03832062).
The position will involve sample processing, quality control, library preparation, and targeted next generation sequencing using Illumina NextSeq and NovaSeq platforms in the ASF laboratory. The post holder will be supervised by a Senior Laboratory Research Scientist, but will be expected to work with some degree of independence and to troubleshoot and use their own initiative to overcome problems that may occur. The successful applicant will be integrated closely with the Cancer Dynamics research team, partaking in regular lab meetings, journal club, and internal and external collaborator meetings. There will be a close interaction with the research team at the Renal and Skin Unit at the Royal Marsden NHS Foundation Trust. There will be ample opportunities for training both at the Francis Crick Institute and more widely, including training workshops and conferences, nationally and internationally.
We are looking for an enthusiastic and highly motivated early career scientist eager to hone their molecular biology techniques, develop NGS skills, and work as an integral part of a busy and experienced team of scientists. The post holder will have the opportunity to contribute to the development and implementation of novel genomics applications in cutting-edge research areas such as single cell biology to enhance our understanding of human biology and disease.
The post holder will also play a role in supporting the team’s research projects further by preparing samples for testing from biological material, for example, preparation of serum, plasma and PBMCs from whole blood, and DNA/RNA extraction from tissue or FFPE (formalin-fixed paraffin-embedded) material. This will include the CAPTURE Study (COVID-19 antiviral response in a pan-tumour immune study); a prospective observational cohort study, established in response to the COVID-19 pandemic, with the aim of understanding the effects of the SARS-CoV-2 pandemic in patients with cancer and in healthcare workers who may be exposed to the virus in the course of their work.
The post holder will also be expected to take an active role in supporting senior staff in setting up and maintaining quality control procedures, including good laboratory practice, document management and sample storage and tracking.
The successful applicant will work within the ASF to support specifically the Cancer Dynamics Lab and the translational studies within this group, including Renal and Melanoma TRACERx projects, from receiving samples, through quality control checking, library preparation and sequencing. This is a unique opportunity to work at the interface of a science platform and a specific research programme which is aimed at improving our understanding of cancer and ultimately translating these findings for patient benefit.
The incidence of renal cell carcinoma (RCC) has more than doubled in the UK since the late 1970s. Half of all patients will have advanced disease, which is associated with a five-year survival of only 5%. An improved understanding of the factors that drive metastatic disease and treatment resistance is fundamental for improving these outcomes. We have previously revealed extensive intra-tumour heterogeneity present within RCC demonstrating that genetically distinct, physically and temporally separated subclones evolving in a branched pattern contribute to the make-up of the tumour as a whole. The use of NGS was instrumental to generating these insights. This type of heterogeneity appears to play a central role in tumour evolution, progression and treatment resistance and is also a significant hurdle for precision medicine, not least through the effect of tumour sampling bias on prognostic and predictive markers development.
The principal objectives of TRACERx Renal are to use Next Generation Sequencing methodologies to define drivers and intratumour heterogeneity in RCC and determine the relationship between heterogeneity and disease stage, clinical outcome and treatment response. Additional objectives include the identification of drivers of metastatic progression and drug response, or resistance and establishing the utility of cell-free tumour DNA in patients’ blood and urine as a predictive biomarker in RCC. Experience and methods gained from this sequencing work are being used to develop experimental approaches for the Melanoma TRACERx project, PEACE and HOLST-F studies.
The successful candidate will join the diverse TRACERx team of surgeons, clinicians, pathologists, scientists and bioinformaticians working together to address these challenges (for further information see www.tracerx.co.uk).
These include but are not limited to the following:
- The primary responsibility will be to provide support for next generation sequencing on the translational studies, chiefly TRACERx projects
- Operation and maintenance of Illumina sequencing platforms
- Operation of liquid handling robotic platforms
- Be willing to learn how to use laboratory computers and associated software applications
- Liaising with equipment providers for standard problems and issues
- General maintenance of laboratory areas and equipment and monitoring stock levels
- Training in additional sample processing methods, such as DNA/RNA extraction techniques, as required
- Preparing DNA and RNA libraries for sequencing
- Assisting the team to investigate, assess and set up appropriate methodologies to enhance translational research
- Keeping accurate laboratory records both on paper and electronically
- Collaborating in the preparation of scientific reports, journal articles, presentations and posters, and occasionally presenting papers and posters
- Participating in developing methods and refining experimental strategies in collaboration with ASF staff, scientists and Cancer Dynamics Lab
- Keeping up to date with subject related and professional issues, in particular, developments in the specific subject area
- In addition, the post holder will be expected to carry out any other duties and responsibilities within the scope, spirit and purpose of the post and its grading as requested by the line managers. These will include sharing in departmental duties and possibly out of hours working.
Note: This job description reflects the present requirements of the post. As duties and responsibilities change and develop the job description will be reviewed and be subject to amendment in consultation with the post holder.
Key experience and competencies
The post holder should embody and demonstrate our core Crick values: bold, imaginative, open, dynamic and collegial, in addition to the following:
Qualifications, experience and competencies:
- Degree in biological sciences or equivalent
- A strong understanding of molecular biology, including next generation sequencing, library preparation and quality control
- Proven practical experience in molecular biology, genetics or genomics
- Excellent attention to detail
- Excellent time management and laboratory record keeping
- Strong written and oral communications skills with the ability to communicate complex information to others
- Very good experience with Microsoft Excel and competency in other standard Office packages
- Organisational and problem-solving skills
- Flexible and cooperative approach to working with others
- Proactive, showing initiative and independent thought
- The nature of running the sequencing equipment requires occasional out of hours working. The role holder will therefore need to show willingness to work flexibly when necessary
Qualifications, experience and competencies:
- Experience working in a genomics/sequencing lab in an academic, clinical or industrial setting
- Next Generation Sequencing experience using the Illumina and/or Life Technologies sequencing platforms
- Experience in library preparation from DNA and RNA
- Experience in sample preparation methods such as DNA/RNA extraction, serum, plasma and PBMC isolation
- Experience with laboratory automation and high throughput methods
- An understanding or knowledge of bioinformatics approaches to sequence analysis, data mining and the use of genomic database resources
- Experience of routinely using a Laboratory Information Management System (LIMS)