The Cancer Genomics working group of the Alleanza contro il Cancro national network is seeking 2 motivated bioinformaticians for positions based at the European Institute of Oncology (IEO) in Milan
Alleanza Contro il Cancro (ACC) is the largest oncology network in Italy, with 22 participating institutions devoted to oncological research producing more than 5000 publications/year with a normalized impact factor of > 20k, with > 4000 researchers and thousands of active clinical trials. Activity within ACC is conducted under the framework of 6 pathology-oriented working groups (WG breast, glioblastoma, colon, melanoma, lung and sarcoma tumors) and 2 cross-disciplinary WG (genomics and immuno-oncology). Specifically, the aim of the ACC genomics WG is to foster the integration of high throughput next generation sequencing in clinical diagnostic workflow, with a particular focus on identifying inovative methodologies that maximize clinically relevant information and provide genomics data interpretation. ACC genomics recently launched multiple projects in which large DNA/RNA sequencing panels are applied to prospectively recruited cancer patients, in collaboration with the 6 pathology-oriented WGs. The first pilot project, currently up and running, aims at sequencing germline and somatic genomes from 1000 prospectively recruited non-small cell lung cancer patients, with several ancillary projects (liquid biopsy, immuno-oncology biomarkers, and others). Additional projects have been designed and are due to open in 2018. The current sequencing platform is aimed at characterizing single nucleotide variants and structural alterations using medium-sized (0.8-3 Mb) targeted sequencing, but ongoing projects are aimed at developing methodologies to detect additional parameters (mutational burden, mismatch repair defects, mutational signatures) and at testing new sequencing methodologies (long-read sequencing, HLA typing, TCR clonality, RNAseq from FFPE clinical specimens, etc)
A dedicated bioinformatic infrastructure has been built in collaboration with Elixir/CINECA, and a network of bioinformaticians within participating institutions has been formed (ACC bioinformatics). The group periodically meets and works in collaboration to develop dedicated analytical pipelines for the project.
ACC genomics is seeking 2 motivated bioinformaticians to coordinate the bioinformatics efforts within the multiple projects. A junior (1-4 years post- PhD) and a senior (>4 years post-PhD) profile are seeked. The candidate will be based at the IEO in Milan, where he/she will also interact with one of the largest computational biology communities in Italy This is an excellent opportunity to conduct cutting-edge bioinformatics in the clinical field and to pioneer the emerging field of clinical bioinformatics.
- Perform routine analyses of clinical samples with next-generation sequencing (NGS);
- Participate in designing, implementing, validating and maintaining bioinformatics pipelines;
- Contribute to bioinformatics process optimization and standardization;
- Participate to the development of scientific databases and their application in a growing clinical genomics environment;
- Implement, update and maintain locally stored data resources required for various analysis tasks;
- Writing bioinformatics protocols and documentation;
- for the senior figure: coordination of the activities of the ACC bioinformatics group
- BSc. or MSc. in Bioinformatics-related subject (biology, bioinformatics, mathematics, statistics, physics, etc.);
- Programming skills (Python, R, preferable);
- Experience with NGS data analysis;
- Proficiency with Unix/Linux operating system;
- Good English level;
- Attention to details;
- Ability to multitask, work and learn independently, and be self-motivated;
- Ability to work in team and desire to collaborate with other bioinformaticians in the group is essential;
- A strong work ethic and commitment to timely delivery of results.
- Ph.D. in Bioinformatics or equal experience;
- Experience with genomics data analysis;
- Prior experience working with large-scale datasets using high performance computing environments is desirable.
- Experience with Cancer genomics and bioinformatics related resources (TCGA, ICGC, COSMIC, etc.)
- Experience with database construction and maintenance
If interested, please send your cv and contact details for two referees to email@example.com, firstname.lastname@example.org and email@example.com
Deadline for application is 31st january 2018