The Vall d´Hebron Institute of Oncology (VHIO) Seeks a “Post-doctoral Scientist (Cancer Genomics Lab)”
Reference: Ref. 76-2023
Application deadline: until position filled
Number of vacancies: 1
Job description:
The Cancer Genomics Lab and the Breast Cancer Group, under the leadership of Dr. Ana Vivancos and Dr Cristina Saura, invites you to be a part of our mission to unravel the molecular intricacies behind presence of ctDNA in breast milk and its application as a biomarker.
In recent years, liquid biopsy has emerged as a transformative alternative to traditional tissue biopsy analysis. Liquid biopsy provides a minimally invasive, real-time assessment of tumor heterogeneity and treatment response. It becomes especially relevant when traditional biopsies fall short. Our lab is at the forefront of using circulating tumor DNA (ctDNA) due to its exceptional diagnostic and prognostic potential (4).
Our foremost objective is to enhance the sensitivity of ctDNA detection methods, with Next-Generation Sequencing (NGS) at the forefront of our endeavors. We firmly believe that augmenting ctDNA resources can significantly enhance sensitivity and broaden its applicability. In a milestone achievement in September 2023, our lab published an article that demonstrated the feasibility of isolating ctDNA from breast milk. This breakthrough opens doors to the early detection of pregnancy-associated breast cancer, where ctDNA emerges as a promising ally (11).
Our groundbreaking study reported, for the first time, the presence of cell-free tumor DNA (ctDNA) in breast milk (BM) collected from patients with breast cancer. Through droplet digital PCR, we detected tumor variants in an astonishing 87% of BM cases, while only 8% of matched plasma samples yielded results. Retrospective next-generation sequencing analysis of BM ctDNA recapitulated tumor variants, with an impressive clinical sensitivity of 71.4% and a remarkable specificity of 100%. In two cases, ctDNA was detectable in BM collected 18 and 6 months before standard diagnosis. This discovery opens up the potential use of BM as a novel source for liquid biopsy for pregnancy-associated breast cancer (PPBC) detection (11).
This post-doctoral position is a great opportunity to enter the biomarker filed in cancer genomics. Your work will not only contribute to the understanding of ctDNA as a biomarker but also have the potential to redefine cancer diagnostics and treatment. We are particularly excited about the possibilities that studying ctDNA in breast milk opens for early breast cancer detection, making a real impact on women’s health.
If you are passionate about cancer genomics, eager to explore the mysteries of ctDNA, and dedicated to pushing the boundaries of scientific knowledge, we invite you to be a part of our team. Together, we can pioneer the future of cancer diagnostics and treatment.
References
(1) Kustanovich, A., Schwartz, R., Peretz, T. & Grinshpun, A. Life and death of circulating cell-free DNA. Cancer Biol. Ther. 20, (2019).
(2) Paweletz, C. P., Lau, C. J. & Oxnard, G. R. Does Testing Error Underlie Liquid Biopsy Discordance? https://doi.org/10.1200/PO.18.00408 1–3 (2019). doi:10.1200/PO.18.00408
(3) Vivancos A, Tabernero J. Circulating tumor DNA as a novel prognosti indicator. Nat Med. 2022 Nov;28(11):2255-2256. doi: 10.1038/s41591-022-02068-8. PMID: 36357679.
(4) Alix-Panabières C, Pantel K. Liquid Biopsy: From Discovery to Clinical Application. Cancer Discov. 2021 Apr;11(4):858-873. doi: 10.1158/2159-8290.CD-20-1311. PMID: 33811121.
(5) Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, Pacey S, Baird R, Rosenfeld N. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017 Apr;17(4):223-238. doi: 10.1038/nrc.2017.7. Epub 2017 Feb 24. PMID: 28233803.
(6) Grabuschnig S, Bronkhorst AJ, Holdenrieder S, Rosales Rodriguez I, Schliep KP, Schwendenwein D, Ungerer V, Sensen CW. Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms. Int J Mol Sci. 2020 Oct 29;21(21):8062. doi: 10.3390/ijms21218062. PMID: 33137955; PMCID: PMC7662960.
(7) Angeles AK, Janke F, Bauer S, Christopoulos P, Riediger AL, Sültmann H. Liquid Biopsies beyond Mutation Calling: Genomic and Epigenomic Features of Cell-Free DNA in Cancer. Cancers (Basel). 2021 Nov 10;13(22):5615. doi: 10.3390/cancers13225615. PMID: 34830770; PMCID: PMC8616179.
(8) Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, Thornton K, Agrawal N, Sokoll L, Szabo SA, Kinzler KW, Vogelstein B, Diaz LA Jr. Circulating mutant DNA to assess tumor dynamics. Nat Med. 2008 Sep;14(9):985-90. doi: 10.1038/nm.1789. Epub 2007 Jul 31. PMID: 18670422; PMCID: PMC2820391.
(9) Bettegowda, C. et al. Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies. Sci. Transl. Med. 6, 224ra24 (2014).
(10) Serrano, C. et al. Clinical value of next generation sequencing of plasma cell-free DNA in gastrointestinal stromal tumors. BMC Cancer 20, 1–12 (2020).
(11) Saura C, Ortiz C, Matito J, Arenas EJ, Suñol A, Martín Á, Córdoba O, Martínez-Sabadell A, García-Ruiz I, Miranda I, Morales-Comas C, Carrasco E, Viaplana C, Peg V, Nuciforo P, Bayó-Puxan N, Gonzalez-Medina A, Miquel JM, Gómez-Rey M, Villacampa G, Arévalo S, Espinosa-Bravo M, Balmaña J, Dienstmann R, Arribas J, Tabernero J, Vivancos A, Sansó M. Early-Stage Breast Cancer Detection in Breast Milk. Cancer Discov. 2023 Oct 5;13(10):2180-2191. doi: 10.1158/2159-8290.CD-22-1340. PMID: 37704212; PMCID: PMC10551665.
Requirements:
PhD in Computational Oncology, Bioinformatics, Biology, Biochemistry, Biomedicine, Bioengineering, Molecular Biology, or a related scientific area: Your advanced degree is essential for this role, as it forms the foundation for your expertise in computational oncology.
At least one paper as the first author: Your publication record showcases your ability to lead and contribute to scientific research.
Experience/knowledge in bioinformatics (R, Python) and cancer: Proficiency in bioinformatics tools and programming languages like R and Python, coupled with a strong understanding of cancer biology, will be instrumental in your work.
Proficiency in English: Effective communication in English is crucial, as it is the primary language used in our scientific discussions and collaborations.
Additional information:
Knowledge of statistical modeling or machine learning (a plus): Familiarity with statistical modeling or machine learning techniques will be considered an asset in this role.
Application:
To embark on this transformative journey with us, please submit your CV and a cover letter outlining your research interests and relevant experience via email: selecciorrhh@vhio.net, including the reference number.
We deeply appreciate your interest in the Cancer Genomics Lab and eagerly await your application. Please do not hesitate to reach out for any inquiries or further information.
Salary conditions will be set according to experience and profile.
About the Cancer Genomics Lab:
The Cancer Genomics Lab provides cutting-edge applications in cancer genomics through state-of-the-art technologies and, importantly, the development of novel, fully validated tests. Our novel genomic tests provide an important added value to our activity, enabling routine patient testing in the clinical research setting (Prescreening Program) as well as in translational research.
The Cancer Genomics Lab has developed and implemented several tests during the last 10 years that have been in use in the Prescreening Program routine. Tests for DNA profiling in tissue are NGS-based: an Amplicon-seq hotspot panel to sequence 67 genes (developed back in 2012) and a custom 435-gene hybrid capture panel (VHIO-300, developed in 2018), and an nCounter (Nanostring) panel for RNA gene fusion detection (with the capacity of detecting over 100 recurrent gene fusions) and perform gene expression profiling. As a reflection of our dedication to excellence and quality in the services we provide, both NGS-DNA based tests have been accredited according to the UNE-EN ISO 15189 quality system, that specifies requirements for quality and competence in medical laboratories. In recognition to our track, VHIO-300’s UNE-EN ISO 15189 accreditation was awarded in its flexible version, allowing us to include new analytes directly in the accredited test (following a standard operating procedure).
In 2021, we initiated the technical transfer of the Food and Drug Administration (FDA)-approved Guardant360® CDx liquid biopsy test for comprehensive genomic profiling. VHIO es the first cancer research center in Europe to have a laboratory equipped with this cutting-edge platform.
About VHIO:
Under the leadership of Josep Tabernero, the Vall d’Hebron Institute of Oncology (VHIO), has established itself as a comprehensive cancer center of proven excellence internationally. It is also thanks to VHIO’s optimal organizational structure based on a purely multidisciplinary and translational model that VHIO talents continue to anticipate and tackle the many unresolved questions in combatting this multifaceted and heterogeneous disease.
Located within the Vall d’Hebron Barcelona Hospital Campus, our researchers closely collaborate and interact with Vall d’Hebron physician-scientists. Translational science and clinical research are therefore tightly connected which promotes superb interaction and teamwork which, in turn, accelerates the bench-bedside-bed cycle of knowledge. This privileged environment affords VHIO direct access to patients as well as the entire spectrum of oncology professionals who care for them, and a second-to-none appreciation of how cancer science can translate into more powerful, targeted treatments and better practice for the care of patients.
VHIO’s pioneering model and programs, coupled with its belief in combining strengths through cross-border collaborations, continue to spur advances in reversing cancer resistance, halting metastatic spread, and more effectively treating even the most undruggable tumor types.
VHIO’s translation toward precision oncology: https://www.vhio.net
Vall d’Hebron Institute Oncology (VHIO) endorses the Requirements and Principles of the European Charter for Researchers, the Code of Conduct for the Recruitment of Researchers promoted by the European Commission and follows Equal Opportunities policies.
On 10th April 2018 VHIO was awarded the “HR Excellence in Research” logo. Our Institute was consequently granted permission to use the HR Excellence in Research Award logo as demonstration of its stimulating and favourable work environment in line with the Charter & Code.
