Instand-NGS4P is a 60-month PCP project federating 7 leading medical centers (two are coordinating ERNs) as buyers’ group with major experience in using different NGS platforms in research and routine diagnostics. The consortium is further strengthened by European patient advocacy groups, a standardization organization and partners participating in the European infrastructures BBMRI-ERIC, ELIXIR as well as several NGS-related EU programs to cover all technical aspects and transversal needs & requirements. Driven by patient and clinical needs, innovative NGS workflows from sample-pre-analytics to medical decision making will be developed. The modular design of the workflow will particularly enable SEMs to contribute, and provides flexibility to adopt emerging user needs and technologies. Specifications will address regulatory requirements for IVDs and refer to international standards and requests development of reference materials and implementation of EQA schemes covering the whole workflow. R&D suppliers will be selected based on a public tender all along this PCP process in 3 phases according to the best-value for money solution. The 3 phases foresee the leverage of 4 technical modules (pre-analytics, sequencing, bioinformatics, e-reporting/e-medication) and their standardized interfaces – from design (Phase 1) to prototypes (Phase 2), and full integration in Phase 3. At the end, this PCP will provide 2 fully integrated, standardized NGS workflows for routine diagnostics of common and rare cancers from adults to children. In order to enable broad implementation in healthcare systems throughout Europe and beyond and to increase benefit to patients a series of support activities are planned including communication and dissemination activities targeting a broad stakeholder community, development of training and education material for healthcare professionals and patients, health economic assessment and engagement with healthcare payers and policy makers.

Functional non-coding regions of the genome play a fundamental role in gene expression and are enriched for disease associated variants. Perturbation of non-coding regions harbouring disease-associated variants is now the rationale of ongoing clinical trials (e.g. NCT03432364), highlighting the translational potential of basic research in the non-coding space. However, our ability to systematically identify disease-associated functional elements in the non-coding genome, understand its grammar, and subsequently develop new therapies is limited. CRISPR-based pooled screens targeting non-coding elements in situ have been successful in uncovering complex gene regulatory architecture in a variety of biological systems. However, these approaches are limited to a few loci, lack of direct genotype-phenotype correlation, and do not target large chromatin structures that determine gene expression programs. To overcome these limitations, I propose a multi-scale approach platform that is generalizable to different cell types and phenotypes. Under this proposal, I will focus on the role of non-coding sequences in the context of blood malignancies. I will investigate non-coding sequences whose change in chromatin state (activation or repression) is associated with drug resistance in Chronic Myelogenous Leukemia (CML). I will study alterations in the chromatin structure (i.e. at chromatin loops or topologically associated domains) that are causal to imatinib resistance in CML. Finally, to learn enhancer grammar and mechanistically link non-coding variants to disease, I will focus on non-coding sequence variation in leukemia and dissect non-coding sequences at base pair resolution using dense mutagenesis coupled with long-reads sequencing. A deeper understanding of the non-coding regulatory architecture in diseases will provide the basis for development of innovative therapies targeting the non-coding genome.

Almost 500,000 former childhood cancer patients (CCS) are now living in Europe. Compared to the general population, CCS represent a vulnerable population as they are at an increased risk of developing health problems, known as late effects, resulting in excess morbidity and mortality. Many survivors are unaware of their personal risk for specific late effects, which reduces their ability to manage their own follow-up care. Similarly, their treating healthcare professionals (HCPs) lack information about care required for CCS and access to treatment data from their childhood cancer. The Survivorship Passport (SurPass) is an innovative, digital tool, developed in previous EU-funded projects, that can be used to overcome these knowledge gaps to improve people-centred long-term survivorship care. Importantly, end users (CCS, HCPs) are integral to the research, represented by three key stakeholder networks (PanCare, SIOP Europe, CCI Europe). PanCareSurPass will conduct a robust assessment of the implementation of the SurPass by first conducting a pre-implementation study in six countries (Austria, Belgium, Germany, Italy, Lithuania, Spain) representing three infrastructural scenarios in Europe. Ethical, structural, organisational, economical, national, local, privacy issues, health systems, and particular national circumstances will be taken into account throughout. An Implementation Strategy will be developed and the SurPass will be updated and validated before use in an implementation study in the six countries. The study will look at a range of outcomes including CCS activation and empowerment, CCS/HCP satisfaction with the tool, feasibility and health economics. Based on the results of the study, a Prediction Model will be developed to promote and support future implementation of the SurPass across Europe.

The central challenge for the immune system is to efficiently recognize and neutralize foreign antigen while protecting self. If the latter fails, autoimmunity and/or autoinflammation may occur, as observed in many human diseases. Though several human genes involved in the process have been identified we still lack: i) a comprehensive appreciation of all contributing molecular pathways, ii) an understanding of the interplay and epistatic relationships among the various elements and iii) a satisfactory strategy to counteract dysregulation based on an understanding of the regulatory logic. I hypothesize that there is only a finite number of pathways involved and that it should be possible to mount a synergistic strategy to create a first chart of the entire “territory”. Key to this endeavor is the identification of sufficient elements by mapping immune dysregulation genes to “anchor” the chart onto signposts of which the human pathophysiological relevance is certain. From these signposts, contextualization and integration is achieved by interaction proteomics and network informatics mining the existing data universe, validated through biochemical and imaging tools to power an established set of immune assays. While it may be preposterous to claim feasibility with one ERC grant, I propose that once such a chart exists, even at initial low resolution, it can help reconcile disconnected observations and coalesce future work while being immensely improved in accuracy and mechanistic understanding by the entire community. iDysChart will work towards these goals by 1) identifying novel monogenic causes of autoimmune/autoinflammatory diseases, enabling elucidation of fundamental mechanisms, 2) creating a network-level understanding of molecular pathways of immune dysregulation and 3) employing chemical and genetic screens to complement human disease gene discovery in predicting the core human immune dysregulome and investigating potential avenues for therapeutic modulation.

Vilnius University Hospital Santaros Klinikos (VULSK) acts as a coordinator of the TREL (Twinning in Research and Education to improve survival in Childhood Solid Tumours in Lithuania) project that aims to enhance translational, clinical and late-effect research in paediatric solid tumours (ST). The project concept is based on the existing shortcomings in paediatric oncology at VULSK and Lithuania – scarce research indicators and inferior survival rates in children with ST. TREL has a goal to increase scientific excellence in the most common paediatric ST (brain tumours, neuroblastoma and renal tumours). VULSK and 8 leading research intensive institutions each covering different areas of the project activities according to their expertise form the TREL consortium. TREL will be delivered in 7 working packages addressing training in tumour specific laboratory research and clinical trials, cross-cutting education on genome-wide sequencing and treatment innovations, enhancing skills in observational studies on the quality of survivorship including fertility preservation and research methodology as well as project and innovation management. Training exercise will focus on the implementation of secondments of VULSK staff to the partner premises, organisation of multidisciplinary transfer-of-knowledge meetings, and participation in strategic scientific meetings corresponging objectives of each working package. As a consequence of the twinning activities with internationally-leading research active counterparts VULSK will improve its research profile and reputation, enhance international, regional and national visibility and competitiveness. Fostering of existing and establishment of new networking channels will facilitate incorporation of VULSK professionals to the ongoing collaborative projects that will improve research indicators of individual researchers and VULSK as well as will increase survival rate of children with ST in Lithuania in a long-term perspective.