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- Access to high-throughput genomic technologies: We have outstanding experience with high-throughput (single-cell) (epi)genomic and transcriptomic profiling. State-of-the-art genomic studies are typically driven by the rapid development of novel and expensive technologies. In our laboratory, we have direct access to and extensive experience in handling various sequencing technologies, including an Illumina iSCAN, MiSeq, NextSeq, HiSeq2500, HiSeq4000 and NovaSeq6000. This allows us to rapidly perform whole-genome sequencing (WGS), targeted (re-)sequencing (e.g., exome sequencing), (targeted) bisulphite sequencing [5(h)mC-Seq], as well as RNA sequencing. These techniques can be applied on fresh frozen (tumor) tissue, FFPE-based (tumor) tissue and liquid biopsies. Moreover, via a single-cell accelerator initiative at VIB (https://techwatch.vib.be/?page_id=528), our lab has early access to the newest single-cell multi-omics technologies (scRNA-seq, ATAC-seq, DNA-seq, CITE-seq, CROP-seq and spatial profiling). We manage the access to the 10X Genomics technology and Illumina NovaSeq system for all the single-cell RNA sequencing experiments at UZ Leuven and KU Leuven via our VIB – KU Leuven Single Cell Core Facility (https://cbd.vib.be/research/expertise-units/single-cell-core/).
- Cutting edge genomic data analysis through advanced bio-informatics and data integration approaches: The required experience to cluster the omics-type of data into molecular subtypes and develop specific classifier to be used in a clinical context is available within our lab. We have significantly invested in attracting computational biologists to analyze and integrate large genomic datasets. Currently, there are 5 experienced postdocs, > 10 PhD students (including MDs), 3 omics data analysts as well as a staff scientist in our group focusing on the analysis of several large-scale genomic data sets. To perform these large computational analyses, our lab has a state-of-the-art computing infrastructure in-house (updated beginning 2019 to over 340 processors and 66 TB storage), and for high-performance computing we have access to the Flemish Supercomputer Center (Vlaams Supercomputer Centrum, VSC).
- Numerous collaborative projects at the national and international level:
- We have longstanding ongoing collaborations with most oncologists at UZ Leuven, which are often internationally highly recognized leaders in the field, such as E Van Cutsem (gastro-intestinal cancer), I Vergote and D Timmerman (gynaecological cancer), P Schöffski (solid tumors and lymphomas), J Van steenkiste (lung cancer), S Jacobs (paediatric cancer), M Garmyn (melanoma) etc. These collaborations are of tremendous value for my group, as they guarantee access to a large number of clinically well-characterized patient samples for our genomic studies, positioning ourself at the center of translational cancer research in Leuven.
- Diether Lambrechts is a board member of the directors of the Genomics Core Facility from UZ Leuven – KU Leuven, a founding member of the Single Cell Omics Institute (SCOI) from KU Leuven and a board member of the steering committee of the Single Cell Core Facility from the VIB-KU Leuven Center for Cancer Biology (in collaboration with the Genomics Core Leuven).
- Our publication about single-cell analysis in Lung Cancer (Nature Medicine, 2018) spurred interest with Chinese collaborators (Fudan and Zhejiang University, both top 5 Chinese universities), with whom we have now set-up 3 China-based laboratories that mirror our single-cell analysis set-up in Leuven, with the ambition to embark on joint projects using the same experimental infrastructure. Diether Lambrechts is Scientific Director of the Sino-Belgian Lab for Single-Cell Analysis Technologies.
- We have ongoing collaborations with many other institutions for our expertise in next generation sequencing and cancer genomics, e.g. J De Greve (UZ Brussels); C Sotiriou (Jules Bordet Institute, Brussels); C Blanpain (ULB, Brussels); P Fasching (University Hospital Erlangen, Germany); Jeremy Cheadle (Cardiff University, UK); Darran O’Connor, Jochen Prehn and Annette Byrne (University College Dublin, Ireland); Vessela Kristensen (University of Oslo, Norway); VHIO, Spain); INSERM, France; Louis Chesler (The Institute of Cancer Research in London, UK); the EORTC; Comprehensive Cancer Center Zurich, the University Hospital of Zurich, Switzerland; Fudan University in Shanghai, the School of Medicine, Zheijiang University in Hangzhou, China etc.
- We are an active contributor to international genetic consortia (BCAC, OCAC, E2C2) and currently partner (work package leader) of different European collaboration projects:
- 2015-2020: EU H2020-PHC-2014-2015 – Breast cancer stratification: understanding the determinants of risk and prognosis of molecular subtypes (B_CAST) (51k€; promoter)
- 2017-2021: EU H2020-MSCA-ITN-2017 – Exploiting GLIOblastoma intractability to address European research TRAINing needs in translational brain tumour research, cancer systems medicine and integrative multi-omics (GLIOTRAIN) (207k€; promoter)
- 2018-2022: EU H2020-SC1-2016-2017 - Advancing a Precision Medicine Paradigm in metastatic Colorectal Cancer: Systems based patient stratification solutions (COLOSSUS) – (481k€; co- promoter)
- 2019-2024: EU H2020-SC1-BHC-2018-2020 - Resistance under combinatorial treatment in ER+ and ER- breast cancer (RESCUER) – project is accepted, but not active (co-promoter)
- 2019-2022: ERACoSysMed - Resistance under combinatorial treatment in ER+ and ER- breast cancer (RESCUER) – project is accepted, but not active (co-promoter)
- Excellent contacts and collaborations with the Flemish Biotech scene and international key pharmaceutical companies: We are very keen on collaborating with the pharmaceutical and biotechnical companies (Hoffman-La-Roche, Sanofi-Aventis, Bayer AG, Eisai, Eli-Lilly, Novartis Oncology, Boehringer Mannheim, Merck Serono, Brystol Myers Squibb, Agilent, Biocartis, J&J etc.). We were able to file 5 patent applications (as co-inventor and co-owner) with them. Following an intense collaboration with Biocartis, a 7-marker assay fully compatible with the Idylla platform was launched in 2018 to detect microsatellite instability (MSI). Idylla™ MSI is nowadays the only MSI test that already received CE-IVD clearance, and it is distributed on a world-wide scale (sub-licenced to Wondfo in China and Nichirei Biosciences in Japan). In 2018, the FDA approved checkpoint immunotherapy as the first cancer treatment for any solid tumor with a specific genetic feature (MSI). Currently, Idylla™ MSI is used in 2 registration studies from Bristol-Myers-Squib to seek FDA registration of the test as a companion diagnostic.
In 2016, we started a VLAIO project with Multiplicom NV (now Agilent Technologies). As a result of our efforts in this project, a new sequencing kit encompassing 19 genes involved in homologous recombination deficiency (HRD) has been commercialized (launch: early 2020). Additionally, an HRD scarring assay to detect HRD-driven genomic instability has been optimized and will be launched. HRD status is guiding the treatment of ovarian and triple-negative breast cancer with PARP inhibitors. These success stories illustrate how we combine top-level research while keeping a strong focus on the clinical impact and technology transfer potential of our research.