VHIO’s Cancer Genomics Group serves as a Core Technology laboratory. We are also dedicated to translational research as well as novel genomic test development.
Our group provides cutting-edge applications in cancer genomics through state-of-the-art technologies and the development of novel, fully validated tests that are used in the clinical research setting (Prescreening Program). Our lab is equipped with an n-Counter (Nanostring) platform, two digital PCR platforms (BEAMing Sysmex and ddPCR, BIO-RAD) and three NextGen Sequencers; MiSeq, NextSeq and HiSeq2500, Illumina. We are also starting to work with Minion Oxford Nanopore technology.
VHIO’s Prescreening Program, is nucleated around the activity of two VHIO groups – Cancer Genomics and Molecular Oncology, led by Paolo Nuciforo, in collaboration with VHIO’s Elena Garralda (PI of our Early Clinical Drug Development Group), and Rodrigo Dienstmann (PI, Oncology Data Science – ODysSey Group), together with Susana Aguilar and Jenifer Gonzalez. Our Advanced Molecular Diagnostics Program - DIAMAV, is supported by the FERO Foundation.
We perform molecular profiling in over 1100 patients each year as potential candidates for enrollment in our Phase I clinical trials led by VHIO’s Research Unit for Molecular Therapy of Cancer (UITM) – ”la Caixa”, directed by Elena Garralda.
Patients’ suitability for inclusion in any given clinical trial is assessed based on their respective genomic or pathologic profile. Our Group has developed and routinely implemented several tests for our Prescreening Program. Two are based on NGS: an Amplicon-seq approach to sequence 67 genes as well as a 450-gene capture panel (Illumina). We use nCounter (Nanostring) for our RNA-based gene fusion panel, with the capacity of detecting over 100 recurrent gene fusions (also enabling us to assess gene expression patterns in tumors), and our Copy Number Alterations panel, evaluating a 59 gene panel for genes with frequent gains or losses in cancer.
As a reflection of our dedication to excellence and quality in the services we provide, we have attained ISO 15189 flexible accreditation for our Amplicon-seq testing method and will soon obtain it for our large 450-gene capture panel.
Research activities focus on developing novel multiplexed tests that are optimized to FFPE-derived nucleic acids. Once developed, they are validated and used in both clinical and translational research.
We are also involved in a number of translational research projects including the identification of mechanisms of resistance to targeted therapies, as well as predictive biomarkers for immunotherapeutics. Our group is particularly interested in liquid biopsy and on RNA-based analysis of tumors for microenvironment profiling.
The mission of VHIO’s Molecular Oncology Group is to apply state-of-the-art tissue-based technologies to basic, translational, and clinical research with a clear focus on developing and validating novel tumor biomarkers for precision medicine in oncology.
Together with VHIO’s Cancer Genomics Group (PI Ana Vivancos), and Oncology Data Science - ODysSey Group (PI Rodrigo Dienstmann), along with Susana Aguilar and Jenifer Gonzalez, our group participates in VHIO’s Molecular Prescreening Program. We molecularly profile over 1100 patients per year as candidates for enrolment in early phase clinical trials at our Research Unit for Molecular Therapy of Cancer (UITM) – ”la Caixa”). We also serve as one of VHIO’s Core Technology Platforms and our laboratory is therefore key to our translational research lines and programs.
We actively participate in all projects involving the use of human tissue collected from patients, including biomarker analyses for patient stratification and inclusion in clinical trials, digital pathology, tissue banking and the development of primary patient-derived xenograft (PDX) models. Our contribution is reflected by several high-impact factor collaborative papers published throughout 2019.
Our group also continues to work both independently as well as in partnership to establish the impact of microbiome in colorectal cancer development and progression. In particular, we are developing a Fusobacterium nucleatum diagnostic assay that permits the simultaneous visualization and quantification of bacteria within tumors.
As a Core Facility we have provided support for approximately 280 clinical studies conducted at Vall d’Hebron, representing around 70% of all currently open trials at our institution. Our involvement in clinical trials ranges from the coordination of sample collection, storage and shipment, developing and running multiple assays for real-time patient inclusion, as well as pharmacodynamic monitoring and dose finding.
In 2019 we performed more than 4000 molecular determinations on samples for patient inclusion in clinical trials, and over 23,000 tests to support basic and translation research. We have also served as the central laboratory of choice for 10 international studies, and successfully maintained the prestigious ISO15189 accreditation that endorses quality and competence.
We participate in the following studies as a Central Lab:
VHIO’s Proteomics Group serves as a Core Technology Platform, provides state-of-the-art proteomic methodologies to VHIO researchers, and incorporates new developments within the field to offer the very latest strategies and technologies in the field.
We employ mass spectrometry-based proteomic strategies for the screening and validation of biomarkers for cancer diagnostics, precision therapy and the closer monitoring of disease.
One of our research lines focuses on the development of mass spectrometry-based assays for the analysis of biomarkers in clinical samples. We have been developing immune-MS based assays with improved selectivity and accuracy in the analysis of low abundance biomarker proteins in plasma or CSF samples.
Our group also develops MS based assays for marker proteins in FFPE tissue samples, aimed at providing accurate quantitative measurements that can translate in superior stratification compared with routine IHC scoring methods.
We have set up workflows for the proteomic and phosphoproteomic characterization of patient-derived xenograft (PDX) models of colorectal cancer. PDX constitute an ideal platform for the molecular characterization at the proteomic level of this tumor type. Complementary to genomic classification, we are exploring the suitability of this characterization as a tool for tumor subtype classification.
VHIO’s Proteomics Group is a member of the Spanish Consortium Chromosome 16 HPP which forms part of the HUPO Human Proteome Project. Following a chromosome-centric strategy, this multicenter and international project seeks to develop an entire map of the proteins encoded by the human genome to advance our understanding of human biology in health and disease.