PO21

Precision Oncology

Dissecting cancer genomes for tailored cancer treatments

   IMPORTANT DATES for this Course
   Deadline for applications: Oct 20th 2021
   Course dates: Oct 25th - Oct 29th 2021

Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants.

Instructors:

Fátima Al-Shahrour is the head of the Bioinformatics Unit at Spanish National Cancer Research Centre (CNIO, Madrid, ES). She has extensive experience in the study of cancer under a genomic perspective. Her research focuses on applying and developing computational methods to precision medicine, for the interpretation of cancer genomes, drug repositioning and prediction of anticancer therapies. Her group belongs to the National Bioinformatics platform and ELIXIR-ES as a node (https://inb-elixir.es/) and it participates in the ISCIII IMPaCT-Data project. She is also a co-director of the Master in Bioinformatics Applied to Personalized Medicine and Health (INS-ISCIII) (https://masterbioinformatica.com/). She obtained her PhD from Universidad Autónoma de Madrid (UAM) in 2006. During her PhD she worked at the Bioinformatics Unit at CNIO and Centro de Investigación Príncipe Felipe (CIPF) in Valencia, ES under the supervision of Joaquín Dopazo. In this period, her research dealt with the development of new Bioinformatics tools for microarray gene expression analysis, with a particular focus on computational methods for the functional interpretation of high-throughput experiments. In 2007, she joined the Computational Biology and Bioinformatics group at Cancer Program under supervision of Jill P. Mesirov at the Broad Institute (Cambridge, MA, USA). Her project was focusing mainly in the development of a computational methodology for identifying molecular signatures of oncogenes and tumor suppressor genes based on gene expression data. In 2008, she got a staff position at Broad Institute and the Brigham and Women's Hospital in Boston, Massachusetts (BWH) as a Computational Biologist working at Dr. MD. Benjamin L. Ebert's lab. During this period, her research was focused on the study of the biology and treatment of cancer under a genomic perspective using hematopoiesis as a model system. After four years at the Broad Institute and BWH, in 2012 she joined the CNIO to lead the Translational Bioinformatics Unit in the Clinical Research and Structural Biology and Biocomputing Programmes. In 2017, she got a permanent position at the CNIO where she leads the Bioinformatics Unit. As a result of her scientific career, Dr. Al-Shahrour has published 96 peer-reviewed articles in bioinformatics and cancer genomics fields.

Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES

Elena Piñeiro obtained her MSc in Bioinformatics and Computational Biology from Universidad Complutense de Madrid (UCM) in 2012, working since then as a bioinformatician in the Translational Bioinformatics Unit, and then, in the Bioinformatics Unit at CNIO. Her work was mainly focused on the elaboration and execution of workflows for the analysis and prioritization of genomic variation obtained from NGS technologies. In 2021 she obtained her PhD in Molecular Biosciences from Universidad Autónoma de Madrid (UAM) with a study on methodologies for the in silico drug prescription in precision oncology based on genomics data.

Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES

Coral Fustero joined the Bioinformatics Unit in 2015, where she specialized the analysis of Next Generation Sequencing data (from microarrays, to RNA-seq, Chip-seq or single-cell RNA-seq). She completed her Master studies in Bioinformatics and Computational Biology from the Universidad Autónoma de Madrid (UAM). Currently, she is working on her PhD thesis, focused on the use of single-cell RNA-seq in personalized cancer treatment.

Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES

Maria Jose Himenez got her MSc in Bioinformatics and Computational Biology at the Universidad Autónoma de Madrid. In 2018 she joined the Bioinformatics Unit of CNIO to complete her master’s thesis, which was focused in detecting germinal variants associated with adverse drug reactions in order to improve PanDrugs, our personalized drug prescription tool for cancer patients. Then she stayed over, in order to pursue her PhD, which aims to explore tumor clonality and how it can be tackled therapeutically.

Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES

Course Description

Precision Oncology (PO) is already revolutionizing healthcare and will play a dominant role in the future of cancer therapy. PO integrates tumor multi-omic profiles and data that reflect the course of the disease, lifestyle and environment to guide clinical decisions during cancer patient journey such as prevention, diagnosis and treatment. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of the course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and the recently developed computational strategies for the analysis of NGS data with a particular emphasis on the interpretation of the results, selection of biomarkers of drug response and afford opportunities to match therapies with the characteristics of the individual patient's tumor. Exercises and case studies focused on cancer will be used to illustrate the principles of how genetics influence led to refining diagnoses and personalized treatment of cancer disease. Although focused on cancer, some of the principles and steps could be extrapolated to other complex diseases.

Target audience

This course is designed for both healthcare professionals and Bioinformaticians working in the area.

Pre-requisites

Course participants should understand some of the science behind high-throughput DNA sequencing and sequence analysis, as we will not go deeply into the underlying theory (or the mechanics of given algorithms, for example) as such. They should not feel intimidated by the prospect of gaining experience working on UNIX-like operating systems (including the shell, and shell scripting) as a tailored, mild introduction will be provided which will include (but is not limited to) beginner-level programming. They In this training course, participants will become familiarised with reproducible technical solutions for automating such analyses in shareable compute environments. General computer literacy, (e.g. editing plain text data files) will be assumed.

Applications

Detailed Program

Support




The Oeiras Valley support allows us to waive 50% of the course fee to accepted candidates that reside or work in the Oeiras council.
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Last updated:  Oct 4th 2021