DETAILED PROGRAMME
Pre-module
The Pre-workshop Module is the welcome module, and it will give a general overview of the Master Class programme outlining the course organization and expectations.
Topics such as “Why is NGS important for blood cancer” and “Diagnosis, prognosis, prediction / Precision medicine”, based on the use of NGS for clonality of lymphoid disorders, will exemplify the potentials of the NGS implementation in the clinical practice. They will serve as examples translatable to other scenarios.
Further introductory sections on “Patient selection and sample quality” and “bioinformatics” will set the ground for the later modules.
Weeks 2-5
This module will provide an overview of well-established NGS technologies such as DNA targeted sequencing and how it can be applied for patient care (examples of current applications), to more advanced technologies such as nanopore sequencing and single cell analytics, which can provide deeper insights into a patient’s disease.
Weeks 2-3
A1: Using NGS technology for diagnosis?
As translational laboratories with experience in NGS analysis applied to hematological cancer, this section will cover our experience in developing targeted DNA NGS solutions and how they can be applied in the clinical practice.
- Examples of NGS applications in different hematological diseases: (i) acute lymphoblastic leukemia; (ii) chronic lymphocytic leukemia; (iii) myelodysplastic syndromes; (iv) inherited platelets disorders.
- Targeted panel design & validation.
- NGS interpretation.
Week 4
A2: Sequencing analysis applications
To follow up on Module A1, this section will provide additional practical examples of innovative NGS applications in the clinical setting.
- Targeted approach: Application of short-read NGS technology for Monitoring of Measurable Residual Disease in acute myeloid leukemia with FLT3 internal tandem duplications (ITDs) (illumina): overview, wet lab, bioinformatics.
- Genome-wide approach: Application of long-read NGS technology for copy number variation profiling and in daily routine hemato- oncology (Oxford Nanopore Technology).
Week 5
This session will go beyond DNA-seq and will cover RNA sequencing, as well as single cell analytics, plus cell free DNA-seq, and how these technologies can be applied to interrogate changes in the tumor and surrounding environment.
Weeks 6-7
This module will cover the basics of the NGS data analysis, including file formats and how to analyze data, and a practical workshop based on an open-source and user-friendly resource such as Galaxy.
- Raw data processing and key steps of the bioinformatics workflow.
- Variant calling, filtering, and interpretation.
- Commonly used tools for data processing.
- An in-house bioinformatics pipeline step-by-step: advantages & disadvantages.
- Workshop on sequencing & NGS analysis using Galaxy.
Week 8
Module C
This module will focus on the technical, regulatory, and ethical limitations that are frequently encountered when implementing NGS technologies for research and patient care.
- Possible barriers and risks in wide implementation of NGS into health care
systems. - Ethical issues connected with DNA/RNA testing.
Weeks 9-10
Module D
Linked Data & Knowledge Graph
The main goal of this module, providing an introduction to Linked Data and Knowledge Graph, is to transmit the main foundations of a Linked and Open data culture. Students will find their way around the different types of open data available on the Web and target the data sources and formats relevant to their fields. They will know the main principles of the Web of linked data, known as the Semantic Web, and will be able to find, query and exploit data in RDF format. The most advanced students will be able to start producing their own knowledge graphs and linked data sets.
Week 11
Module E
Entrepreneurship & Innovation
This workshop aims to improve innovation and entrepreneurial skills of the participants, and how their research can be spun off to improve patient care.
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