ID:
510331
Durata (ore):
48
CFU:
6
SSD:
GENETICA
Anno:
2025
Dati Generali
Periodo di attività
Primo Semestre (29/09/2025 - 16/01/2026)
Syllabus
Obiettivi Formativi
The primary objective of this course is to deepen students' understanding of pharmacogenomics, emphasizing its crucial role in cancer therapy and the innovative use of omic technologies in cancer genomics and epigenomics for the discovery of new molecular features and processes. It also aims to provide students with an updated and critical overview of advanced genomic approaches and technologies, with a particular focus on somatic mosaicism, single-cell DNA sequencing, and their clinical applications. The course will foster a deep understanding of high-resolution genomic analysis methodologies and their relevance to translational research and personalized medicine. Furthermore, students will learn practical skills in data mining of cancer genomic databases.
Prerequisiti
A background in genetics, cancer genetics, molecular biology, and bioinformatics is essential for participants in this course. It is highly recommended that students have completed courses in Basic Molecular Biology or Advanced Molecular Biology, Basic Genetics and Cell Biology, or Human Molecular Genetics and Bioinformatics (1st year).
Metodi didattici
The course adopts an interactive approach, blending frontal lessons supported by PowerPoint presentations with real-time quizzes, hands-on training with tutors, expert seminars, and small group activities (e.g., flipped-classroom). The PowerPoint presentations will be made available on the Kiro Moodle platform for students enrolled in the course. The most appropriate inclusive educational methods will be implemented to accommodate the needs of specific categories of students (such as working students, students with disabilities, and those engaged in caring for family members) as defined by the University of Pavia.
Verifica Apprendimento
The exam consists of an individual written test, including both multiple-choice and open-ended questions, aimed at assessing the skills acquired in relation to the course content. In addition, participation in small-group activities is required and will be evaluated as part of the exam. In the evaluation, particular consideration will be given to communication skills and the use of appropriate scientific language.
Testi
The course will use scientific articles, reviews, and videos. The teacher will provide lecture slides, scientific articles, tutorials, and videos, accessible via the Kiro platform throughout the course.
While the use of a textbook is entirely optional, we suggest the following textbooks:
- Strachan, T., & Read, A. (Latest Edition). Human Molecular Genetics. Taylor & Francis Group.
- Strachan, T., & Lucassen, A. (Latest Edition). Genetics and Genomics in Medicine. Taylor & Francis Group.
While the use of a textbook is entirely optional, we suggest the following textbooks:
- Strachan, T., & Read, A. (Latest Edition). Human Molecular Genetics. Taylor & Francis Group.
- Strachan, T., & Lucassen, A. (Latest Edition). Genetics and Genomics in Medicine. Taylor & Francis Group.
Contenuti
Part I: - Fundamentals of Pharmacogenomics: This section introduces pharmacogenomics, covering the identification and types of pharmacogenes with examples. It highlights the influence of genetic variations, such as Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs), on drug efficacy in cancer treatment. Additionally, it discusses haplotypes, star allele nomenclature, and provides an overview of the PharmGKB database. - Application of Pharmacogenomics in cancer treatment: Explores the application of pharmacogenomic insights in cancer therapy. It emphasizes the role of genetic profiling and introduces the concept of pharmaco-omics, underlining its significance in personalized medicine. Part II – Omic Technologies. Overview of current NGS-based omic technologies used in cancer research, including:
Genomics: targeted genotyping/sequencing, Whole-Exome Sequencing (WES), Whole-Genome Sequencing (WGS);
Transcriptomics: bulk and single-cell RNA sequencing, spatial transcriptomics;
Epigenomics: RRBS-seq, MeDIP-seq, Hi-C, ATAC-seq;
Epitranscriptomics: emerging methods to study RNA modification.
Part III: - Cancer Genomics and Epigenomics: This section offers insight into the hallmarks of cancer, with a focus on the genetic and epigenetic mechanisms that drive cancer development. It underscores the impact of recent advancements in genomic, transcriptomic, and epigenomic technologies in uncovering new features and processes related to cancer. Specifically, it will examine emerging types of mutational hotspots, such as Chromothripsis and Kataegis, along with mutational signatures, and analyze the underlying mechanisms. Moreover, it will offer an overview of the processes involved in DNA, histone, and chromatin remodeling, as well as RNA modifications and their changes in cancer. Additionally, the interaction between epigenomics and the exposome, and the use of epidrugs in cancer treatment will be discussed. Part IV: - Revealing the hidden genome: somatic mosaicism in health and disease. Introduction to somatic mosaicism, its biological basis, and its role in physiological and pathological contexts, including implications for oncology. - Reading genomes one strand at a time: Strand-seq 101: fundamentals of single-strand sequencing (Strand-seq), its applications, and advantages compared to other single-cell genomics approaches. - Harnessing single-cell genomes in the clinic: from precision genomics to personalized yherapeutics. Clinical applications of single-cell genome analysis, with a focus on precision genomics, personalized medicine, and future perspectives in diagnostics and therapeutic development.
Part V – Hands-on Training: Data Mining of Cancer Genomic Databases
This practical module focuses on data mining of cancer genomic databases and introduces bioinformatics tools to evaluate the clinical and biological significance of DNA variants identified through Next-Generation Sequencing (NGS) in cancer. Students will work with genomic data from resources such as AACR GENIE and The Cancer Genome Atlas (TCGA), accessed via platforms like cBioPortal, for selected cancer types.
Genomics: targeted genotyping/sequencing, Whole-Exome Sequencing (WES), Whole-Genome Sequencing (WGS);
Transcriptomics: bulk and single-cell RNA sequencing, spatial transcriptomics;
Epigenomics: RRBS-seq, MeDIP-seq, Hi-C, ATAC-seq;
Epitranscriptomics: emerging methods to study RNA modification.
Part III: - Cancer Genomics and Epigenomics: This section offers insight into the hallmarks of cancer, with a focus on the genetic and epigenetic mechanisms that drive cancer development. It underscores the impact of recent advancements in genomic, transcriptomic, and epigenomic technologies in uncovering new features and processes related to cancer. Specifically, it will examine emerging types of mutational hotspots, such as Chromothripsis and Kataegis, along with mutational signatures, and analyze the underlying mechanisms. Moreover, it will offer an overview of the processes involved in DNA, histone, and chromatin remodeling, as well as RNA modifications and their changes in cancer. Additionally, the interaction between epigenomics and the exposome, and the use of epidrugs in cancer treatment will be discussed. Part IV: - Revealing the hidden genome: somatic mosaicism in health and disease. Introduction to somatic mosaicism, its biological basis, and its role in physiological and pathological contexts, including implications for oncology. - Reading genomes one strand at a time: Strand-seq 101: fundamentals of single-strand sequencing (Strand-seq), its applications, and advantages compared to other single-cell genomics approaches. - Harnessing single-cell genomes in the clinic: from precision genomics to personalized yherapeutics. Clinical applications of single-cell genome analysis, with a focus on precision genomics, personalized medicine, and future perspectives in diagnostics and therapeutic development.
Part V – Hands-on Training: Data Mining of Cancer Genomic Databases
This practical module focuses on data mining of cancer genomic databases and introduces bioinformatics tools to evaluate the clinical and biological significance of DNA variants identified through Next-Generation Sequencing (NGS) in cancer. Students will work with genomic data from resources such as AACR GENIE and The Cancer Genome Atlas (TCGA), accessed via platforms like cBioPortal, for selected cancer types.
Lingua Insegnamento
INGLESE
Altre informazioni
The course features a dedicated website on the University of Pavia's e-learning portal, Kiro, which students can access by using their login credentials.
Corsi
Corsi
MOLECULAR BIOLOGY AND GENETICS
Laurea Magistrale
2 anni
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Persone
Persone (2)
Docente
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