Ateneo - UPO

The course offers an in-depth examination of modern genomic analysis technologies and their bioclinical applications, organized into the following major areas:Review of Fundamental Genetics and GenomicsGenome Reorganization and EpigeneticsAmplification Technologies, DNA Sequencing, and Genotyping

Tom Strachan, Andrew P Read. Human Molecular Genetics. Ed. ISBN 2019

The course aims to provide students with theoretical and practical knowledge of the major omics disciplines, with an in-depth focus on genomic and epigenetic analyses.Specifically, the learning objectives aim to enable students to:Understand biological and omics information flows: Acquire an integrated view of genome structure and gene regulation mechanisms in order to critically evaluate the functional impact of DNA mutations and polymorphisms.Evaluate and select sequencing and analysis technologies: Understand the operating principles of Sanger sequencing and Next-Generation Sequencing (NGS) platforms, developing the ability to select the most appropriate omics strategy (whole exome, whole genome, or targeted panels) based on the specific biological or clinical question.Interpret bioinformatics analysis workflows in the omics sciences: Understand the logic and structure of the computational pipelines used for processing NGS data, with particular attention to the stages of quality control, alignment, variant calling, and annotation of genomic variants.Understanding epigenomic regulation: To contextualize the molecular basis of epigenetics and the main methodological and analytical approaches applied to the study of DNA methylation profiles.The course is worth a total of 5 CFU, all of which are delivered through face-to-face instruction (DE)

Basic information on cell biology and genetics

The course is primarily delivered through in-person lectures (delivered teaching - DE), supported by slides, technical diagrams, and the guided analysis of case studies or bioinformatics pipelines sourced from recent scientific literature.

To encourage the development of independent, critical thinking and active participation, the lectures are structured to maintain continuous interaction with the students (interactive teaching - DI). The professor will regularly present stimulating questions, short quizzes, or practical problems during class.

Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services- students-physical-or-learning-disabilities Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

The assessment of the expected learning outcomes consists of a final oral examination. The exam is conducted as an interview (averaging 2-3 main questions) designed to verify the student's understanding of the theoretical and applied topics covered during lectures, as well as their ability to establish critical connections between different areas of the syllabus.

The evaluation criteria are based on the following key metrics:

Depth of knowledge and understanding of the course topics (omics sciences, genomics, NGS, bioinformatics, and epigenetics).
Command of scientific language, terminological accuracy, and clarity when explaining complex scientific concepts.
Ability to apply knowledge and use critical reasoning when handling methodological questions

Fundamentals of Genetics and Genomics
• In-depth review of key concepts and the fundamentals of genetics
• Structure and organization of genomes, molecular mechanisms of DNA replication, and regulation of the flow of genetic information.
• Study of genetic variability: structural polymorphisms and DNA mutations.
Genome Rearrangements and Epigenetics
• Chromosomal rearrangements
• Mutations involving entire chromosomes: aneuploidy and polyploidy
• Introduction to molecular epigenetics: regulatory mechanisms and analytical methods for studying DNA methylation profiles.
• X-chromosome inactivation
• Methods for analyzing chromosomal rearrangements
Amplification Technologies, DNA Sequencing, and Genotyping
• Theoretical principles and applications of PCR (Polymerase Chain Reaction) techniques.
• Evolution of sequencing systems: from the Sanger method to modern Next-Generation Sequencing (NGS) platforms.
• Application strategies for Next-Generation Sequencing
• Structure of the computational pipeline for processing raw data from genomic sequencing runs.
• Crucial stages of the bioinformatics process: quality control, alignment of reads to the reference genome, variant calling, and subsequent functional and clinical annotation.
• Advanced techniques and methodologies for genotyping known DNA polymorphisms.

1. Knowledge and Understanding
Provide an in-depth description of the structure of the genome and the molecular mechanisms underlying the flow of genetic information.
Understand the theoretical and biochemical principles underlying PCR, Sanger sequencing, and Next-Generation Sequencing (NGS) technologies.
Understand the differences between whole-exome sequencing (WES), whole-genome sequencing (WGS), and genotyping techniques.
Understand the computational logic of bioinformatics pipelines (alignment, variant calling, annotation) for the analysis of genomic data.
Understand the molecular epigenetic mechanisms and the related methodologies for analyzing DNA methylation.

2. Ability to Apply Knowledge and Understanding
Select the most appropriate omics technology or sequencing strategy to address a specific biological or clinical question
Interpret the main results derived from a bioinformatics analysis pipeline for genomic sequencing.
Evaluate the suitability of different genotyping platforms in experimental contexts

3. Independent Judgment
Be able to critically evaluate the quality of genomic data and the reliability of the various analytical methods covered.
Demonstrate the ability to reason independently in associating a specific genomic or epigenetic variation with its potential functional impact.

4. Communication Skills
Explain scientific concepts related to the omics sciences using appropriate language
Being able to correctly use the specific scientific terminology of genomics and bioinformatics during the exam interview.

5. Learning Skills
Develop self-directed learning skills useful for independent and continuous professional development in the field of omics, by consulting the relevant scientific literature.