Genomics an Epigenomics

The course will be divided in formal lessons, international seminars, journal clubs and non-formal theoretical and practical activities.

Formal Lessons

Lesson 1: Introduction to the Genomic and Epigenomic course
· Introduction to the contents and aims of the course
· Description of the evaluation modalities and requirements
· Assignment of the articles for Journal Clubs
· Information related to the preparation of the mini review

Lesson 2: How to prepare a Journal Club
· How to read a scientific article
· How to prepare a journal club

PART 1- Principles of genomic and epigenomic analyses

Lesson 3: Principles of Evolution and its molecular implications (Part 1)
· Evolution and common ancestor
· Anatomy of mutations and functional consequences
· Selection processes: natural selection, neutral selection and genetic drift
· Pluricellularity and sexual selection
· Germline mutations

Lesson 4: Principles of Evolution and its molecular implications (Part 2)
· Complex genetic diseases
· GWAS and predisposition
· From genetics to epigenetics
· Mutator phenotype, driver and passenger mutations

Lesson 5: Somatic hallmarks of cancer
· Principles of cancer genetics: oncogenes, tumor suppressors (gatekeepers and caretakers)
· Epigenetic micro- and macro-environmental implications (inflammation, angiogenesis, metastasis)
· Driver vs. passenger molecular mechanisms in the natural history of cancer

Lesson 6: Next Generation Sequencing approaches
· From Sanger to next-generation sequencing
· Library preparation approaches and multiplexing
· Emulsion, solid and in solution clustering
· Sequencing by ligation: SOLiD, Complete Genome
· Sequencing by synthesis: Pyrosequencing, Ion Torrent and Illumina
· Development of SBS Illumina chemistry
· Next next generation sequencing: Nanopore and PacBio

Lesson 7: Approaches for genomic analyses (Part 1)
· Molecular oncology and new treatments
· Molecular oncology and examples of precision medicine
· Limits of precision medicine in oncology

Lesson 8: Approaches for genomic analyses (Part 2)
· From whole genome to gene panel sequencing
· Actionable genome and its clinical value
· Development of gene panels: from disease specific to pan-cancer and germline
· Liquid biopsies
· Application studies

Lesson 9: Epigenetic regulation by DNA modification (2 hours, Testa)
· DNA methylation and its functional roles
· Passive and active DNA de-methylation
· Oxidation of DNA methylation by TET proteins
· Approaches to study DNA methylation

Lesson 10: Gene expression analyses by RNA-seq
· RNA species
· Overview of RNA-seq
· PolyA RNAseq and variants
· GRO-seq
· NET-seq
· 4sU-seq
· Translatome analysis (ribosome footprinting etc)
· CAGE-seq
· Smrt-seq

Lesson 11: Epigenome Mapping Using Next Generation Sequencing Technologies
· The functional repertoire of the human genome
· Identification of cis-regulatory elements
· Principles of Chip and chip-seq
· Enhancer mapping by chip-seq
· ATAC-seq
· Issues with ChIP-seq experiments (mappability, technical issues)

Lesson 12: Three dimensional genome organization and 3C-based approaches
· Principles of enhancer promoter regulatory interactions
· Chromosome conformation capture approaches
· Principles of polymer physics
· HiC maps and chromosome territories
· A-B compartments
· Topologically associated domains (TADs)
· CTCF/Cohesin loops
· 3D conformation and gene transcription regulation
· Contact probability and time dependent structural fluctuations
· Transcription and contact probabilities

Lesson 13: Principles of Single Cell Analyses
· Introduction to single cell analyses
· Dimensionality reduction
· SMART-seq
· DROP-seq
· Barcoding
· 10X Genomics
· Single cell DNA and ATAC-seq
· CITE-seq
· Multiplexing by genotype
· Non-genetic multiplexing approaches
· Microwell parallel single cell sequencing
· Combinatorial indexing

Lesson 14: Spatial transcriptomics
· Laser capture microdissection
· Multiplexed single molecule fluorescence in situ hybridization (FISH)
· In situ transcript capturing
· Integration of single cell with spatial data in silico

PART 2- Pathological and clinical implications of genomic and epigenomic analyses

Lesson 15: Role of DNA methylation in development and diseases
· Connection between development, differentiation and cancer
· Molecular view of epigenetic regulatory mechanisms
· DNA vs. histone modifications
· DNA methylation and cell identity
· Cancer of unknown primary origin
· Cancer cell of origin: the example of HGSOC

Lesson 16: Epi-genomic architecture of Cancer
· Genome-driven oncology, the reclassification of tumor types on the basis of genetic lesions and its translational challenge
· showcase examples from solid cancers (Ovarian cancer, Gliomas etc.) on the omic-based reconstruction of cancer cell and cancer-associated cell heterogeneity

Lesson 17: Epi-genomic architecture of Neurological and Neuropsychiatric disorders
· Genome-wide association studies and the results from the Brainstorm consortium
· Rare variants, polygenic inheritance and their interplay
· Polygenic risk scores
· Key examples from neurology and psychiatry

Lesson 18: Models for capturing patients-specific genomes and epigenomes
· Complexity and heterogeneity of biological systems and disease
· Patient-derived experimental models (both iPSC- and adult tissue/tumor-based)
· Principles and examples of benchmarking genomic and epigenomic profiles in patient-derived experimental models versus the primary in vivo counterpart

Lesson 19: The multi-omic architecture of COVID19
· The systemic impact of COVID19 as defines by multi tissue omics (both bulk and single cell
· Genomic and epigenomic layers of analysis in COVID19 (both bulk and single cell) and their impact on diagnosis, prognosis, and care
· Live interactive session for visualization of public omic COVIFD19 datasets

Seminar series
· Six seminar lectures by ad hoc invited scientists related to the course contents

Journal Clubs
· Presentation of preassigned scientific articles by each student followed by an open discussion with the entire class with professors acting as moderators

Experimental design and practical activities
· Study sessions related to the genomic and epigenomic technologies to which the students have been exposed during the course. This will involve a detailed analysis of the technological approaches and of the related experimental procedures. This will be followed by discussions of related scientific literature in the form of Journal Clubs and by the design of experimental strategies to solve related scientific questions.
This will involve the following technological approaches:
- Preparation of samples for next generation sequencing
- Whole genome and whole exome sequencing
- Liquid biopsies
- RNA and ChIP sequencing
- Novel approaches in epigenome mapping
- Assay for Transposase-Accessible Chromatin using sequencing
- Three-dimensional epigenomic analyses
- Single cell analyses
- Spatial transcriptomics
- Nanopore sequencing

The course will be divided in formal lessons, international seminars, journal clubs and non-formal theoretical and practical activities.

Formal Lessons

Lesson 1: Introduction to the Genomic and Epigenomic course
· Introduction to the contents and aims of the course
· Description of the evaluation modalities and requirements
· Assignment of the articles for Journal Clubs
· Information related to the preparation of the mini review

Lesson 2: How to prepare a Journal Club
· How to read a scientific article
· How to prepare a journal club

PART 1- Principles of genomic and epigenomic analyses

Lesson 3: Principles of Evolution and its molecular implications (Part 1)
· Evolution and common ancestor
· Anatomy of mutations and functional consequences
· Selection processes: natural selection, neutral selection and genetic drift
· Pluricellularity and sexual selection
· Germline mutations

Lesson 4: Principles of Evolution and its molecular implications (Part 2)
· Complex genetic diseases
· GWAS and predisposition
· From genetics to epigenetics
· Mutator phenotype, driver and passenger mutations

Lesson 5: Somatic hallmarks of cancer
· Principles of cancer genetics: oncogenes, tumor suppressors (gatekeepers and caretakers)
· Epigenetic micro- and macro-environmental implications (inflammation, angiogenesis, metastasis)
· Driver vs. passenger molecular mechanisms in the natural history of cancer

Lesson 6: Next Generation Sequencing approaches
· From Sanger to next-generation sequencing
· Library preparation approaches and multiplexing
· Emulsion, solid and in solution clustering
· Sequencing by ligation: SOLiD, Complete Genome
· Sequencing by synthesis: Pyrosequencing, Ion Torrent and Illumina
· Development of SBS Illumina chemistry
· Next next generation sequencing: Nanopore and PacBio

Lesson 7: Approaches for genomic analyses (Part 1)
· Molecular oncology and new treatments
· Molecular oncology and examples of precision medicine
· Limits of precision medicine in oncology

Lesson 8: Approaches for genomic analyses (Part 2)
· From whole genome to gene panel sequencing
· Actionable genome and its clinical value
· Development of gene panels: from disease specific to pan-cancer and germline
· Liquid biopsies
· Application studies

Lesson 9: Epigenetic regulation by DNA modification (2 hours, Testa)
· DNA methylation and its functional roles
· Passive and active DNA de-methylation
· Oxidation of DNA methylation by TET proteins
· Approaches to study DNA methylation

Lesson 10: Gene expression analyses by RNA-seq
· RNA species
· Overview of RNA-seq
· PolyA RNAseq and variants
· GRO-seq
· NET-seq
· 4sU-seq
· Translatome analysis (ribosome footprinting etc)
· CAGE-seq
· Smrt-seq

Lesson 11: Epigenome Mapping Using Next Generation Sequencing Technologies
· The functional repertoire of the human genome
· Identification of cis-regulatory elements
· Principles of Chip and chip-seq
· Enhancer mapping by chip-seq
· ATAC-seq
· Issues with ChIP-seq experiments (mappability, technical issues)

Lesson 12: Three dimensional genome organization and 3C-based approaches
· Principles of enhancer promoter regulatory interactions
· Chromosome conformation capture approaches
· Principles of polymer physics
· HiC maps and chromosome territories
· A-B compartments
· Topologically associated domains (TADs)
· CTCF/Cohesin loops
· 3D conformation and gene transcription regulation
· Contact probability and time dependent structural fluctuations
· Transcription and contact probabilities

Lesson 13: Principles of Single Cell Analyses
· Introduction to single cell analyses
· Dimensionality reduction
· SMART-seq
· DROP-seq
· Barcoding
· 10X Genomics
· Single cell DNA and ATAC-seq
· CITE-seq
· Multiplexing by genotype
· Non-genetic multiplexing approaches
· Microwell parallel single cell sequencing
· Combinatorial indexing

Lesson 14: Spatial transcriptomics
· Laser capture microdissection
· Multiplexed single molecule fluorescence in situ hybridization (FISH)
· In situ transcript capturing
· Integration of single cell with spatial data in silico

PART 2- Pathological and clinical implications of genomic and epigenomic analyses

Lesson 15: Role of DNA methylation in development and diseases
· Connection between development, differentiation and cancer
· Molecular view of epigenetic regulatory mechanisms
· DNA vs. histone modifications
· DNA methylation and cell identity
· Cancer of unknown primary origin
· Cancer cell of origin: the example of HGSOC

Lesson 16: Epi-genomic architecture of Cancer
· Genome-driven oncology, the reclassification of tumor types on the basis of genetic lesions and its translational challenge
· showcase examples from solid cancers (Ovarian cancer, Gliomas etc.) on the omic-based reconstruction of cancer cell and cancer-associated cell heterogeneity

Lesson 17: Epi-genomic architecture of Neurological and Neuropsychiatric disorders
· Genome-wide association studies and the results from the Brainstorm consortium
· Rare variants, polygenic inheritance and their interplay
· Polygenic risk scores
· Key examples from neurology and psychiatry

Lesson 18: Models for capturing patients-specific genomes and epigenomes
· Complexity and heterogeneity of biological systems and disease
· Patient-derived experimental models (both iPSC- and adult tissue/tumor-based)
· Principles and examples of benchmarking genomic and epigenomic profiles in patient-derived experimental models versus the primary in vivo counterpart

Lesson 19: The multi-omic architecture of COVID19
· The systemic impact of COVID19 as defines by multi tissue omics (both bulk and single cell
· Genomic and epigenomic layers of analysis in COVID19 (both bulk and single cell) and their impact on diagnosis, prognosis, and care
· Live interactive session for visualization of public omic COVIFD19 datasets

Seminar series
· Six seminar lectures by ad hoc invited scientists related to the course contents

Journal Clubs
· Presentation of preassigned scientific articles by each student followed by an open discussion with the entire class with professors acting as moderators

Experimental design and practical activities
· Study sessions related to the genomic and epigenomic technologies to which the students have been exposed during the course. This will involve a detailed analysis of the technological approaches and of the related experimental procedures. This will be followed by discussions of related scientific literature in the form of Journal Clubs and by the design of experimental strategies to solve related scientific questions.
This will involve the following technological approaches:
- Preparation of samples for next generation sequencing
- Whole genome and whole exome sequencing
- Liquid biopsies
- RNA and ChIP sequencing
- Novel approaches in epigenome mapping
- Assay for Transposase-Accessible Chromatin using sequencing
- Three-dimensional epigenomic analyses
- Single cell analyses
- Spatial transcriptomics
- Nanopore sequencing