Omics: from Bench to Bedside
A.Y. 2020/2021
Learning objectives
The aim of the course is to present to the students the fundamental logic in the use of omic methodologies, to introduce the theoretical and practical bases and the principles on which the different omic techniques are based, to describe the main protocols of use both in the preparation of the sample and of the instrumentation and their control, and finally to provide the basis for the management and analysis of the results including the possibility of integration of the data obtained with different omic methodologies.
In addition, since omics-based recent approaches have unveiled the molecular mechanism behind tumorigenesis of several human tumors and promoted the identification of next-generation molecular markers for early diagnosis, prognosis and even personalized targeted therapy, the course will introduce the student to the most promising omics approaches and their outcomes for the diagnosis and therapy of cancer.
In addition, since omics-based recent approaches have unveiled the molecular mechanism behind tumorigenesis of several human tumors and promoted the identification of next-generation molecular markers for early diagnosis, prognosis and even personalized targeted therapy, the course will introduce the student to the most promising omics approaches and their outcomes for the diagnosis and therapy of cancer.
Expected learning outcomes
At the end of the course, the students will be able to address different scientific issues and to choose and apply the best omics approaches to understand the biochemical bases of tissue functions in health and disease. The student will be prepared to discuss the available modern high technologies to identify novel tumor markers and understand personalized therapies; they will learn the "omics" work flow from different clinical matrices (i.e. tumor specimen) to data analysis.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Lesson period
Second semester
If the situation allows it, lessons will be held in the classroom. Each lesson will be video-recorded and made available asynchronously through the Ariel platform. If the situation worsens or there are no classrooms suitable to contain all the students of the course respecting the social distancing, the lessons will be delivered through the Microsoft Teams platform and can be followed synchronously according to the scheduled time and asynchronously because recorded through the same platform.
Course syllabus
The following topics will be covered during the section of Omics technology and approaches:
- Introduction to genomics
- Sequencing technology platform
- Single Nucleotide polymorphisms (SNPs), exome sequencing and genome-wide association study (GWAS)
- DNA-protein interaction at the genome level (chromatin immunoprecipitation coupled to next-generation sequencing-ChIP-Seq)
- Functional genomics screens
- Epigenomics
- Metagenomics
- Introduction to transcriptomics
- Nascent RNA and total RNA sequencing
- Splicing analysis
- Other RNAs analysis (miRNAs, long non-coding RNAs, small nuclear RNAs, and others)
- Introduction to proteomics
- Proteomic platform and instrumentation (high resolution nanoLC-MS/MS system)
- Labelled and label-free proteomics
- Imaging proteomics and applications
- Structural proteomics
- Introduction to metabolomics
- Metabolic platform: targeted vs untargeted metabolomics
- Lipidomics
- Fluxomics
- Introduction to bioinformatics
- Omics data integration
- Principle of system biology and application to disease.
The following topics will be covered during the section of "Omics approaches in oncodiagnostics and therapy"
- Elements of oncogenic transformation, tumor classification, and phenotype, epidemiology and risk factors of most common neoplasia. Hereditary cancers
- Omics-based approaches to investigate the molecular mechanism of cancer transformation
- Omics-based approaches to identify molecular markers for early diagnosis and prognosis of the most common tumors (from histology to liquid biopsy). Hereditary cancers.
- Cancer therapy and immunotherapy: examples of personalized treatments based on novel biotech drugs and/or treatments
- Introduction to genomics
- Sequencing technology platform
- Single Nucleotide polymorphisms (SNPs), exome sequencing and genome-wide association study (GWAS)
- DNA-protein interaction at the genome level (chromatin immunoprecipitation coupled to next-generation sequencing-ChIP-Seq)
- Functional genomics screens
- Epigenomics
- Metagenomics
- Introduction to transcriptomics
- Nascent RNA and total RNA sequencing
- Splicing analysis
- Other RNAs analysis (miRNAs, long non-coding RNAs, small nuclear RNAs, and others)
- Introduction to proteomics
- Proteomic platform and instrumentation (high resolution nanoLC-MS/MS system)
- Labelled and label-free proteomics
- Imaging proteomics and applications
- Structural proteomics
- Introduction to metabolomics
- Metabolic platform: targeted vs untargeted metabolomics
- Lipidomics
- Fluxomics
- Introduction to bioinformatics
- Omics data integration
- Principle of system biology and application to disease.
The following topics will be covered during the section of "Omics approaches in oncodiagnostics and therapy"
- Elements of oncogenic transformation, tumor classification, and phenotype, epidemiology and risk factors of most common neoplasia. Hereditary cancers
- Omics-based approaches to investigate the molecular mechanism of cancer transformation
- Omics-based approaches to identify molecular markers for early diagnosis and prognosis of the most common tumors (from histology to liquid biopsy). Hereditary cancers.
- Cancer therapy and immunotherapy: examples of personalized treatments based on novel biotech drugs and/or treatments
Prerequisites for admission
Basic knowledge in Biochemistry, Applied Biochemistry and Immunology and elements Human physio-pathology is strongly recommended.
Teaching methods
The course is composed of two sections: 1. Omics technology and approaches (32 h) and 2. Omics approaches in oncodiagnostics and therapy (16 h) of frontal lectures for a total of 48 hours.
Both sections consist of lectures given by the Teachers and occasionally seminars by external experts on particular subjects.
Power point presentations or short videos are usually used and are provided to the students in the Ariel site of the course.
Both sections consist of lectures given by the Teachers and occasionally seminars by external experts on particular subjects.
Power point presentations or short videos are usually used and are provided to the students in the Ariel site of the course.
Teaching Resources
The iconographic material shown during the lessons and bibliographic references can be downloaded from the Ariel portal.
Assessment methods and Criteria
The students' learning outcomes will be evaluated by the teacher through an oral examination of the learning of the program carried out during the course.
Omics approaches in oncodiagnostics and therapy
BIO/10 - BIOCHEMISTRY
MED/04 - EXPERIMENTAL MEDICINE AND PATHOPHYSIOLOGY
MED/04 - EXPERIMENTAL MEDICINE AND PATHOPHYSIOLOGY
Lessons: 16 hours
Professors:
D'Alessandro Sarah, Taramelli Donatella
Omics technology and approaches
BIO/10 - BIOCHEMISTRY
MED/04 - EXPERIMENTAL MEDICINE AND PATHOPHYSIOLOGY
MED/04 - EXPERIMENTAL MEDICINE AND PATHOPHYSIOLOGY
Lessons: 32 hours
Professors:
Caruso Donatella Maria, Mitro Nico
Professor(s)
Reception:
to be defined
via Carlo Pascal, 36 - 20133 MILANO