APPLIED GENOMICS
- Overview
- Assessment methods
- Learning objectives
- Contents
- Bibliography
- Delivery method
- Teaching methods
- Contacts/Info
To follow this course the student must have a good understanding of basic molecular biology, genetics and recombinant DNA technology. A proper familiarity with Web-based programs and browers and with the basic bionformatic tools is required as well. Moreover, a good knowledge of English language will be important to read and understand texts and publications that will be provided to the students as teaching material.
The learning outcomes will be assessed through an oral interview lasting approximately 25-30 minutes, during which several topics selected from the syllabus will be discussed .The final evaluation will include an overall assessment regarding: 1) the level of knowledge about different topics related to the course content and the precision and overall quality of the answers (50%); 2) the student’s ability to properly motivate his/her statements and to sustain an adequate discussion (30%) and 3) the communication skills (20%). At least one question concerning the experimental laboratory module will be asked. The final mark will be calculated on the above-mentioned criteria and the exam will be considered passed if the final mark will be equal or over 18/30.
This course is organized in two distinct modules, represented by class lessons and a laboratory training section. The course is mainly focused on the recently developed genomic sciences and will provide students with a detailed overview of the most important achievements in this scientific area since the conception of the Human Genome Project up to the most recent developments. The laboratory section will be focused on the use of several online platforms mostly used in bioinformatics approaches to genomics. This course covers essential topics in the frame of the Master Degree Course in Molecular and Industrial Biotechnologies, since many applications in the above mentioned context heavily rely on both a detailed knowledge of the informational content of the human genome and the technological achievements who made the achievement of such critical information possible.
The expected learning outcomes for this course will be the following:
• A detailed knowledge of the principles of genomic sciences at both the experimental approaches level and the main achievements in the field of genomics, together with a deep comprehension of the rational bases underlying the full elucidation of the human genome and its countless applications.
• The ability to carry out bioinformatics analyses on the currently used genome browsers, in order to elaborate genomic experimental plans as well.
• The ability to carry out bibliography searches and to synthesize the retrieved informations in oral and/or visual representation.
• The ability to achieve an informed judgment, adequate expertise and communication skills in relation to both the experimental approaches and the main scientific achievements in genome sciences.
• The ability to develop both a critic awareness and ability to analyze and discuss issues related to the course contents and the comprehension skills required to develop and maintain issues related to the acquired knowledge, by means of critical reasoning and problem-solving attitudes.
CLASS LESSONS (5 CFUs, 40 hours)
• From Genetics to Genomics: introduction.
• The Human Genome project, part 1: Rationale, aims and planning. Polymorphic genetic markers and genetic maps. Theoretical basis of linkage analysis in humans (LOD scores) Autozygosity mapping.
• The Human Genome project, part 2: Building physical maps of a genome. Somatic cell and radiation hybrids-based mapping approaches. Physical maps based on FISH assays. Genomic libraries and assembly of clone contigs by fingerprinting or STS-content mapping. Transcriptional maps of the genome. The EST project.
• The Human Genome project, part 3: Human genome sequencing: the “clone-by-clone” vs. “whole genome shotgun” approaches. The public and private human genome projects. Validation of the human genome sequence assembly.
• The post-genomic era: Genome annotation. The informational content of the human genome. Gene number and biological complexity. The GeneOntology and EnCODE projects.
• Genome transplantation: an avenue for synthetic life.
• Functional Genomics: Forward and reverse genomics approaches. Molecular pathology.
• Basics of comparative genomics.
• Genomic approaches for the genetic dissection of complex diseases.
• Linkage disequilibrium. mapping. The advent of SNP markers and the HapMap project. Genome-wide association studies. Potential and limitation of GWAS. The missing heritability issue.
• Approaches for next generation sequencing. The 1000 genome project. Mapping human disease genes by exome sequencing.
• Introduction and applications of personal genomics.
LABORATORY LESSONS (1 CFU, 12 hours)
The Laboratory section is organized in three lessons, with a preliminary introduction followed by training activities carried out in the bioinformatics laboratory. The lab section envisages the use of bioinformatics databases and algorithms for the planning and resolution of a set of topics and problems in the field of genome sciences, mainly by means of the most popular genome browser, such as those hosted at NCBI, UCSC e Ensembl. The lab program will be carried t according to the following schedule:
• Analysis of a human pedigree in which a genetic disease is segregating.
• Definition of the map position of candidate genes for the above mentioned disease.
• Search for putative mutations segregating with a human genetic disease.
• Planning of an experimental strategy to isolate the gene and express the corresponding gene product form a mutated allele underlying a genetic disease
• Planning of a site-specific mutagenesis assay in order to produce a functionally inactive form of a disease gene-derived protein.
• Bioinformatic search to define the expression levels of a gene of interest in a panel of healthy and cancer-derived human tissues and in silico planning of a qPCR assay to confirm the reported expression levels.
• Planning a cloning strategy to express a recombinant fusion protein carrying a FLAG epitope in frame with the coding sequence for a gene of interest, in order to define the intracellular localization of the corresponding gene product.
• Implementation of a strategy to silence a gene of interest by RNA interference
To carry out the above mentioned tasks, students will make use of several free-access bioinformatic programs and databases, such as Restriction mapper, OFRfinder, NCBI BLAST, Primer3, rVista, TransFac, ClustalW, Oligo calculator, Gene Cards, siRNA Design.
The teaching material is regularly updated and will be provided to all students in the e-learning online platform as Powerpoint slides file, short notes, animation files and articles from scientific literature on selected issues. For the laboratory session, printed folders and extracts from the scientific literature will be provided. All didactic material will be made available to the students through the online e-learning tool.
Recommended textbook:
• T Strachan & A. Read – “Human Molecular Genetics”, 5th edition” (CRC Press, Ed., 2019)
• T Strachan, J Goodship & P Chinnery – “Genetics and Genomics in Medicine” (Routledge Ed., 2019)
The course envisions both class lessons (5 CFUs) and laboratory training (1 CFU). Class lessons will be held with the aid of Power Point slide presentation sessions, coupled to projection of didactic movies when required. Selected scientific papers focused on topics of major interest will also be provided to students through the e-learning platform. The laboratory training section will be held in the bioinformatics laboratories at the teaching headquarter in via Monte Generoso in Varese. Each student will be given a designated workstation with an online PC (in order to individually carry out the module program) together with a printed folder describing each training section. Assistance to the students will be granted throughout the whole lab sessions. Lab attendance is mandatory for all students, which can skip no more than one lesson for explained reasons.
The teacher is available under appointment for conversations with the students focussed on both topics discussed in the course and organizing issues related to the course, either by phone or e-mail. Students are kindly required not to ask bureaucratic/administrative question unrelated to the course content, if not really urgent.
Telephone: ++39-0332-421512
Email address: francesco.acquati@uninsubria.it