GENOMICS
- Overview
- Assessment methods
- Learning objectives
- Contents
- Bibliography
- Delivery method
- Teaching methods
- Contacts/Info
A detailed knowledge of Genetics, Molecular Biology and Recombinant DNA Technologies is required. Moreover, a solid experience with the World Wide Web and a basic background in Bioinformatics are strongly recommended. A good knowledge of English will be important to read and understand texts and publications that will be provided to the students as teaching material.
At the end of the module, students will undergo an oral examination aimed at verify the proper achievement of the expected knowledge and abilities. During the exam, the acquired knowledge will be evaluated by asking the student to answer and further discuss at least three different topics selected from the syllabus.
Informed judgment and critical analysis skills will also be evaluated, also in relation to the laboratory module, by means of a practical exam session to be carried out on a bioinformatics workstation.
For each student, the final judgement will consider the quality and precision of the answers (70%), the ability to motivate statements (20%) and the communication skills (10%). The overall evaluation will be expressed by a final mark, which will be calculated as the weighted average of marks attained in the oral exam (70%) and in the online bioinformatics topic. The scheduled time for each exam will be about 20-25 minutes and the exam will be considered passed if the final mark will be equal or higher than a 18/30 threshold.
This course is organized in two distinct modules, represented by class lessons and a laboratory training section.
The aim of the class lessons is to provide the students with a detailed knowledge in the most recent topics and achievements in the field of genomics, in order to give the students a proper level of knowledge on the most recent advancements in the field of genetics and genomics applied to Homo sapiens.
Modern approaches within these fields will be described and discussed in this course to provide a comprehensive picture of the recent field of human genome science. The topics of the course have been selected focusing on the conceptual and methodological current approaches in genome science, with a special attention on both the relevant potentials and pitfalls in these areas. This course thus aims to provide the knowledge and abilities needed for the understanding the structural and functional content of the human genome, with frequent references to the genetic mechanisms underlying biological processes in normal and pathological conditions in humans.
The laboratory section will be focused on the use of several online platforms mostly used in bioinformatics approaches to genomics.
The expected learning outcomes for this course will be the following:
-A detailed knowledge of the principles of genomic sciences and both the experimental approaches and main achievements in the field of genomics.
-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 main scientific achievements in genome sciences.
- The ability to develop 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 will also include an overview of the most recent technological and experimental approaches within the frame of the different topisc of the course.
MODULE OF GENOMICS, CLASS LESSONS (5 CFUs, 40 hours)
• From Genetics to Genomics: an introduction to genome science (2 hours)
• Genome project, part 1: Rationale, aims and planning. Polymorphic genetic markers and genetic maps. Assembly of the first genetic maps. The concept of human disease gene. Rational bases of positional cloning. Linkage analysis in humans and calculation of LOD scores. Autozygosity and linkage disequilibrium mapping approaches for human Mendelian disorders. (6 hours)
• Genome project, part 2: Introduction to physical maps of a genome. Somatic cell and radiation hybrids. Physical maps based on FISH assays. Genomic libraries and assembly of recombinant clone contigs by fingerprinting or STS-content mapping. Transcription maps of the genome: the EST project. The concept of positional candidate cloning (4 hours)
• Genome project, part 3: Theoretical bases of genome sequencing. The first complete non-human genome sequences. 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 (4 hours)
• The post-genomic era: Preliminary comparison of public and Celera human genome assemblies. Anatomy of the human genome. Genome “paradoxes”. Genome annotation: the informational content of the human genome. The GeneOntology and EnCODE projects (6 hours)
• Genome transplantation: towards artificial life (3 hours)
• Functional Genomics: Forward and reverse genomics approaches in the most widely used model organisms (3 hours)
• Genomic approaches for the genetic dissection of complex diseases: Theoretical bases. Parametric and nonparametric inkage analysis approaches for complex diseases. Linkage disequilibrium mapping. The advent of SNP markers and the HapMap project. Genome-wide association studies(GWAS): potentials and limitations. The concept of missing heritability (8 hours)
• 21st century’s Genomics: approaches for next generation sequencing. The first personal genomes. The 1000 genome project. Modern approaches to identify genes underlying monogenic disorders: exome sequencing Personal Genomics: potentials and limitations. (4 hours)
MODULE OF GENOMICS, LABORATORY LESSONS (1 CFU, 16 hours)
The Laboratory section is organized in four lessons (4 hours each), with a preliminary introduction followed by training activities carried out in a 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 and definition of the map position of candidate disease genes.
• Search for putative mutations segregating with a human genetic disease.
• Planning of an experimental strategy to clone and express the gene product from a mutated allele underlying a genetic disease
• Bioinformatic search on the structural and functional features of a gene of interest and planning of a a site-specific mutagenesis and a realtime qPCR assay to evaluate gene 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.
• In silico definition of the role of SNP polymorphic site in the pathogenesis of a human genetic disease.
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.
All teaching material is updated regularly and will be provided to all students in the e-learning online platform as Powerpoint or Pdf files, short notes, animation files and articles from scientific literature on selected issues related to the course’s topics.
Printed folders describing each exercise to be carried out in the laboratory module will also be provided to each student.
Recommended textbook:
• T Strachan & A. Read – “Human Molecular Genetics” (Garland Science Publ.)
• T Strachan, J Goodship & P Chinnery – “Genetics and Genomics in Medicine” (Garland Science Publ.)
The course envisions both class lessons (5 CFUs) and laboratory training (1 CFU). Class lessons will be held with the aid of slide presentation sessions, coupled to projection of didactic movies when required. 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 section 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 25% of the total hours assigned to the laboratory module.
The teacher will answer questions regarding the topics discussed in the course following an appointment by e-mail. Students may also ask bureaucratic/administrative question concerning the course. Email address: francesco.acquati@uninsubria.it