Teaching plan for the course unit

 

 

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General information

 

Course unit name: The Human Genome

Course unit code: 568763

Academic year: 2021-2022

Coordinator: Raquel Rabionet Janssen

Department: Department of Genetics, Microbiology and Statistics

Credits: 2,5

Single program: S

 

 

Professors participants

 

Coordinadors: Raquel Rabionet, Ferran Casals

Altres professors: Susanna Balcells, Gemma Marfany, other professors from the Department of Genetics, Microbiology and Statistics, including researchers from the CRG-CNAG and specialized researchers as invited speakers.

 

 

Estimated learning time

Total number of hours 62.5

 

Face-to-face and/or online activities

16

 

-  Lecture

Face-to-face

 

4

 

-  Lecture with practical component

Face-to-face

 

2

 

-  IT-based class

Face-to-face

 

6

 

-  Field trip

Face-to-face

 

2

 

-  Seminar

Face-to-face

 

2

Supervised project

6

Independent learning

40.5

(the student should spend a few hours after each computer session to get familiarized with the tools presented in class. )

 

 

Competences to be gained during study

 

Basic competences
 — To acquire knowledge that will provide a base or an opportunity to be original in the development or application of ideas in a research context.  

—  Capacity of applying the acquired knowledge and to solve problems in new or poorly known environments within broader contexts related to the study subject.

— Capacity to integrate knowledge and face the complexity to emit judgment based on information that, despite being incomplete or limited, will include a reflection about the social ant ethical responsibilities linked to the application of said knowledge or judgements.

— Ability to communicate the conclusions, and the knowledge and reasoning behind them, to a specialized or unspecialized audience, in a clear an unambiguous manner.  

— To acquire learning abilities that will allow them to continue studying in a autonomous and self-directed manner

General Competences

—  Ability to structure a logical and rational presentation to discuss any scientific aspect in front of an heterogeneous audience.

—  To develop the ability of logical, critical and creative thinking, and analytical and synthetic abilities.

—  To develop the ability of interaction and knowledge transfer in their environment.

— Ability of teamworking and collaborating with other researchers.  

—  In a more academic area, the master has the objective of providing the student with a habit and ability of critical reading and interpretation of scientific publications related to their study subject and to be able to design, write and defend a research project.

Specific competences

— To develop the ability to choose among different basic cellular and genetic analysis technologies to analyze the structure, regulation, function and evolution of genes and genomes.

— To be able to analyze the impact in a specific cell, of the genetic and epigenetic mechanisms that control cellular memory. To be knowledgable about the Human Genome Project (PGH) and of subsequent projects, which have addressed the variation and function of the human genome

— To be knowledgable about the structure, paterns of variation and funcional elements of the human genome.

— To know how to access the databases which integrate the públic information on the human genome; and how to retrieve information from them.

— To be able to read specialized and updated literature on some aspect of the human genome; to be able to summarize and give a critical vision of it.

— To be knowledgable about outstanding researchers involved in any of the projects and about the particular investigations they are currently developing.

 

 

 

 

Learning objectives

 

Referring to knowledge

Why this Subject:
Progress on the knowledge of the human genome in the past 25 years has been dramatic. The large amount of information generated and the application of new technologies to obtain and analyze large amounts of various types of sequence information have radically changed society. Students who complete a master’s degree in genetics and genomics must be very aware that the human genome project (and the sequencing and massive analyses of the genomes of other organisms) has given rise to the field of genomics, which is now at the forefront in science and in society.

General Aims:
The main objective of this course is twofold: first, students should become familiar with the general and unique characteristics of the human genome, regarding both its structure and its functions. In addition, the student must know the scientific and political initiatives that have culminated in obtaining the complete nucleotide sequence of the human genome and subsequently the catalog of sequence variation between individuals and populations (HapMap Project, Human Variome, 1000 genomes, ExAC, GnomAD), and the characterization of the expression patterns and other functional elements of the human genome (ENCODE, Roadmap epigenomics and GTEX projects), and be familiarized with the tools to examine these resources, such as genome browsers and websites like GnomAD, and those of the GTEX and ENCODE projects.

In this context, it is intended that students become familiar with the main databases containing all this information on the human genome and that they get practical training on browsing and information retrieval.

Another goal is for students to consider the human genome as a model genome, which provides sequence data (structure and regulation) and which has launched bioinformatics projects, data processing and hypotheses that can be applied to the analysis of genomes of other organisms.

A final objective is for students to gain a clear picture of the current frontier of knowledge about the human genome.

 

 

Teaching blocks

 

1. The Human Genome Project;Structure of the human genome (2 hours)

2. Patterns of variation of the human genome: background on the HapMap and 1000 genomes projects; GnomAD/ExAC (1 hour)

3. The ENCODE and GTEx projects; the funcional human genome (one hour)

4. Computer sessions (6 hours)

*  Navigating, consulting and using online databases and resources generated by the large projects related to and derived from the Human Genome Project: ENCODE, GTEX, UCSC and Ensembl Genome Browsers, GnomAD, etc.

Identification of causal genetic variants within patient’s genomes.

5. CNAG Field visit (2 hours)

*  Visit to the CNAG sequencing facilities

6. Conferences (2 hours)

*  Invited speakers will present their research on some of the issues arising from the human genome, followed by a debate on the subject above. Additionally, papers by the presenters will be handed to the students in advance for a discussion on relevant topics.

7. Theorico-practical session: integration and wrap up (2 hours)

*  Integration of the knowledge presented in the various sessions and wrap up of the course.

 

 

Teaching methods and general organization

 

Classroom teaching:
Classroom teaching will consist of lectures, seminars and practical computer sessions. It will also include lectures by guest lecturers experts on the topic.

Individual Learning:
The personal work by the student will consist of reading the suggested reading of the course in order to grasp the concepts taught during lectures, and to access and explore the diferent databases and websites shown during the course to solve the excercises proposed. He/she is encouraged to search further readings on his/her own.


Tutorial Assistance:
Students may ask the teachers any question or problem related to the subject, both in pre-established office hours and by email.

 

 

Official assessment of learning outcomes

 

Attendance to all sessions is compulsory. If you cannot attend more than one session you will need to provide a justified reason.

 Evaluation will consist of

a written excercise (80% of the grade) to be done individually after the completion of the course. The evaluation will cover all aspects of the course: theoretical classes (35% final grade); computer sessions and field visit (35% final grade) and the invited speaker sessions (10% of the final grade).

Participation (20%) will be assessed by formulating questions regarding the two invited speaker presentations, and by participation in the discussion in the theorico-practical session.

 

 

Examination-based assessment

Evaluation will consist of

a written excercise  to be done individually after the completion of the course. The evaluation will cover all aspects of the course: theoretical classes (35%); computer sessions and field visit (35%) and the invited speaker sessions (10%). Submission of two written questions, one regarding each of the invited speaker presentations (20%).