Identifying Data 2022/23
Subject (*) Genomics Code 614522006
Study programme
Mestrado Universitario en Bioinformática para Ciencias da Saúde
Descriptors Cycle Period Year Type Credits
Official Master's Degree 1st four-month period
 First Optional 6
Language
Spanish
Teaching method Face-to-face
Prerequisites
Department Bioloxía
Coordinador
Vila Taboada, Marta
 E-mail
marta.vila.taboada@udc.es
Lecturers
Becerra Fernandez, Manuel
Cerdan Villanueva, Maria Esperanza
De Castro De Antonio, María Eugenia
Vila Taboada, Marta
 E-mail
manuel.becerra@udc.es
esper.cerdan@udc.es
m.decastro@udc.es
marta.vila.taboada@udc.es
Web
General description Denomínase xenómica ao conxunto de ciencias e técnicas dedicadas ao estudo integral do funcionamento, a evolución e a orixe dos xenomas. A xenómica usa coñecementos derivados de distintas ciencias como son: xenética, bioloxía molecular, bioquímica, informática, estatística, matemáticas, física, etc.
A diferenza da xenética clásica que a partir dun fenotipo, xeralmente mutante, busca o ou os xenes responsables de devandito fenotipo, a xenómica ten como obxectivo predicir a función dos xenes a partir da súa secuencia ou das súas interaccións con outros xenes.
As ciencias xenómicas están en plena expansión, sobre todo grazas ás tecnoloxías avanzadas de secuenciación de ADN e aos avances en bioinformática.

Study programme competencies
Code Study programme competences
A8 CE8 - Understanding the basis of the information of the hereditary material, its transmission, analysis and evolution
A9 CE9 – To understand the benefits and the problems associated with the sequencing and the use of biological sequences, as well as knowing the structures and techniques for their processing
B1 CB6 - Own and understand knowledge that can provide a base or opportunity to be original in the development and/or application of ideas, often in a context of research
B2 CB7 - Students should know how to apply the acquired knowledge and ability to problem solving in new environments or little known within broad (or multidisciplinary) contexts related to their field of study
B5 CB10 - Students should possess learning skills that allow them to continue studying in a way that will largely be self-directed or autonomous.
B6 CG1 -Search for and select the useful information needed to solve complex problems, driving fluently bibliographical sources for the field
B7 CG2 - Maintain and extend well-founded theoretical approaches to enable the introduction and exploitation of new and advanced technologies
B8 CG3 - Be able to work in a team, especially of interdisciplinary nature
C1 CT1 - Express oneself correctly, both orally writing, in the official languages of the autonomous community
C2 CT2 - Dominate the expression and understanding of oral and written form of a foreign language
C3 CT3 - Use the basic tools of the information technology and communications (ICT) necessary for the exercise of their profession and lifelong learning
C7 CT7 – To maintain and establish strategies for scientific updating as a criterion for professional improvement.
C8 CT8 - Rating the importance that has the research, innovation and technological development in the socio-economic and cultural progress of society

Learning aims
Learning outcomes Study programme competences
Knowledge about the molecular tools used in genomics AJ8
AJ9
Knowledge about structural, functional and evolutionary genomics AJ8
 BJ1
BJ2
 CJ8
To set up experiments and analyse and interpret data using DNA microarrays and RNAseq BJ6
BJ7
 CJ2
CJ3
Knowledge about the mechanisms involved in the evolution of genomes and the molecular and bioinformatic tools used in that kind of studies BJ5
BJ8
 CJ1
CJ7

Contents
Topic Sub-topic
Introduction: from Molecular Genetics to Genomics Molecular markers
Applications ot recombinant DNA technologies
PCR and real-time quantitative PCR
Sanger sequencing
DNA editing techniques
The Human Genome Project Approaches for whole genome sequencing
Next Generation Sequencing (NGS) Platforms
Paired-end libraries
Data files
Whole genome sequencing Annotation
Comparative genomics
Metagenomics Metabarcoding
Clinical Genomics Amplicon-seq
Panel-seq
Exome-seq
Pharmacogenomics
Single Nucleotide Polymorphisms (SNPs) Genome wide association studies (GWAS)
Digital genetic testing
Functional Genomics Transcriptome analysis: microarrays and RNAseq
Hands on Introduction to the Integrative Genomics Viewer (IGV)
Solving exercises using GALAXY
Gene expression analysis using GALAXY
Pharmacogenomic analysis using PHARMGKB

Planning
Methodologies / tests Competencies Ordinary class hours Student’s personal work hours Total hours
ICT practicals B2 B5 B8 C3 21 42 63
Mixed objective/subjective test A8 A9 B2 C1 C2 C3 2 8 10
Guest lecture / keynote speech A8 A9 B1 B6 B7 C1 C2 C7 C8 21 52.5 73.5
 
Personalized attention 3.5 0 3.5
 
(*)The information in the planning table is for guidance only and does not take into account the heterogeneity of the students.

Methodologies
Methodologies Description
ICT practicals Hands on: students solve exercises using their own laptop.
Mixed objective/subjective test Assessment of the learning process. Tests may include multiple choice questions, problem solving and computer exercises. Instructors will decide whether scheduling a separate test for the computer exercises depending on the progress of the group.
Guest lecture / keynote speech Each instructor will explain the basic contents of each topic interacting as much as possible with the students.

Personalized attention
Methodologies
ICT practicals
Description
The instructors will carefully supervise the student's work during the hands-on sessions.
In the event of having officially certified "part-time" students, the instructors will take the appropriate measures so that their scores are not affected.

Assessment
Methodologies Competencies Description Qualification
Guest lecture / keynote speech A8 A9 B1 B6 B7 C1 C2 C7 C8 In order to pass the subject, all students will have to take a multiple choice test and/or short-answer questionnaire. 70
ICT practicals B2 B5 B8 C3 All students will have to submit several reports following the guidelines provided by each instructor. In these reports, students will answer questions and/or solve exercises using their own computer and the software introduced during the computer labs. 30
 
Assessment comments

Students scoring at least 50 (out of 100) points but not reaching the minimum thresholds (ICT practicals: 15 out of 30 points; Objective test; 28 out of 70 points) will be awarded a 4.5 (out of 10) score. When resitting, they can choose to take both parts or only the failed one.

Evaluation criteria and methodology will be same for the first and second opportunities, except for mark "A with distinction" which will only be awarded to outstanding students passing the subject in the first opportunity.

Students will be scored as "ABSENT" (Non presentado) only when not involved in any of the assessed activities.

In the case of exceptional circumstances, lecturers may assist the student to improve his/her learning process and/or catch up on missed work/assessments. The student is responsible for liaising with his/her lecturer to organise this assistance by e.g. applying for: an extended deadline to present his/her work or taking an exam in a different date. The coordinator can request evidence about the reason for such an application.

In the event of having officially certified "part-time" students, the instructors will take the appropriate measures so that their scores are not affected.

Sources of information
Basic Pevsner J (2015). Bioinformatics and Functional Genomics. Wiley Blackwell
Kulkarni S, Pfeifer J (2015). Clinical Genomics. A guide to Clinical NGS. Academic Press, Elsevier
Robison PN, Piro RM, Jäger M (2018). Computational Exome and Genome Analysis. CRC Press, Taylor & Francis Group
Brown TA (2018). Genomes4. Garland Science, Taylor & Francis Group

Complementary


Recommendations
Subjects that it is recommended to have taken before
Introduction to molecular biology/614522004
Genetics and molecular evolution/614522005

Subjects that are recommended to be taken simultaneously

Subjects that continue the syllabus
Fundamentals of bioinformatics/614522008

Other comments

Do not take this course unless your level of English is B1 or higher.


(*)The teaching guide is the document in which the URV publishes the information about all its courses. It is a public document and cannot be modified. Only in exceptional cases can it be revised by the competent agent or duly revised so that it is in line with current legislation.