This course brings together students from the Biotechnology and Biochemistry and Molecular Biology degrees. Genomics is aimed at those students interested in delving into the area of Genetics.

In this subject the general principles of genomics in eukaryotes, bacteria and viruses are worked on. The foundations of the study of complete genomes are established. Methods for the analysis of eukaryotic genomes and critical analysis of scientific articles are worked on.

The contents that are worked on are integrated and related to various subjects in the areas of Cellular and Molecular Biology, Microbiology, Genetics, etc. The subject is basic for the professional practice of any graduate in Biosciences.

The knowledge and skills acquired by the students after successfully completing the subject are detailed below:

1. Know the fundamentals of Genomics and master the procedure to follow for annotating a genome (T8).

2. Know the most appropriate methodological approach to each biological question and be able to apply appropriate genomic analyzes to the specific requirements of the genomic study of animals, plants, viruses, as well as the microbiome. (T2; T6).

3. Understand the complexity of the annotation process and its limitations and know different strategies to overcome them (T6).

4. Know how to use the bioinformatics tools developed for genome annotation (T2; T20).

5. Know how to read scientific articles on Genomics research. Knowing how to critically read and interpret articles on different methodologies, being able to understand the reasons for the differences in workflows in each case. Ability to perform a critical reading of articles and papers (T4; T20; T24).

6. Know different graphs to represent results and know how to make presentations through a web page (T22).

The competences/learning results are related to the following competences of the Biochemistry and Molecular Biology and Biotechnology degree:

T2. Develop the capacity for autonomous learning and adaptation to new situations.

T6. Develop the ability to create and undertake: formulate projects, design and manage, search for and integrate new knowledge and behaviors.

T8. Know the scientific foundations to understand the behavior, properties and interactions of Biological Molecules.

T20. Analyze and interpret appropriately data and experimental results specific to the area.

T22. Know the procedures commonly used by the scientific community to create, transmit and disseminate scientific information.

T24. Evaluate and interpret the scientific literature of the area.

Likewise, the competencies worked on in this subject are related to the transversal competencies of the faculty, especially "teamwork", "the capacity for creation and entrepreneurship" and "autonomy and responsibility". (https://www.ehu.eus/eu/web/ztf-fct/transversal-competences)

GENOMES PROJECT ORGANIZATION AND OBJECTIVES

UNIT 1.-Basic objectives of genomics. Mapping genomes. Genetic maps. Physical maps

UNIT 2.-Human genome project: Objectives. History. Perspectives the human genome project. Internet resources.

UNIT 3. ENCODE project: Historical context. Objectives. Experiments. Phases. Cell lines. Conclusions. Criticisms.

UNIT 4.- Animal genome projects. Rodentia. Other vertebrates. Invertebrate genome projects

UNIT 5.- Plant genomes project: Arabidopsis thaliana. Legumes. other plants

UNIT 6.- Microbial genome projects. Sequencing microbial genomes. Yeast genomes. Parasite genome. Minimal Genome concept. Metagenomics and environmental genomics

GENOME SEQUENCING AND ANNOTATION

UNIT 7.- Automatic sequencing. Sanger's method. NGS. Masive sequencing by Next Generation Sequiencing (NGS) and Third Generation Sequencing (TGS). Sequence assembly.

UNIT 8.- Genome sequencing. Hierarchical Sequencing, Shotgun, Sequence Check

UNIT 9.- Structural annotation. Location of genes in the sequence of a genome. Gene search: extrinsic, intrinsic and integrated methods. Localization of genes in prokaryotic organisms. ORF search. Search for genes in eukaryotic organisms. Location of functional RNA genes.

UNIT 10.- Comparative genomics. Clustering of sequences by homology. Orthologous genes. phylogenies.

UNIT 11.- Determination of the function of the genes. Computerized analysis of gene function. Gene Ontology. Assignment of functions by experimental analysis. Annotation. Genome comparison

UNIT 12.-Functional annotation. Identification of regulatory sequences, other non-protein-coding genes.

ANALYSIS OF GENOMIC VARIATION

UNIT 13.- Genetic variation. Types of markers: SNPs and copy number changes (CNV). Nature of the variations. Classification and distribution. Linkage disequilibrium and haplotypic maps

UNIT 14.-Technology. Discovering new SNPs. SNP genotyping. Genome-Wide Association Studies (GWAS). SNPs and complex diseases.

UNIT 15.- Pharmacogenomics. Other SNP genotyping applications in Forensics, Nutrigenetics. Sport Genetics and Genetic Doping.

ANALYSIS OF GENOMIC EXPRESSION. TRANSCRIPTOMIC

UNIT 16.- Analysis of expression microarrays. Types and methods. Experimental design. Statistical analysis. Data mining. RNA Sequencing (RNA-Seq) and single cell RNA-Seq (scRNA-Seq). eQTL analysis.

UNIT 17.- Validation of array and RNA-Seq results. Single gene analysis (qRT-PCR, etc). Expression databases

UNIT 18.- Epigenomics. Epigenetic marks: histone modifications and DNA methylation. DNA methylation analysis: methylation arrays and Whole Genome Bisulphite Sequencing (WGBS). mQTL analysis.

PRACTICAL PROGRAM

1. Sequence alignment

2. ORF search, gene search (homology analysis), analysis of repetitive sequences

3. Transcrptomics.

4. Search and analysis of SNPs

5. Global genome analysis, bioinformatic tools.

The teaching methodology is based on student participation in the development of the subject. We encourage the interaction with the student by asking questions about specific aspects both addressed to the class in general and to part of the student body in particular.

In the theoretical classes, in addition to the teacher's explanations, analysis of scientific articles on various topics will be interspersed. The student must analyze a minimum of 5 articles during the course. Students must comment and discuss various readings that are proposed during the course. This analysis of scientific articles will be carried out both individually and in groups.

Genomics Project: Students will have to assemble and annotate a problem genome.

The research project will be guided, but since each group can follow different strategies in the analysis of the genome, the path and rhythms of each group will be respected. Each group has a different genome, with its own specifications, therefore, there is no single workflow, so that each group can follow its own strategy, following a methodology and using specific software, etc. There are different ways to approach the same problem.

The teacher makes a guide but does not provide protocols. For each session, a common objective is established for the groups and each one must find a way to overcome it. So it is the responsibility of each group to find the right tools and workflow, explaining the processes and software followed, as well as the reason for their strategy.

The teacher will make sure that each group manages to overcome the challenge, providing in each case the help that is necessary for it.

The way to prove that the challenge is met is to provide the teacher with a small report (200 words maximum) with the results of each session. The teacher will give them feedback so that each group knows if they have passed the challenge or not, pointing out their strengths and weaknesses.

By the tenth week of class, they will have the results of all the challenges, and from that moment until the end of the course, they will have 5 weeks to work on their presentation. In that time interval, each group will have two tutorials to explain her work in detail to the teacher.

Reading articles

The articles have to be read individually, underlining the 10 main ideas and agreeing on these ideas as a group. Subsequently, the selection of these ideas is defended against the rest of the class. So each group presents their ideas and the article is underlined among all. The reason for each idea is analyzed in class. The teacher helps to carry out a critical reading of the article, validating or rejecting the underlined ideas.

• Final Assessment System
• Tools and qualification percentages:
  • Written test to be taken (%): 50
  • Team projects (problem solving, project design)) (%): 50

The written exam is 50% of the qualification and the other 50% is the group work "genomics project". It is necessary to obtain a grade of 4 or higher to pass the course in both sections (exam and group work).

For the students, subject to both continuous and final evaluation, it will be enough to not take the final test for the final grade of the subject to be “not presented”.

During the development of the evaluation tests, the use of books, notes or notes, as well as telephone, electronic, computer or other devices or devices, by the students will be prohibited. In any case of dishonest or fraudulent practice, the provisions of the protocol on academic ethics and prevention of dishonest or fraudulent practices in assessment tests and academic work at the UPV/EHU will be applied.

The evaluation criteria will be the same as in the ordinary exam. In exceptional situations the criteria will be established with the student.

For the students, subject to both continuous and final evaluation, it will be enough to not take the final test for the final grade of the subject to be not presented or not presented.

During the development of the evaluation tests, the use of books, notes or notes, as well as telephone, electronic, computer or other devices or devices, by the students will be prohibited. In any case of dishonest or fraudulent practice, the provisions of the protocol on academic ethics and prevention of dishonest or fraudulent practices in assessment tests and academic work at the UPV/EHU will be applied.

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Basic bibliography

Greg Gibson, Spencer V. Muse (2004) A primer genome science 2nd edition. Editorial Sinauer

In-depth bibliography

Terry A. Brown, Ed Panamericana (2008) Genomas. 3º Edición
Malcolm Campbell, Laurie J. Heyer (2006) Discovering Genomics, Proteomics, and Bioinformatics. Editorial Cold Spring Harbor Laboratory Press, 2ª edición
Reece R.J. (2004) Analysis of Genes and Genomes Ed. Wiley

Journals

Nature
Science
Nature Review Genetics
Genomics

Web addresses

http://www.biomedcentral.com/bmcgenomics/
http://www.biomedcentral.com/bmcmedgenomics/
http://genomebiology.com/
http://www.ebi.ac.uk/microarray-as/ae/
http://www.hapmap.org/
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed
http://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome&itool=toolbar
http://www.ensembl.org/index.html