Teaching plan for the course unit



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General information


Course unit name: Molecular Diagnosis

Course unit code: 569699

Academic year: 2021-2022

Coordinator: Cristina Garcia Aljaro

Department: Department of Genetics, Microbiology and Statistics

Credits: 5

Single program: S





If students have any questions or doubts about a subject that is taught, they can consult the lecturer during office hours or by email.



Estimated learning time

Total number of hours 125


Face-to-face and/or online activities



-  Lecture





-  Lecture with practical component





-  Group tutorial




Independent learning




Competences to be gained during study


Criteria for designing the most appropriate diagnostic strategy for a specific inherited disorder or infectious disease.
Knowledge about the use of molecular methods to identify the main groups of viruses, bacteria and pathogenic protozoa in different matrices.
Criteria for assessing the suitability of a specific diagnostic test for a specific genetic disorder, taking into account technical, socioeconomic and ethical factors. Capacity to critically evaluate data produced by the main molecular techniques used in the diagnosis, and to analyse new methods.





Learning objectives


Referring to knowledge

Justification of the subject One area in which new technologies are increasingly used is the molecular diagnosis of various disorders. In this area, technologies can increase the sensitivity and specificity of a diagnosis and the speed of detection. This helps us to act on the course of a disease, and decide between treatment options. Therefore, students of this master’s degree in Biotechnology should have an understanding of the applicability of these technologies not only in fields as important as industry and the environment, but also in the field of health.

Objectives: The main objective of this subject is to provide the knowledge required to understand the molecular bases of the diagnosis of genetic disorders; how  infectious agents can be detected and identified by molecular biology techniques in clinical samples and also in the environment, water or food; the applicability of these techniques to different situations (clinical, epidemiological and treatment); and the advantages and disadvantages of molecular versus traditional techniques. The objective is also to provide a detailed explanation of the various experimental techniques that can be used to make different types of diagnoses, and to use some of these techniques in laboratory practicals.



Teaching blocks


1. Introduction

*  Topic 1. Molecular diagnosis. Hereditary and infectious pathologies. Experimental design and bioinformatics resources to use in the laboratory (databases). Molecular Biology Techniques applied to molecular diagnosis. DNA, RNA or protein diagnosis. "In situ" diagnosis.

Topic 2. Quality controls in molecular diagnosis. Molecular assays verification. Standards and standardization of molecular diagnosis. Tests development in molecular diagnosis. Ethical, social and legal aspects related to molecular diagnosis. Interest in molecular epidemiology. Considerations of the genetic counsel in molecular diagnosis. Why, when and how.

2. Genetic Diseases

*  Topic 3. Monogenic diseases. 1) Direct diagnosis. Detection of different types of known mutations by Southern, PCR-RFLP, HRM, MLPA or sequencing. Techniques to identify unknown mutations. Advantages and disadvantages of analyzes from DNA and RNA. Examples: Duchenne muscular dystrophy, cystic fibrosis, fragile X chromosome syndrome. 2) Indirect diagnosis. Types of markers for indirect diagnosis: SNPs, VNTRs and microsatellites. Recombination, cosegregation and genetic distance. Evaluation of an indirect diagnosis based on the genetic distance.

Topic 4. Techniques for exploring the whole genome at molecular level. 1) Arrays: array-CGH and SNP-arrays; sensitivity and applications. 2) High throughput sequencing applied to the discovery of new genes responsible for genetic diseases and/or their diagnosis. Excess of genetic information.

Topic 5. Diagnosis of chromosomal abnormalities. Techniques: karyotype, G-banding cytogenetics and FISH. Genomic microarrays. Chromosomal fragility and cancer. Prenatal and preimplantation diagnosis. Translocations, aneuploidies.

Topic 6. Diagnosis of metabolic diseases. Mitochondrial diseases. Maternal inheritance, and heteroplasmy. Clinical evaluation and measures in blood and urine. Biomarkers. Newborn screening. Use of specific techniques: determinations of enzymatic activities, metabolomics, whole exome sequencing.

Topic 7. Diagnosis of the risk of developing complex diseases. Pathogenesis of type 2 diabetes mellitus.  Molecular markers and diagnosis. Applications of molecular diagnosis in the prevention and treatment of complex diseases.

3. Infectious Diseases

*  Topic 8. Molecular diagnosis of viruses in clinical samples. Molecular epidemiology of viral infections. NGS applied to the analysis of viruses in clinical samples, water and food. Virus typing for sequence and phylogenetic analysis. Standardization and quality control.

Topic 9. Techniques for sample’s treatment for molecular diagnosis of viruses in water and food. Outbreak investigation.

Topic 10. Molecular diagnosis of viruses producing acute infections: hepatitis A and E, norovirus. Diagnostic techniques with microarrays and multiplex arrays based on microspheres and microchips for the diagnosis of respiratory and gastrointestinal viruses.

Topic 11. Diagnosis and monitoring of chronic viral infections. Molecular diagnosis of Hepatitis Viruses of Blood Transmission: Hepatitis C and Hepatitis B. Retrovirus, HIV.

Topic 12. Diagnosis of bacterial infections. Molecular techniques for clinical diagnosis and epidemiological investigations. Molecular techniques vs traditional methods in laboratory diagnosis of infectious diseases. Diagnosis of gastrointestinal and respiratory infections.

Topic 13. Molecular diagnosis of tuberculosis.

Topic 14. Diagnosis of parasitic diseases. The biological and structural complexity of the parasites and their repercussions in the diagnosis. Molecular diagnosis of protozoa/helminths.

Topic 15. Molecular diagnosis applied to systemic protozoa. Leishmaniasis / Chagas disease. Diagnostic in the laboratory: traditional vs molecular methods.

4. Pharmacogenetics and pharmacogenomics

*  Topic 16. Response to drugs, nutrients and toxic compounds. Molecular diagnosis applications  to identify genetic factors responsible for different response to drugs, nutrients and xenobiotics. Pharmacogenetics and pharmacogenomics. Toxicogenetics and toxicogenomics. Nutrigenomics.



Teaching methods and general organization


Face-to-face learning: theoretical classes, seminars and  learning activities. A total of nineteen, 90-minute lectures will be given and one with learning activities (30 hours in total), in which the lecturers will teach the topics described in the programme and the students will work in groups on a specific topic. These sessions could include specialized talks and seminars given by guest lecturers. A range of useful material for students will be posted on the virtual campus or similar platforms, to make it easy to access. The lecturer will encourage the group to engage in critical analysis and discuss contents.

Practical classes: students will complete 12 hours of practicals, in four three-hour sessions. In these sessions, the students will perform experiments for making a direct molecular diagnosis of a monogenic disease, identifying specific mutations; an indirect diagnosis of another disease by analysing polymorphic markers in a family;  and the diagnostic of a parasitic disease. The experiments require the use of various laboratory techniques (including PCR, agarose gel and acrylamide gel electrophoresis, among others). A series of practical case studies on the diagnosis of genetic and infectious diseases will be given to the students in the form of problems and then discussed in class.

Distance learning task:  Find and read suitable reference works to assimilate the concepts taught in the theoretical classes. - Solve a series of problems on cases of diagnosing different diseases. - Discuss a scientific paper related to one of the topics covered in the subject.

Study - For every hour of face-to-face class, students should study an additional 1.5 to 2 hours. - Solving problems presented in the practical classes: students must spend 5 hours on this task. - Reading and discussing the scientific paper requires 5 hours of study.


As far as possible, the gender perspective will be incorporated in the subject content.



Official assessment of learning outcomes


In order to obtain the final grade, the students will present a total of 6 questionnaires to the professors (70%) and a review of a scientific article (30%). It will be positively valued the continued active participation of the student during the course in the different activities proposed (debates, conferences, practical sessions ...)