Ateneo - UPO

The course addresses the principles and clinical applications of clinical biochemistry and molecular laboratory medicine within the framework of precision medicine.The first part focuses on molecular diagnostics, from the evolution of genomic technologies to the selection and management of biological samples. Next-generation sequencing and complementary molecular technologies, pre-analytical variables, the main classes of genomic variants, and the essential criteria for interpreting molecular reports will be discussed. Applications in genetic disease diagnosis and pharmacogenetics will be examined, with particular emphasis on variant classification, the management of variants of uncertain significance, and the translation of genotypes into therapeutic recommendations.Molecular oncology will be addressed through the distinction between germline and somatic alterations, liquid biopsy and circulating tumour DNA, the selection of predictive biomarkers, treatment-response monitoring, and the identification of resistance mechanisms. Colorectal cancer, non-small-cell lung cancer, and gynecological cancers will be used as the main clinical models.The course will also cover circulating biomarkers of neurodegenerative diseases, with particular reference to the A/T/N framework, plasma biomarkers of amyloid pathology, tau pathology, axonal damage, and astrocyte activation, as well as the available analytical technologies and the criteria for appropriate clinical use and interpretation.A section will be devoted to laboratory medicine in ageing and frailty, including age-dependent reference values, assessment of renal function in older adults, biomarkers of sarcopenia, malnutrition, immunosenescence and inflammageing in older patients, analytical interferences associated with polypharmacy, and an introduction to biological clocks.The final part will introduce metabolomics and proteomics in laboratory medicine, the main analytical platforms, and their clinical applications. The role of biobanks, the evolution of laboratory samples and data, the digital lifecycle of laboratory reports, interoperability standards, the Italian Electronic Health Record, the European Health Data Space, and the potential applications of artificial intelligence in laboratory processes will also be discussed.

The teaching materials required for exam preparation consist of the lecture slides and the supplementary materials provided by the lecturer and made available through the DIR platform. These materials reflect the topics actually covered during the course.The following textbooks are recommended for consultation and further study:M. Ciaccio (Coordinator), Trattato di Biochimica Clinica e Medicina di Laboratorio, EdiSES, 1st edition, 2021. ISBN 9788836230440.N. Rifai (Ed.), Tietz Textbook of Laboratory Medicine, Elsevier/Saunders, 7th edition, 2022. ISBN 9780323775724. In particular: Section VI, Molecular Diagnostics.For rapidly evolving topics, the most recent versions of the guidelines and consensus documents referred to during the lectures and made available through the DIR platform will be used.

The course aims to provide students with the conceptual and methodological tools required to understand the role of clinical biochemistry and molecular biology in diagnosis, prognostic stratification, treatment selection, and monitoring of major pathological conditions.
In particular, the course aims to:
- understand the principles of the main technologies used in molecular diagnostics, including their indications, potential, and limitations;
- acquire the tools needed to critically interpret molecular diagnostic reports, distinguish germline from somatic variants, and recognise the diagnostic, prognostic, predictive, and - -therapeutic significance of biomarkers;
- develop the ability to appropriately select and interpret laboratory tests, taking into account biological sample characteristics, pre-analytical and analytical variables, and the patient’s clinical context;
- integrate biochemical, molecular, and clinical data into diagnostic and therapeutic pathways, with particular reference to precision oncology, neurodegenerative diseases, ageing, and frailty;
- understand the role of advanced omics technologies, particularly genomics, proteomics, and metabolomics, in the development of innovative diagnostic approaches and precision medicine, including their clinical applications, level of maturity, and main limitations;
- acquire knowledge of the integrated management of biological samples and associated data across the continuum from diagnostics to research, with particular reference to biobanks, sample quality and traceability, storage, sharing, and data reuse;
- understand the digital lifecycle of laboratory data and the role of the Italian Electronic Health Record, the European Health Data Space, and the secondary use of health data, including the principles of interoperability, data protection, quality, governance, and accountability;
- develop a critical and responsible approach to the use of digital technologies and artificial intelligence in laboratory medicine, recognising their opportunities, limitations, risks of bias, and clinical implications.

The course integrates basic biomedical sciences with clinical and translational research applications, showing how biochemical, molecular, and omics knowledge, together with the appropriate management of samples and data, can be transferred into clinical practice to improve diagnosis, personalised treatment, and patient monitoring.

The course requires basic knowledge of general and organic chemistry, biochemistry, cell and molecular biology, genetics, and human physiology. In particular, students should be familiar with the structure and function of the main biological macromolecules, the fundamental mechanisms of gene expression, cellular metabolism, and the main mechanisms of biochemical regulation.Introductory knowledge of general pathology and the basic principles of laboratory medicine is also useful, particularly with regard to the concepts of biomarkers, reference intervals, sensitivity, specificity, and pre-analytical and analytical variability.No previous specific knowledge of sequencing technologies, omics sciences, bioinformatics, biobank management, or digital health systems is required, as these topics will be introduced during the course.

The course is delivered through lectures supported by presentations, interpretative frameworks, examples of laboratory reports, and materials selected from the scientific literature and relevant professional guidelines.Lectures are complemented by interactive sessions based on the guided discussion of clinical cases and laboratory medicine problems. Students will be involved in the interpretation of biochemical and molecular reports, the assessment of test appropriateness, the identification of major pre-analytical and analytical issues, and the integration of biomarkers with the clinical context and potential diagnostic and therapeutic decisions.Particular attention will be paid to the critical interpretation of molecular diagnostic reports, the distinction between germline and somatic variants, and the interpretation of circulating biomarkers and data generated by omics technologies. Applied examples will also be used to discuss the pathway of biological samples and associated data from diagnostics to research, the role of biobanks, the secondary use of health data, and the applications of digital technologies in laboratory medicine.Prompting questions, short reasoning exercises, and collective discussion will be used to promote active participation, independent judgement, and the ability to integrate biochemical, molecular, and clinical knowledge.Presentations used during the lectures, supplementary learning materials, and information relevant to exam preparation will be made available through the University’s teaching platform.

Teaching materials used during the lectures, supplementary readings, examples of laboratory reports, and clinical cases will be made available through the University’s DIR/Moodle learning platform. Course announcements and information relevant to exam preparation will also be published on the same platform.Students with disabilities, Specific Learning Disorders or Special Educational Needs may request the dedicated services and support tools provided by the University by contacting the relevant Student Careers and Services Office and consulting the dedicated UPO webpage: https://www.uniupo.it/it/servizi/servizi-studentesse-e-studenti-condizione-di-disabilit%C3%A0-e-dsaAfter contacting the University support service, students may contact the course lecturer to agree on how the approved measures will be applied to teaching activities and examination procedures.

Learning outcomes are assessed through an in-person computer-based written examination, held in a computer room using the University Moodle DIR platform.The examination lasts 30 minutes and consists of 20 questions covering the topics included in the course program. Question formats may include:multiple-choice questions;completion or fill-in-the-blank questions;matching, ordering, or classification questions;application-based questions involving the interpretation of laboratory data, biomarkers, molecular reports, or short clinical cases.The examination is designed to assess:knowledge and understanding of the biochemical and molecular principles underlying laboratory diagnostics;the ability to recognize the indications, potential, and limitations of the main diagnostic and omics technologies;the ability to interpret biochemical and molecular data and reports within the relevant clinical context;understanding of the pathway of biological samples and associated data from diagnostics to research;knowledge of the role of biobanks, digital health systems, and the secondary use of health data;the ability to apply acquired knowledge to simple diagnostic problems.Incorrect and unanswered questions do not result in penalties. The overall score is based on the number of correct answers and is converted into a mark out of 30. The examination is passed with a minimum mark of 18/30.A passing grade requires knowledge of the fundamental course contents, correct understanding of the main biomarkers and diagnostic methods, and the ability to interpret simple situations. Higher grades reflect progressively more complete knowledge, the ability to connect different topics, and the correct application of knowledge to laboratory data and clinical cases. An excellent grade requires comprehensive and in-depth knowledge and the ability to critically integrate biochemical, molecular, and clinical information.As the module is part of an integrated course, the final assessment will be determined collegially by the teaching staff, according to the procedures described in the integrated course syllabus.

1. Molecular diagnostics and precision medicine
Evolution of molecular diagnostics from the Human Genome Project to current clinical applications. Organisation of the human genome, coding and non-coding regions, and major classes of genomic variants: single-nucleotide variants, insertions and deletions, copy-number variations, gene fusions and structural variants. Evolution of the human reference genome: GRCh38, the telomere-to-telomere sequence and the human pangenome; relevance to variant detection and interpretation.
Principles of the main technologies used in molecular diagnostics: Sanger sequencing, quantitative and digital PCR, next-generation sequencing, gene panels, exome, genome and transcriptome analysis. Complementary technologies: fluorescence in situ hybridisation, immunohistochemistry, array-CGH and SNP arrays. Concepts of coverage, sequencing depth and variant allele frequency.
Selection and management of biological samples according to diagnostic purpose. Formalin-fixed paraffin-embedded tissue, fresh or frozen tissue, peripheral blood, plasma and other biological materials. Main pre-analytical issues and their impact on nucleic-acid quality and result reliability.
2. Genetic diagnostics and pharmacogenetics
Applications of molecular diagnostics to genetic and rare diseases. Gene panels, clinical exome sequencing and whole-genome sequencing: indications, potential and limitations. Classification of germline variants by pathogenicity and management of variants of uncertain significance. Interpretation of genetic reports and implications for patients and relatives. Principles of informed consent in advanced genetic diagnostics.
Principles of pharmacogenetics and pharmacogenomics. Relationships among genotype, metabolic phenotype, treatment efficacy and risk of adverse reactions. Examples involving cytochrome P450 genes, thiopurine and fluoropyrimidine metabolism, and associations between HLA alleles and adverse drug reactions. Interpretation of pharmacogenetic reports and translation of molecular findings into clinical recommendations.
3. Liquid biopsy and molecular diagnostics
Biology of circulating cell-free DNA. Principles of non-invasive prenatal testing based on circulating cell-free fetal DNA.
Circulating tumour DNA and technologies for detecting and quantifying low-frequency variants. Applications of liquid biopsy to treatment-response monitoring, minimal residual disease assessment, early detection of relapse and investigation of resistance mechanisms. Analytical and clinical limitations and complementarity between liquid and tissue biopsy.
Distinction between germline and somatic variants and related clinical implications. Principles for selecting diagnostic, prognostic and predictive biomarkers and assessing their clinical actionability.
Applications of molecular diagnostics in three cancer models:
• colorectal cancer;
• non-small-cell lung cancer;
• ovarian and endometrial cancer.
Structure and interpretation of molecular oncology reports, with attention to terminology, analytical quality and the relationship between results and therapeutic decisions.
4. Circulating biomarkers in neurodegenerative diseases
Evolution of Alzheimer’s disease diagnosis from a predominantly clinical to a biological model. The A/T/N framework and the meaning of biomarkers of amyloid pathology, tau pathology and neurodegeneration.
Main blood-based biomarkers: Aβ42/Aβ40 ratio, phosphorylated tau, neurofilament light chain and glial fibrillary acidic protein. Biological meaning, specificity and potential clinical applications. Principles of ultrasensitive analytical technologies. Pre-analytical and clinical variables affecting results, appropriateness of test requests, and limitations in screening and differential diagnosis of neurodegenerative diseases.
5. Laboratory medicine in ageing and frailty
Effects of age on laboratory-result interpretation and reference values. Assessment of renal function in older adults: creatinine, estimated glomerular filtration rate and cystatin C, with particular reference to sarcopenia.
Biomarkers and laboratory parameters associated with frailty, sarcopenia, malnutrition, immunosenescence and inflamm-ageing. Effects of multimorbidity and polypharmacy on result interpretation and analytical interference. Integrated interpretation of laboratory data in frail older adults. Introduction to biological age and the main biological and molecular clocks.
6. Advanced omics technologies for innovative diagnostics
Positioning of genomics, transcriptomics, proteomics and metabolomics along the pathway linking molecular information to the clinical phenotype.
Principles of targeted and untargeted metabolomics. Mass spectrometry- and nuclear magnetic resonance-based technologies. Established applications, including expanded newborn screening and diagnosis of inborn errors of metabolism, and emerging applications in oncology and neurodegenerative diseases. Limitations related to standardisation, reproducibility, interpretation, costs and turnaround time.
Principles of proteomics applied to laboratory medicine. Mass-spectrometry-based analyses and high-throughput platforms. Identification and validation of new protein biomarkers and integration of proteomic data with other omics data.
Potential and challenges of transferring omics technologies from research to diagnostic practice.
7. Samples and data from diagnostics to research
The pathway of biological samples and associated data from collection and result generation to storage and possible reuse for research. The role of biobanks in ensuring the quality, traceability, preservation and scientific value of biological samples and associated clinical and molecular data. Integration of diagnostic activities, translational research and the development of new biomarkers.
Principles of quality, documentation, pseudonymisation, controlled access and secondary use of biological samples and health data.
8. Digitalisation of laboratory data and the European Health Data Space
The digital lifecycle of laboratory data. The role of the Italian Electronic Health Record and the national Health Data Ecosystem.
Principles and objectives of the European Health Data Space, with particular reference to the primary and secondary use of health data. Semantic and technical interoperability and the main standards used in healthcare systems.
Applications of digital technologies and artificial intelligence to laboratory medicine: consistency checks, alert systems, integration of multimodal data and support for clinical interpretation. Main issues related to data quality, personal-data protection, algorithmic bias, transparency and professional accountability.
9. Integration of the gender dimension
When interpreting biomarkers and clinical data, attention will be paid, where relevant, to biological sex, gender, age and characteristics of the reference population as potential determinants of biological variability, drug response and diagnostic-test performance.

By the end of the course, students are expected to achieve the following learning outcomes.Knowledge and understandingStudents will be able todescribe the principles of the main molecular diagnostic and omics technologies applied to laboratory medicine;recognise the main classes of genomic variants and understand their potential diagnostic, prognostic, predictive and therapeutic significance;understand the applications of genetic diagnostics, pharmacogenetics, liquid biopsy and molecular oncology;explain the biological and clinical significance of the main circulating biomarkers of neurodegenerative diseases, ageing and frailty;understand the pathway of biological samples and associated data from diagnostics to research, the role of biobanks, the secondary use of health data and the principles of the European Health Data Space;describe the main applications and limitations of digital technologies and artificial intelligence in laboratory medicine.Applying knowledge and understandingStudents will be able to:identify the most appropriate technology and biological sample according to the diagnostic question;recognise the main pre-analytical and analytical factors that may affect result quality and reliability;interpret the essential elements of genetic, pharmacogenetic and molecular oncology reports;distinguish germline from somatic variants and assess their different clinical implications;relate biomarker results to the clinical context, potential therapeutic decisions and test limitations;apply acquired knowledge to simple clinical cases and laboratory medicine problems.Making judgementsStudents will be able to critically assess test appropriateness, sample and data quality, the clinical relevance of results and the limitations of the technologies used. They will also be able to recognise the ethical, organisational and data-protection implications of genetic diagnostics, biobanking, secondary use of health data and artificial-intelligence applications.Communication skillsStudents will be able to use biochemical, molecular and laboratory-medicine terminology appropriately and clearly explain the essential meaning of a diagnostic result, distinguishing analytical data from clinical interpretation and from possible implications for patients and their relatives.Learning skillsStudents will be able to update their knowledge through the critical consultation of guidelines, scientific literature and reliable professional sources, recognising the rapid evolution of molecular, omics and digital technologies.Levels of achievementA passing level requires knowledge of the fundamental concepts, recognition of the main technologies and biomarkers covered in the course, and the ability to interpret simple situations.An advanced level requires comprehensive and integrated knowledge, the ability to connect technologies, samples, data and clinical context, and the critical assessment of the appropriateness, limitations and implications of laboratory results.