84437 - In Vivo Neurometabolic Diagnostics

Learning outcomes

Discuss conventional and innovative technologies for the quantitative mapping of in vivo central nervous system and neuromuscular metabolic biomarkers. Describe in vivo neurometabolism in relationship to physiological and pathological conditions. Discuss the application of in vivo connectome imaging for the investigation of ageing and pathogenetic mechanisms, and for diagnostic, prognostic and follow-up purposes in pathological conditions. Develop expertise in the advanced processing and multi-level analyses of neurometabolic networks in line with the rapidly developing biomedical research and clinical settings. Develop skills for working in multidisciplinary team including clinicians, neuropsychologists, physicists, bioinformaticists and technicians.

Course contents

Module 1 (Prof. Tonon)

• Course introduction
  

• In vivo metabolic investigation techniques of the central and peripheral nervous system
  • Elements of acquisition and analysis of magnetic resonance data (brain proton MR spectroscopy, muscle phosphorus MR spectroscopy, diffusion tensor imaging, functional MRI, quantitative susceptibility mapping)
  • Elements of nuclear medicine
  • Application of in vivo metabolic-microstructural investigation methods to the main groups of pathologies of the nervous system (genetic, toxic-metabolic, degenerative, neoplastic and inflammatory)

• Advanced analysis methods and tools: elements of connectome imaging and analysis and elements of machine learning methods for medical research

• Principles of radiogenomics

Module 2 (Prof. Bacalini)

Module 2 will focus on the discovery and validation of biomarkers for brain aging. Specifically, the following topics will be discussed:

• Biomarkers: definitions and characteristics; experimental design and statistical considerations in biomarkers discovery.
• Overview of aging and brain aging pillars; contribution of aging in neurodegenerative diseases.
• Omics for biomarkers discovery in the fields of aging and brain aging.
• Biomarkers of aging in anti-aging interventions.

Module 2 will include a laboratory devoted to the bioinformatic analysis of omic data for biomarkers discovery. In particular, a pipeline for the analysis of genome-wide and sequencing data related to brain aging, with a particular focus on DNA methylation, will be discussed and applied. Through the use of example-oriented exercises, the student will learn how to use R environment and Bioconductor packages to manage genomic data and answer biological questions

Module 3 (Prof. Morandi)

• Course introduction
• • Introduction to clinical biochemistry and biomarkers
  • Laboratory medicine: the pre-analytical, analytical and post-analytical phases
  • Variability and standardization of laboratory testing
  • Performance of a laboratory test: sensibility, specificity, predicting values and ROC curves
• DNA sequencing and personalized medicine
  • DNA sequencing: from Sanger method to 2nd, 3rd and 4th generation sequencing in neurological disorders and brain tumours
  • Cloud computing tools for genomic assay designing
  • Personalized medicine: new diagnostic and bioinformatic approaches that provide understanding of the molecular basis of neurological diseases and brain tumours
  • Espansion repeat analysis using nanopore sequencing
  • HLA genotyping using nanopore long read sequencing
    
• Principle of epigenetics
  • The use of genetic and epigenetic biomarkers in neurological disorders and tumours of the central nervous system
  • The assessment of diagnostic, prognostic and predictive tests with examples from new assays based on Next Generation and nanopore Sequencing
  • Clinical validation of a new diagnostic assay
• Liquid biopsy to monitor the evolution of neurometabolic diseases and brain cancers through a minimally invasive technique
• Cerebrospinal fluid analysis in the central nervous system diseases
• Bioinformatic tools in clinical molecular biology: cloud computing approaches for NGS analysis identifying single point mutation, indels, genome rearrangements, copy number variations, variant allele frequency, gene fusions, epigenetic modifications, hierarchical clustering, principal component analysis, phylogenetic trees, methylation plot, ROC curves, Kaplan-Meier graph
• In Vitro Diagnostic Medical Device Regulation (IVDR)
• Wet lab practice: DNA purification; library preparation for Nanopore sequencing; loading libraries onto MinION platform; data analysis for expansion repeat disorders genetic biomarkers

Readings/Bibliography

Teaching materials in PDF

Teaching methods

Lectures and group practice exercises (wet lab practice).

E-learning module General Training and Specific Training part I on general health and safety training for students pursuant to art. 37 of Legislative Decree 81/2008.

Assessment methods

The exam consists of an oral interview with specific questions on at least two topics.

Gradation of the final grade

Insufficient: lack of preparation. Serious and repeated conceptual errors.

18-19: knowledge of the basic concepts without serious gaps. Exposition of concepts and language as a whole acceptable.

20-24: knowledge of the basic concepts without gaps. Ability to analyze and link in partial autonomy. Exposure of discrete concepts and language.

25-29: preparation of good or very good level or even excellent preparation but with inaccuracies in the presentation that compromise the achievement of full marks. Ability to analyze and link independently. Exposure of concepts in the right succession and mastery of the language.

30-30L: full preparation, consolidated and without inaccuracies on the topics covered in the course. Ability to promptly frame the topic. Ability to analyze and connect independently. Concepts in the right succession and full command of the specific language.

The obtained grade will be the average (weighted average for credits) with that obtained in the course of Neurometabolic and Neurodegenerative Disorders.

Students with learning disorders and\or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en/for-students) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives.

Teaching tools

Power point slides

Office hours

See the website of Luca Morandi

See the website of Caterina Tonon

See the website of Maria Giulia Bacalini