Human genome sequencing and interpretation (2018/2019)

Course code
4S003666
Credits
6
Coordinator
Massimo Delledonne
Other available courses
Other available courses
    Academic sector
    BIO/18 - GENETICS
    Language of instruction
    English
    Teaching is organised as follows:
    Activity Credits Period Academic staff Timetable
    teoria 5 I semestre Massimo Delledonne

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    esercitazioni 1 I semestre Massimo Delledonne

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    Learning outcomes

    Scope of the course is to provide the most important concepts of clinical genomics, describing the structure and the function of the human genome as well as the most advanced approaches for its clinical interpretation

    A key point of the course is the detailed description of the human genome sequencing and annotation approaches carried out by the international public consortium, and by the private (Celera) initiative. The reference genome is indeed a fundamental component of nowadays human resequencing in precision medicine, and describes many key points about the structure and the function of the human genome.

    Then, the course will focus on the technologies of next generation sequencing and their use in detecting single nucleotide variants as well as large genomic structural variations


    At the completion of the course the students will be able to properly analyze and interpret a whole human genome.

    Syllabus

    THE HUMAN GENOME

    The human genome sequencing consortium project
    • CG content and CpG islands
    • Repetitive sequences in the human genome
    • Segmental duplications
    • Gene content

    The human genome sequencing project by Celera
    • Shot gun sequencing and hybrid assembly
    • Gene prediction and annotation
    • SNPs in the human genome

    Epigenetics and epigenomics
    • Chromatine modification
    • DNA methylation
    • miRNA

    The ENCODE project
    • Methods and set of materials
    • Transcribed and protein-coding regions (GENCODE)
    • Protein bound regions
    • DNase I hypersensitive sites and footprints
    • Regions of histone modifications
    • DNA methylations
    • Chromosome interacting regions
    • ENCODE data integration with known genomic features
    • ENCODE data integration independent of genomic landmarks: Enhancers

    CLINICAL GENOMICS

    Clinical Genome Sequencing
    • Overview of Technical Aspects and Chemistries of Next Generation Sequencing
    • Targeted Capture Methods for exome and gene panels
    • RNA Sequencing and Methylome Analysis
    Base Calling, Read Mapping and Coverage Analysis

    Clinical Genome Analysis
    • Detection of Single Nucleotide Variant
    • Detection of Insertions and Deletions (Indels)
    • Detection of Translocations
    • Detecion of Copy Number Variants

    Clinical Genome Interpretation
    • Clinical Genomics for Constitutional Diseases
    • Clinical Genomics for Somatic Diseases (Cancer)
    • Reference Databases for Disease Associations
    • Reporting of Clinical Genomics Test Results

    Textbook:
    Clinical Genomics, Kulkarni and Pfeifer eds, Elsevier, ISBN: 978-0-12-404748-8
    Slides and articles are available on http://profs.scienze.univr.it/delledonne/Education.html

    Assessment methods and criteria

    written, usually 10 open questions. The answers are evaluated on the basis of proper reporting of the key concepts of the question's topics. Voting is expressed in thirty.

    Reference books
    Activity Author Title Publisher Year ISBN Note
    teoria KULKARNI & PFEIFER CLINICAL GENOMICS (Edizione 1) Elsevier 2015 978-0-12-404748-8
    teoria Brown Genomes 4 (Edizione 4) Taylor & Francis 2017 978-0-8153-4508-4

    STUDENT MODULE EVALUATION - 2017/2018