Human genome sequencing and interpretation (2015/2016)

Course code
4S003666
Name of lecturer
Massimo Delledonne
Coordinator
Massimo Delledonne
Number of ECTS credits allocated
6
Academic sector
BIO/18 - GENETICS
Language of instruction
English
Location
VERONA
Period
II semestre dal Mar 1, 2016 al Jun 10, 2016.

Lesson timetable

Learning outcomes

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

Assessment methods and criteria

written, open questions

STUDENT MODULE EVALUATION - 2015/2016