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

II semestre
Day Time Type Place Note
Monday 4:30 PM - 7:30 PM lesson Lecture Hall F  
Wednesday 9:30 AM - 11:30 AM lesson Lecture Hall F  

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