An Introduction to the Analysis of the Next-generation Sequencing Data [GE13]

Course highlights

EC points

1.4

Start date

04-03-2019

End date

08-03-2019

Course days

Monday to Friday

Faculty

To be announced

Course fee

€ 870

Location

Erasmus MC, Rotterdam NL

Level

Introductory

Disciplines

  • Genetic Epidemiology

Application

How to apply

Detailed information about this course:

Description

This course provides an introduction to working with Next-Generation Sequencing (NGS) data. It targets individuals who have access to NGS data and want to learn how to work with this data and what the possibilities and limitations of NGS are. Lectures will be complemented with practical sessions in which the student will gain hands-on experience with various tools and techniques.Subjects that will be covered include:

  • NGS: an introduction to methodology and techniques;
  • Basic statistics of NGS data, e.g. coverage;
  • Aligning the sequence reads;
  • Calling sequence and structural variants;
  • Dealing with various file formats (samtools, VCFtools, GATK);
  • Annotating sequence and structural variants;
  • Evaluating functional effects of the genetic variants on proteins;
  • Conversion to other formats;
  • Single variant and Collapsed genotype analyses with various tools (e.g. seqMeta, RAREMETAL and RVtest);
  • Finding variants with recessive effects and compound heterozygosity;
  • Search for rare variants in families and population based studies for complex phenotypes;
  • Search for rare variants in Mendelian disorders, and
  • Imputation of sequence variants.

Assessment

Assignment(s)


Reduction on fees

PLEASE NOTE THIS DOES NOT APPLY TO THE RESEARCH MASTERS (120 ECTS)

50% reduction on our fees for participating institutes of NIHES

This 50% reduction is offered to participants formally appointed at the departments or sections participating in NIHES.

University Medical Center Rotterdam/Erasmus University Rotterdam:

  • Department of Epidemiology
  • Department of Public Health
  • Department of Psychiatry, Section of Medical Psychology and Psychotherapy
  • Department of Child and Adolescent Psychiatry/Psychology
  • Department of Medical Informatics
  • Department of General Practice
  • Erasmus School of Health Policy & Management
  • Generation R

50% reduction on our fees for NIHES affiliated partners

This 50% reduction is offered to participants formally appointed at the following NIHES affiliated partners:

University Medical Center Rotterdam/Erasmus University Rotterdam, departments of:

  • Dermatology
  • General Paediatrics
  • Plastic and Reconstructive Surgery
  • Rehabilitation Medicine

Institute of Medical Education Research Rotterdam (iMERR)

Netherlands Cancer Institute/Antoni van Leeuwenhoek Hospital

  • Department of Cancer Epidemiology

25% reduction on our fees for partner institutes of NIHES

For participants formally appointed at the following departments, institutes:

  • Departments of Erasmus MC (except the departments mentioned above)
  • Addiction Research Institute (IVO)
  • Integraal Kankercentrum Zuid (IKZ)
  • Pallas Health Research and Consultancy
  • Municipal Health Service Amsterdam (GGD Amsterdam)
  • Municipal Health Service Rotterdam (GGD Rotterdam)
  • Havenpolikliniek
  • Admiraal De Ruyter Ziekenhuis

25% reduction for all (international) PhD students
Please state your tutor’s name and email address on the application form (remarks field).

25% reduction on our course fees (maximum 3 EC points per academic year) for all NIHES alumni
Please state that you are a NIHES alumnus/alumna and the academic year you graduated (remarks field).