MGC Next Generation sequencing

30 August 2017 - 1 September 2017

Course language: English

The 11th edition of the “Next Generation Sequencing (NGS) Data analysis” course will be organized at the LUMC, from 30 August, 2017 - 1 September, 2017.
The course aims at PhD students, postdocs and senior researchers who are interested in, planning, or already working with next-generation sequencing. We welcome researchers from both the genomics and bioinformatics fields. Currently available technologies as well as hardware and software solutions will be presented and discussed. The focus of the course will be on the data and ways to analyse the data.


We only have facilities to accommodate 60 participants. All registrants have to send a motivation in the free text field of the web form. Important are your experience in this field and the data you have. When we get more registrations, we have to make a selection. In this case, we will inform you before August 15, 2017.


Provisional Program NGS data analysis 2017, LUMC Leiden

           Wednesday, August 30

09:00    Welcome coffee and sign-in: location the Paleijhs
             1. The technologies, their output, and technology-related problems (lecture hall CZ3)
             chair: Johan den Dunnen (LUMC Leiden)
09:30    Introduction to Next-Generation Sequencing – Johan den Dunnen (LUMC Leiden)
10:00    IIllumina – Wilfred van Ijcken (EMC Rotterdam)
10:30    Coffee break
11:00    10x Genomics – Henk Buermans (LUMC Leiden)
11:30    PacBio RSII – Yahya Anvar (LUMC Leiden)
12:00    Oxford Nanopore – Wigard Kloosterman (UMC Utrecht)
             Lunch 12:30 – 13:30
             2. General Data Analysis (lecture hall CZ3)
             Chair: Jeroen Laros (LUMC Leiden)
13:30    Alignment methods – Wibowo Arindrato (LUMC Leiden)
14:00    Variant calling using GATK – Martin Elferink (UMC Utrecht)
14:30    Combining tools into a pipeline – Jeroen Laros (LUMC Leiden)
15:00    Coffee break
15:30    De Novo Assembly – Erwin Datema (KeyGene)
16:00    Data visualization – Rutger Brouwer (EMC Rotterdam)
16:30    End of Day 1

           Thursday, August 31

              3. Things to Know and Specific Applications I (lecture hall CZ3)
             Chair: Judith Boer (EMC Rotterdam)
09:00    Think before you start – Judith Boer (EMC Rotterdam)
09:30    QC issues – Peter-Bram ’t Hoen (LUMC Leiden)
10:00    ChIP-Seq and DNA methylation – Hendrik Marks (RU Nijmegen)
10:45    Coffee break
11:15    Statistics for NGS – Renee Menezes (VUMC Amsterdam)
11:45    RNA expression profiling – Peter-Bram ’t Hoen (LUMC Leiden)
             Lunch 12:30 – 13:30
             Computer Practicals: Rooms J1-83 and J1-82
              - CLCbio – Andre Koper (CLCbio).
              - NextGene – Fons Elstrodt (Bioke)
13:30    30 participants CLCbio (laptop room), 30 participants NextGene (PC room)
15:00    Coffee break
15:30    30 participants NextGene (PC room), 30 participants CLCbio (laptop room)
17:00    End of Day 2

           Friday September 1

             4. Specific applications II (lecture hall CZ3)
             chair: to be announced
09:00    Metagenomics – Ksenia Arkhipova (Utrecht University)
09:30    Exome sequencing in a diagnostic setting – Claudia Ruivenkamp (LUMC Leiden).
10:00    Analysis of long molecule sequencing data - Walter Pirovano (BaseClear)
10:30    Coffee break
11:00    Structural variation analysis using NGS data – Victor Guryev (ERIBA/UMCG Groningen)
11:30    Non-invasive prenatal testing – Frank Sleutels (EMC Rotterdam)
             Lunch 12:00 – 13:00
              Computer Practicals: Room J1-82
13:00 – 14:30 Introduction to Galaxy – Saskia Hilterman (EMC Rotterdam) and David van Zessen (EMC Rotterdam)
14:30     End of Day 3 – Please return evaluation forms and badges

Start date

30 August 2017


Leiden University Medical Center, building 1
J1-82, J1-84, Lecture hall 3
Albinusdreef 2

Course organiser


Personnel of MGC associated institutes are free of charge  
Participants who are member of BioSB € 175,00  
Participants from the academicworld but outside MGC or BioSB € 250,00  
Participants from outside the academic world € 500,00  
Participants from the research school MGC get a 100% discount  

Terms and conditions

To this course the general terms and conditions of Boerhaave CME are applicable.