2013 - 2014
(GE13) An Introduction to the analysis of the next-generation sequencing data
Period
Lecture time
Course & lecture location
14 – 18 April 2014
09.30 – 12.30 hrs
13.30 – 17.15 hrs
Erasmus MC
Dr. Molewaterplein 50, Rotterdam
Faculty Building
Course coordinator
Dr. N. Amin (n.amin@erasmusmc.nl)
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 (e.g. PLINK)
- Single variant and Collapsed genotype analyses with various tools (e.g.
seqMeta, RAREMETAL, RVtest, SKAT, RVtdt and CMC)
- 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
- Imputation of sequence variants
The course requires working with command line in a LINUX operating
system; experience in working with LINUX will be useful. The course
assumes that the students are knowledgeable in the field of genetic
association analysis and therefore does not aim to teach the statistics
behind the software tools that will be used during the course.
(GE13) An Introduction to the analysis of the next-generation sequencing data
Programme 2014
Date
Monday
14/04/2014
Tuesday
15/04/2014
Time
Topic
Location: COO-5 (Ee-351)
Moderator: R. Kraaij
9:30-10:00
General Introduction
C.M. van Duijn
10:00-11:00
NGS: History and Technologies
R. Kraaij
11:00-12:30
Genome Alignment
R. Kraaij/J. van
Rooij
12:30-13:30
Lunch Break
13:30-15:30
Discovery and annotation of Structural
variants
15:30-15:45
Coffee Break
15:45-17:15
Viewing and working with aligned (*.bam)
files
Location: COO-5 (Ee-351)
Moderator: R. Kraaij
9:30-11:00
11:00-12:00
Wednesday
16/04/2014
Finding homozygous variants in Families
and population-based samples
Evaluating Functional Effects of genetic
variants
Lecturer
V. Guryev
L. Karssen
S. Leal
J. van Meurs
12:00-13:00
Lunch Break
13:00-14:30
Analyzing population-based data using
collapsed genotypes
14:30-15:00
Coffee Break
15:00-16:00
Calling SNPs from the NGS data (Theory)
L. Francioli
16:00-17:00
Calling SNPs from the NGS data (Practical)
J. van Rooij
Location: COO-5 (Ee-351)
Moderator: N. Amin
9:30 -11:00
Creating analyzable datasets: from VCF to
PLINK
N. Amin
11:00-12:30
Annotating sequence variants
N. Amin
12:30-13:15
Lunch Break
13:15-14:45
Rare variants: From population-based to
family-based studies
14:45-15:00
Coffee Break
15:00-17:00
Replication and power analysis of rare
variants
S. Leal
S. Leal
S. Leal
Thursday
Location: COO-5 (Ee-351)
17/04/2014
9:30 -11:00
11:00-12:30
18/04/2014
Analysis of sequence data with RVtest and
RAREMETAL
Application of exome-sequencing in
Mendelian diseases
12:30-13:30
Lunch Break
13:30-14:30
Searching for compound heterozygosity
14:30-14:45
Coffee Break
14:45-16:00
Compound heterozygosity in populationbased Studies
N. Amin
M. Bevova
Y. Aulchenko
F. Liu
Location: COO-5 (Ee-351)
Analysis of sequence data in structured
populations
Moderator: F. Rivadeneira
9:30 -10:30
From common to rare haplotypes
F. Rivadeneira
10:30-12:30
Imputation of sequence variants
P. Deelen
12:30-13:30
Lunch Break
13:30-15:30
Analysis of sequence data using ‘seqMeta’
N. Amin
15:30-16:00
Summary/ Overview
C.M. van Duijn
16:00-17:00
Friday
Moderator: N. Amin
Y. Aulchenko