Bioinformatics for genomics
Kickoff Bioinformatics Expertise Center
10 November 2009
Judith Boer
Dept. of Human Genetics
Omics views of genomes
Genetic variation
SNPs, loss-of-heterozygosity
Copy number variants
Epigenetic variation
DNA methylation
Chromatin
Expression variation
RNA expression
Gene structure
Who are we?
• Johan den Dunnen  always new machines
• Peter-Bram ‘t Hoen  always new applications
• Barend Mons  biosemantics
• Peter Taschner  databases and annotation
• Matt Hestand  next generation sequencing analysis
• Judith Boer  microarray and integrated analysis
Bioinformatics at Human Genetics
Personal view:
"Life science researchers should be able to analyze and
interpret their own genomics data"
• Tools
• Courses
• Research - example
• Expertise
Bioinformatics Tools – Commercial
• Rosetta Resolver
• database, analysis, visualization
• Spotfire
• analysis and visualization
• Ingenuity Pathway Analysis
• literature and high-throughput database mining
• Dedicated platform tools
• Agilent, Illumina, Affymetrix: image analysis, per array
• www.lgtc.nl
Bioinformatics Tools – Open source
• Programming languages
• R, Perl, Bash scripting (Linux), MySQL, Apache, PHP,
Python, Java, …
• Software, e.g. Bioconductor, BioPerl, Ensembl Perl API,
Bowtie, BWA, Velvet, Varscan, Rmap, …
• Alignment, analysis of next-generation sequencing and
microarray data
• Web browsers, e.g. UCSC, Ensembl
• visualize data in relation to genome features
• Gene Ontology, e.g. DAVID
• functional annotation and enrichment
Bioinformatics Research & Tools
• BioSemantics
• Databases and annotation
• Next generation sequencing analysis
• Microarray and integrated analysis
• www.humgen.nl/bioinformatics.html
• www.lgtc.nl
Bioinformatics Tools – BioSemantics
• Anni 2.1 (Jelier / Mons / 't Hoen)
• associations between gene list and other genes, diseases,
processes based on literature mining
• Nermal (van Haagen / Mons / 't Hoen)
• which proteins associate with / bind to my protein?
Bioinformatics Tools – NGS analysis
• GAPSS (Hestand / van Galen / 't Hoen)
• modular pipeline for next-generation sequencing data
analysis
• CORE_TF (Hestand / 't Hoen)
• Conserved and Over-REpresented Transcription Factor
binding sites
Bioinformatics Tools – Databases
• LOVD (Fokkema / Taschner) www.lovd.nl
• locus-specific DNA variation database
• Mutalyzer (Fokkema / Taschner)
• sequence variant nomenclature check
Bioinformatics Tools – Microarray analysis
• Microarray Retriever (Brandt / 't Hoen)
• search and retrieve data from public array repositories
• R packages (Menezes / van Iterson / Boer)
• SIM: Statistical Integration of Microarrays
• SSPA: Sample Size and Power Analysis for microarray data
Bioinformatics Courses
• Analysis of microarray gene expression data (MGC)
• Judith Boer, Peter van der Spek (ErasmusMC)
• 10th edition June 2010 (yearly, 30-40 participants PhD/PD)
• Next-generation sequencing data analysis (MGC)
• Johan den Dunnen, Judith Boer, Matt Hestand
• 3rd edition planned February 2010
• www.medgencentre.nl
• others: MolMed Research School ErasmusMC, NBIC
Bioinformatics Research – Example
• Next generation sequencing data analysis
• ChIP-seq
• gene structure (DeepCAGE)
• expression analysis (DeepSAGE)
• miRNA expression and identification
• (targeted) re-sequencing
• mutation (SNP) detection
• copy number variation detection
• de novo assembly
Bioinformatics Expertise
• Experimental design of microarray and NGS studies
• Choice of analysis software
• Use of analysis software
• Setting up a locus-specific database
• Some cases: help with data analysis
Acknowledgements
• BioSemantics: Herman van Haagen, Bharat Singh, Peter-Bram ‘t
Hoen, Marco Roos, Barend Mons
• Databases and annotation: Ivo Fokkema, Jacopo Celli, Gerard
Schaafsma, Jeroen Laros, Peter Taschner
• NGS analysis: Michiel van Galen, Jaap van der Heijden, Yuching
Lai, Henk Buermans, Matthew Hestand
• Microarray analysis: Maarten van Iterson, Judith Boer
• Michel Villerius, Johan den Dunnen, Gertjan van Ommen