Bioinformatics for genomics Kickoff Bioinformatics Expertise Center 10 November 2009 Judith Boer Dept. of Human Genetics.

Bioinformatics for genomics

Kickoff Bioinformatics Expertise Center

10 November 2009

Judith Boer

Dept. of Human Genetics

Omics views of genomes

RNA expressionGene structure

Genetic variation Expression variation

DNA methylationChromatin

Epigenetic variation

SNPs, loss-of-heterozygosityCopy number variants

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