Enabling Genomic Technologies to support The Strategic Research Programme in Diabetes (

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1 Enabling Genomic Technologies to support The Strategic Research Programme in Diabetes ( Karin Dahlman-Wright BEA, Bioinformatics and Expression Analysis CF and Karin Dahlman-Wright Research Group Karin Dahlman-Wright 24 maj

2 Where are we? KI SLL Bionut KFC KDW Research group BEA Karin Dahlman-Wright Lab Manager: Fredrik Fagerström-Billai Bioinformatics Thomas Svensson MAF Juha Kere Lab Manager: Kristina Duvefelt Affiliated to SciLife Lab Karin Dahlman-Wright 24 maj

3 Hui Gao Established the Affymetrix core facility Later to become the Bioinformatics and Expression Analysis core facility, BEA, PhD, Estrogen signaling in metabolic disease: A functional genomics approach 2006 Post doc with Tom Gingeras at Affymetrix Research Labs. Financed by VR. Presently in Karin Dahlman-Wright research group Karin Dahlman-Wright 24 maj

4 BEA Infrastructure; Platforms Illumina iscan Bead Arrayscanner Gene Titan Real Time PCR ABI 7900 Agilent HiSeq 2000 Affymetrix GeneChip Instrument System Robotics All platforms are supported by extensive data analysis pipe lines Karin Dahlman-Wright 24 maj

5 Available genomic technologies Platforms Applications Bioinformatics support 24 maj

6 Avaliable array platforms Affymetrix Agilent illumina Array Technology Length of the probes Through the use of photolithography and combinatorial chemistry specific DNA probes are constructed on the chip surface. Inkjet printing process is used to deposit oligo monomers onto specially prepared glass slides base by base. 25 mer 60 mer 50 mer Probes are bound to magnetic beads randomly distributed across arrays. The arrays are then scanned to detect the location of each bead. This is based on an individual decoding sequence carried by each probe. Karin Dahlman-Wright 24 maj

7 Gene Expression Analysis Karin Dahlman-Wright 24 maj

8 Most used applications Applications Affymetrix Agilent Illumina Gene expression SNP analysis ChIP-on-chip DNA-methylation Custom array Karin Dahlman-Wright 24 maj

9 Probe design; Affymetrix and Illumina platforms for gene expression Probe design strategy Affymetrix Karin Dahlman-Wright 24 maj

10 Affymetrix and Illumina platforms for gene expression 3' (IVT) Gene ST Exon ST BeadArray Platform Affymetrix Affymetrix Affymetrix Illumina Coverage Known transcripts Known transcripts Known transcripts Known transcripts Species Splicing Analysis Minimum # Arrays Human, mouse, rat + many more Human, mouse, rat Human, mouse, rat No No yes No 2-40 depending on array Human, mouse, rat / 16 / 24 depending on array Karin Dahlman-Wright 24 maj

11 Genotyping Karin Dahlman-Wright 24 maj

12 Genotyping solutions for the Affymetrix platform Single cartridge format 96well format Axiom genotyping solution Karin Dahlman-Wright 24 maj

13 . Genotyping Solutions for the Illumina Platform Goldengate assay Infinium II assay Karin Dahlman-Wright 24 maj

14 Affymetrix and Illumina platforms for genotyping Platform Affymetrix Affymetrix Illumina Illumina Assay names Axiom Genotyping Genechip Goldengate Infinium II Assay type Hybridzation/ligati on Hybridzation Primer extension/ligation Hybridzation/prime r extesion and ligation (I) or SBE(II) Technology basis Oligonucleotide array Oligonucleotide array (96 well format) Bead array Bead array Throughput/week/p erson 700 samples 100 samples 300 samples samples/1-12 sample chip SNP detection 560K SNPs + 6,000 polymorphic regions custom Up to 900K SNPs + 950K CNV markers Up to1500 Up to 1000 K SNPs Application LOH analysis GWAS LOH analysis GWAS Copy number analysis Linkage analysis LOH analysis GWAS Copy number analysis Karin Dahlman-Wright 24 maj

15 Illumina GWA Portfolio Infinium Bead Chips Samples/chip Markers per sample Human1M-Duo 2 >1 million HumanOmni1-Quad 4 >1 million, incl. content from the 1000 Genomes Project HumanOmniExpress 12 >700,000 Human660W-Quad 4 >658,000 Karin Dahlman-Wright 24 maj

16 Affymetrix GWA Portfolio Single cartridge format 10K K SNPs SNP K SNPs + 420K CNV markers SNP K SNPs + 950K CNV markers DMET Plus Content derived from Pharma ADME core panel 1,936 drug metabolism markers in 225 genes 96well format Axiom genotyping solution 560K SNPs + 6,000 polymorphic regions Flexible content including data from the 1000 Genomes Project Karin Dahlman-Wright 24 maj

17 Epigenetics Karin Dahlman-Wright 24 maj

18 Illumina Infinium DNA methylation assay The HumanMethylation27BeadChip interrogate 27,578 CpG loci, covering more than 14,000 genes. HumanMethylation450 BeadChip expert-selected coverage of >450,000 methylation sites. Very good performance Karin Dahlman-Wright 24 maj

19 Affymetrix platform for ChIP-on-chip analysis Karin Dahlman-Wright 24 maj

20 Affymetrix tiling array portfolio Whole genome tiling arrays Human Tiling 2.0R Array Set (7 array set) Mouse 2.0R Array Set (7 array set) Drosophila Tiling 1.0R Array C. elegans Tiling 1.0R Array Other more Focused and Custom Arrays Human Promoter 1.0R Array Mouse Promoter 1.0R Array ENCODE 2.0R Array Karin Dahlman-Wright 24 maj

21 Deep sequencing, we are catching up! HiSeq 2000 Established wet lab and bioinformatics support for ChIP-seq Including DNA-Methylation assay On going pilot study for RNA-seq (Helicos) Karin Dahlman-Wright 24 maj

22 More Information Karin Dahlman-Wright 24 maj