illumina’s mission in complex genetic disease · 5 " explore b cell malignancy...
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© 2014 Illumina, Inc. All rights reserved. Illumina, 24sure, BaseSpace, BeadArray, BlueFish, BlueFuse, BlueGnome, cBot, CSPro, CytoChip, DesignStudio, Epicentre, GAIIx, Genetic Energy, Genome Analyzer, GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X, Infinium, iScan, iSelect, ForenSeq, MiSeq, MiSeqDx, MiSeqFGx, NeoPrep, Nextera, NextBio, NextSeq, Powered by Illumina, SeqMonitor, SureMDA, TruGenome, TruSeq, TruSight, Understand Your Genome, UYG, VeraCode, verifi, VeriSeq, the pumpkin orange color, and the streaming bases design are trademarks of Illumina, Inc. and/or its affiliate(s) in the U.S. and/or other countries. All other names, logos, and other trademarks are the property of their respective owners.
Illumina’s Mission in Complex Genetic Disease: From early discovery to future implementations
Anne Monahan Market Development Manager Complex Disease
2014/Bonn, Germany/ DGFI
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Illumina is a Genomics Company Arrays and Sequencing
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• Hematopoietic Cell Transplantation
• Solid Organ Transplantation
• Autoimmune Diseases • Infectious Diseases • Drug Hypersensitivity
• Hematological Malignancies • Vaccine Development • Autoimmune Diseases • Cancer
• Autoimmune Diseases • Cancer • Cardiovascular Diseases • Infectious Diseases
• Infectious Diseases • Autoimmune Diseases • Immune Development • Cancer
Next-Generation Sequencing in Immunology Research
MHC
Immune Repertoire
Sequencing
Microbiota and Immune Response
miRNA and non-coding
RNA
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" Explore B cell malignancy characteristics
" Discover antibodies specific for antigens of interest
" Inform vaccine development
" Understand autoimmunity
The Antibody Repertoire
Georgiou G, et al. (2014) Nat Biotechnol 32: 158-168
Every B cell creates 1 antibody type
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From Repertoire Sequencing to Single Cells
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" Sorted cells may not reflect the true diversity of the cell population
" RNA-Seq provides an insight into the activity of the cell
" Low population-level expression of transcripts may sometimes reflect high expression in a small subset of cells
From Repertoire Sequencing to Single Cells
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" Use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide
" Bimodal variation in messenger RNA abundance and splicing patterns
Single-Cell Transcriptomics
Shalek AK (2013) Nature 498:236–40
Verified by knockout models and RNA-FISH
▶ Distinct, known maturity states ▶ Differences in the usage of key
regulatory circuits ▶ 137 highly variable, co-
regulated, antiviral response genes
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Splice Variants
Individual cells predominantly express one particular isoform
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RNA-Seq Benefits Better value than GEX arrays
Platform Output Fold change
accuracy Need for updating Any species
GEX Arrays Abundance ++ Yes No
RNA-Seq Abundance & discovery ++++ No Yes
Outperforms GEX arrays at lower cost
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RNA-Seq Benefits Better value than GEX arrays
Platform Output Fold change
accuracy Need for updating Any species $ / sample*
GEX Arrays Abundance ++ Yes No € 347
RNA-Seq Abundance & discovery ++++ No Yes € 168
Outperforms GEX arrays at lower cost
* Includes sample prep, sequencing and cluster reagents. Assumes High-output mode, max samples per run. Pricing based on list. GEX array pricing based on competitor transcriptome array
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RNA-Seq Benefits Better value than GEX arrays
Platform Output Fold change
accuracy Need for updating Any species $ / sample*
GEX Arrays Abundance ++ Yes No € 347
RNA-Seq Abundance & discovery ++++ No Yes € 168
GEX Profiling Abundance ++++ No Yes € 73
Outperforms GEX arrays at lower cost
* Includes sample prep, sequencing and cluster reagents. Assumes High-output mode, max samples per run. Pricing based on list. GEX array pricing based on competitor transcriptome array
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“RNA-Seq is more sensitive in detecting genes with very low expression and more accurate in detecting expression of extremely abundant genes.”
" Report 5 logs vs 3 logs dynamic range for RNA-seq, arrays
" RNA-seq, but not arrays detect previously-observed up-regulation of highly-abundant beta actin upon T cell activation
RNA-Seq Benefits RNA-seq Provides Higher Dynamic Range, Fold Change Accuracy than GEX arrays
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Accessing Illumina technology
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Streamlined End-to-End Workflow Solutions
Enabling Increased Access to Illumina Technology*
▶ TRex ▶ TruSeq RNA ▶ TruSeq DNA ▶ Nextera
▶ BaseSpace Core Apps – BowTie – TopHat – Cufflinks
Data Analysis Applications Sequence
*For Research Use Only.
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" World-class service providers
" Certified to guarantee delivery of high quality data
" Utilize the most widely adopted technology
" Rapid results delivered with no capital investment
Why Illumina Services?
Where to find a service provider? " Contact Illumina Inside Sales
– 1.858.202.4500 – insidesales@illumina.com
" Visit Illumina.com – CSPro providers
§ http://www.illumina.com/services/cspro.ilmn
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" www.illumina.com/immunology
" This presentation
" List of Illumina CSPro providers
Additional Resources
Immunology Research Review Introduction to NGS
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Thank you Any questions?
© 2014 Illumina, Inc. All rights reserved. Illumina, 24sure, BaseSpace, BeadArray, BlueFish, BlueFuse, BlueGnome, cBot, CSPro, CytoChip, DesignStudio, Epicentre, GAIIx, Genetic Energy, Genome Analyzer, GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X, Infinium, iScan, iSelect, ForenSeq, MiSeq, MiSeqDx, MiSeqFGx, NeoPrep, Nextera, NextBio, NextSeq, Powered by Illumina, SeqMonitor, SureMDA, TruGenome, TruSeq, TruSight, Understand Your Genome, UYG, VeraCode, verifi, VeriSeq, the pumpkin orange color, and the streaming bases design are trademarks of Illumina, Inc. and/or its affiliate(s) in the U.S. and/or other countries. All other names, logos, and other trademarks are the property of their respective owners.
Illumina’s Mission in Complex Genetic Disease: From early discovery to future implementations
Anne Monahan Market Development Manager Complex Disease
2014/Bonn, Germany/ DGFI
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