An Overview of Illumina’s Sequencing Technology and its Applications Dr. Epameinondas Fritzilas Computational Biology Group Illumina Cambridge University of Primorska 4 March 2011
© 2009 Illumina, Inc. All rights reserved. Illumina, illuminaDx, Solexa, Making Sense Out of Life, Oligator, Sentrix, GoldenGate, GoldenGate Indexing, DASL, BeadArray, Array of Arrays, Infinium, BeadXpress, VeraCode, IntelliHyb, iSelect, CSPro, and GenomeStudio are registered trademarks or trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.
What is DNA sequencing? Central dogma of molecular biology
We read the DNA: the primary piece of information, the letters of the book. We can get (almost) all letters of the book, but this doesn’t mean that we understand the meaning of everything that is written there.
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More and more organisms are getting completely sequenced
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Who is Illumina?
A company based in San Diego (California, USA) with sites in Singapore, Hayward (California) and Chesterford (near Cambridge, UK) Illumina started as a company making microarrays. The sequencing technology was invented at Cambridge University and developed in a spin-off company called Solexa Ltd. Illumina bought out Solexa in 2006. Other companies in the high-throughput sequencing business: Life Technologies, 454/Roche, Helicos BioSciences, Complete Genomics, Pacific Biosciences, Oxford Nanopore Technologies
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Today’s topic: Illumina’s sequencing workflow Sequencing
Cluster generation
Sample Preparation
Analysis
Collection of raw image data
Nondas Primary analysis
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Secondary analysis
Sequencing workflow Cluster generation
Sequencing
Sample Preparation
Analysis
Collection of raw image data
Primary analysis
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Secondary analysis
Essence of the sample preparation
Cut your DNA randomly and ligate the adapters to each fragment
5’
P
+
T P
5’
A
A
5’
5’ P
Ligation
3’
T A
3’
A T
3’
Make single stranded
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5’
In practice many steps are involved
Quant/QC DNA Clean up
Fragment Genomic DNA Clean up
Fix/Phosphorylate Ends Clean up
A-tail Ends Ligate adapters Clean up
Ligate Size selection adapters Clean up
Size selection Clean up
Amplification Clean up
Quant/QC DNA 8 8
Sequencing workflow Cluster generation
Sequencing
Sample Preparation
Analysis
Collection of raw image data
Primary analysis
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Secondary analysis
Step 1: Cluster generation on the surface DNA (90% bases are >99.9% accurate
>90% bases are >99.9% accurate
Runtime (2x100)
10 days
8 days
Data Rate
5 Gb / day
25 – 40 Gb / day
(95 Gb)
Increasing data volumes are good news for scientists ...
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... but make bioinformaticians struggle like donkeys
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Many thanks to Martin for the invitation …
… and to my colleagues for the slides
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Klaus Maisinger
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David Townley
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Markus Bauer
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Ole Schulz-Trieglaff
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Niall Gormley
