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Old 06-21-2011, 09:49 AM   #1
dan
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Default Reference for Illumina?

Hi, what is the 'canonical' reference for Illumina-Solexa sequencing technology?

I.e. the original paper describing the technology?


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Old 06-21-2011, 10:32 AM   #2
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I'm also looking for a 'canonical reference for the Illumina GoldenGate BeadArray technology, but I think I found that:

http://www.ncbi.nlm.nih.gov/pubmed/15829238



High-throughput SNP genotyping on universal bead arrays.
Shen R, Fan JB, Campbell D, Chang W, Chen J, Doucet D, Yeakley J, Bibikova M, Wickham Garcia E, McBride C, Steemers F, Garcia F, Kermani BG, Gunderson K, Oliphant A.
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Illumina Inc., 9885 Towne Centre Drive, San Diego, CA 92121, USA. rshen@illumina.com
Abstract
We have developed a flexible, accurate and highly multiplexed SNP genotyping assay for high-throughput genetic analysis of large populations on a bead array platform. The novel genotyping system combines high assay conversion rate and data quality with >1500 multiplexing, and Array of Arrays formats. Genotyping assay oligos corresponding to specific SNP sequences are each linked to a unique sequence (address) that can hybridize to its complementary strand on universal arrays. The arrays are made of beads located in microwells of optical fiber bundles (Sentrix Array Matrix) or silicon slides (Sentrix BeadChip). The optical fiber bundles are further organized into a matrix that matches a 96-well microtiter plate. The arrays on the silicon slides are multi-channel pipette compatible for loading multiple samples onto a single silicon slide. These formats allow many samples to be processed in parallel. This genotyping system enables investigators to generate approximately 300,000 genotypes per day with minimal equipment requirements and greater than 1.6 million genotypes per day in a robotics-assisted process. With a streamlined and comprehensive assay, this system brings a new level of flexibility, throughput, and affordability to genetic research.
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Old 06-21-2011, 10:35 AM   #3
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Seems this is the one people cite (weird title!):

http://www.ncbi.nlm.nih.gov/pubmed/15165179

Pharmacogenomics. 2004 Jun;5(4):433-8.
Solexa Ltd.
Bennett S.
Source
Solexa Ltd, Chesterford Research Park, Saffron Walden, CB10 1XL, UK. simon.bennett @solexa.com
Abstract
Solexa Ltd is developing an integrated system, based on a breakthrough single molecule sequencing technology, to address a US$2 billion market that is expected to grow exponentially alongside and as a consequence of further technological enhancements. The system, software and consumables will initially be sold to research organizations, pharmaceutical companies and diagnostic companies that will sequence large regions of genomic DNA, including whole genomes, at costs several orders of magnitude below current levels. Solexa expects to launch its first product in 2006, and as it continues to make time and cost efficiencies, additional products will be launched into the expanding markets that will have broad applications in basic research through to healthcare management.
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Old 06-27-2011, 09:08 PM   #4
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http://www.ncbi.nlm.nih.gov/pubmed/18987734

Nature. 2008 Nov 6;456(7218):53-9.
Accurate whole human genome sequencing using reversible terminator chemistry.
Bentley DR, et al.

Illumina Cambridge Ltd. (Formerly Solexa Ltd), Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK. dbentley@illumina.com
Abstract

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.
Comment in

Nature. 2008 Nov 6;456(7218):49-51.

PMID:
18987734
[PubMed - indexed for MEDLINE]
PMCID: PMC2581791
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