Abstract

This competing supplement request is to upgrade the optical system and base calling algorithms of a Solexa/lllumina 1G Sequencer in order to 1 )demonstrate that the capacity of each sequencer can be readily augmented, and 2) to greatly increase capacity for neuroscience investigators using this important new technology within the Consortium. There is a large demand for this technology (over 1600 sample capacity desired), yet only a limited capacity within the consortium. This proposal seeks to build upon the established experience at the UCLA site with massively parallel sequencing and our experience in scanner fabrication to augment capacity at the UCLA site and poise the consortium to further expand services as neuroscientists embrace sequencing based approaches to genomic analysis.
Aim 1 : To build and test an imaging component for the 1G Sequencer which is 16 fold faster at imaging colonies from the Illumina 1G Sequencer.
Aim 2 : Implement new imaging system within commercial Illumina 1G Sequencer.
Aim 3 : Expand Solexa/lllumina based sequencing services to NIH Neuroscience Microarray Center users. ?

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of Neurological Disorders and Stroke (NINDS)
Type
Resource-Related Research Projects--Cooperative Agreements (U24)
Project #
3U24NS052108-04S1
Application #
7502439
Study Section
National Institute of Neurological Disorders and Stroke Initial Review Group (NSD)
Program Officer
Miller, Thomas
Project Start
2005-07-15
Project End
2009-05-31
Budget Start
2008-06-01
Budget End
2009-05-31
Support Year
4
Fiscal Year
2008
Total Cost
$336,510
Indirect Cost

  Institution

Name
University of California Los Angeles
Department
Genetics
Type
Schools of Medicine
DUNS #
092530369
City
Los Angeles
State
CA
Country
United States
Zip Code
90095

  Publications

Homer, Nils; Nelson, Stanley F (2010) Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol 11:R99
Strom, S P; Stone, J L; Ten Bosch, J R et al. (2010) High-density SNP association study of the 17q21 chromosomal region linked to autism identifies CACNA1G as a novel candidate gene. Mol Psychiatry 15:996-1005
Homer, Nils; Nelson, Stanley F; Merriman, Barry (2010) Local alignment of generalized k-base encoded DNA sequence. BMC Bioinformatics 11:347
Lee, Yohan; Liu, Jason; Patel, Shilpa et al. (2010) Genomic landscape of meningiomas. Brain Pathol 20:751-62
Winden, Kellen D; Oldham, Michael C; Mirnics, Karoly et al. (2009) The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol 5:291
Homer, Nils; Merriman, Barry; Nelson, Stanley F (2009) BFAST: an alignment tool for large scale genome resequencing. PLoS One 4:e7767
Geschwind, Daniel H; Konopka, Genevieve (2009) Neuroscience in the era of functional genomics and systems biology. Nature 461:908-15
Homer, Nils; Merriman, Barry; Nelson, Stanley F (2009) Local alignment of two-base encoded DNA sequence. BMC Bioinformatics 10:175
Day, Allen; Dong, Jun; Funari, Vincent A et al. (2009) Disease gene characterization through large-scale co-expression analysis. PLoS One 4:e8491
Lee, Hane; O'Connor, Brian D; Merriman, Barry et al. (2009) Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing. BMC Genomics 10:646

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