Illumina, Inc. has announced that researchers from the California Institute of Technology and Stanford University School of Medicine, and the National Heart, Lung, and Blood Institute of the National Institutes of Health are the first in the industry to use the Solexa Sequencing technology with the Genome Analyzer to generate significant chromatin immunoprecipitation sequencing, or ChIP-Seq results within months of system installation, and have study findings accepted for publication by high-profile peer-reviewed journals. These studies appear in the June 8, 2007 edition of Science and the May 18, 2007 issue of Cell, respectively.
In both studies, investigators used Illumina's Solexa Sequencing technology to identify how proteins interact with deoxyribonucleic acid (DNA) across the entire human genome.
Findings demonstrate that this next-generation technology offers the scientific community the ability to scan millions of binding sites within one channel of a flow cell for 10 to 30 times lower cost than ChIP-chip approaches. Using the ChIP-Seq method, researchers also obtain resolution, specificity, and signal-to-noise as compared to microarray-based alternatives.
"Our ChIP-Seq study took advantage of the Genome Analyzer's ability to generate tens of millions of sequence reads per run," said Richard M. Myers, Ph.D., Professor and Chair of Genetics at Stanford University School of Medicine and key author on the Science publication.
Myers continued, "This allowed us to turn ChIP into a simple counting assay, in which one sequence read per molecule of DNA was mapped from the sample back onto the reference genome across millions of molecules per sample. By analyzing the distribution of these positive "hits" across the entire genome we mapped and learned new things about thousands of sites that selectively bind to our factor of interest. The amount and nature of these data meant we got exceptional positional resolution and statistical confidence."
"We are excited about applying other similar "sequence census" methods to measure and map RNA expression, DNA modification assays, and the like," said Barbara Wold, Ph.D., Professor of Molecular Biology and Director of the Beckman Institute at Caltech and key author on the Science paper. "It seems inevitable that sequence reads will soon be the common digital currency for genome-scale DNA and RNA measurements."
According to the paper published in Cell on May 18, 2007, researchers at the NHLBI "demonstrated that direct sequencing of ChIP DNA using the Illumina Genome Analyzer is an efficient method for mapping genome-wide distributions of histone modifications and chromatin protein targets." Investigators used the Solexa sequencing technology to generate genome-wide data for more than 20 epigenetic marks in human T cells.
"As indicated by the Science and Cell studies, scientists are now able to explore entire genomes, regardless of organism type, and unearth rich, new information - easily, rapidly, and affordably," said John West, Illumina's Senior Vice President and General Manager, DNA Sequencing.
"The ChIP-SEQ approach is transforming the way scientists are looking at the DNA-protein interactions that alter gene function and regulation, critical to the understanding of many complex diseases."