Tuesday, January 18, 2011

Nextera™ sample prep enables breakthrough study of copy-number variation

The study of copy-number variation (CNV) in humans has contributed to our understanding of genetic uniqueness, as well as disease. Until recently, it was difficult to assess the number of repeated DNA sequences in the genome. In a recent publication, researchers at the 1000 Genomes Project and collaborators have invented new methods to study and find repetitive DNA sequences in the human genome, and have found that CNVs occur in only 7%-9% of human genes. They used the new techniques to compare the entire genomes of 159 individuals and were able to accurately assay previously unidentified duplicated genes.

For sequencing, the researchers picked and cultured 144 fosmid clones (from libraries prepared by shotgun cloning of genomic DNA) from eight selected individuals. After fosmid DNA purification, clone DNA was arrayed in a 96-well plate (two clones combined from unrelated loci for some). Bar-coded sequencing libraries were created separately from each well using the Nextera DNA Sample Prep Kit (Illumina-compatible), using 100 ng of fosmid DNA per well as the starting material. The 96 bar-coded Nextera libraries were pooled and sequenced on two lanes of an Illumina GAII (paired-end, 2 x 76-bp reads, with an additional 9-bp index read). Reads were mapped to the genome and analyzed as described in the supplementary information.

The authors report:
"We identified 4.1 million ‘singly unique nucleotide’ positions informative in distinguishing specific copies…these data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association."

ResearchBlogging.orgSudmant, P. et al. (2010). Diversity of Human Copy Number Variation and Multicopy Genes Science, 330 (6004), 641-646 DOI: 10.1126/science.1197005

Wednesday, January 12, 2011

Illumina acquires Epicentre Biotechnologies

Illumina Acquires Epicentre Biotechnologies, Leading Provider of Nucleic Acid Sample Preparation Reagents and Specialty Enzymes
Combination Enhances Illumina's Sample Preparation and Enzyme Portfolio

SAN DIEGO, Jan 11, 2011 (BUSINESS WIRE) -- Illumina, Inc. (NASDAQ:ILMN) today announced that it has acquired Epicentre Biotechnologies, a leading provider of nucleic acid sample preparation reagents and specialty enzymes used in sequencing and microarray applications. A key component of the acquisition is direct access to Epicentre's proprietary Nextera(TM) technology for next-generation sequencing library preparation, which greatly simplifies genetic analysis workflows and reduces time from sample preparation to answer.

"As next-generation sequencing continues to improve in throughput and cost, there's a critical need for sample prep to evolve as well, to lower costs, handle higher sample volumes and reduce both hands-on and overall processing time," said Jay Flatley, President and CEO of Illumina. "Epicentre's Nextera technology provides a step-change improvement in library prep that will translate into greater ease of use, lower costs, and faster turnaround times for sequencing applications. In addition to Nextera, Epicentre is a leading supplier of specialty enzymes and kits that are beneficial to Illumina's technologies."

The rapid adoption of Nextera sequencing sample prep kits by existing Illumina sequencing customers is indicative of the cost effectiveness, ease of use, and efficiency of Nextera technology. With this patented technology, researchers can prepare sequencer-ready libraries from genomic DNA with less than 15 minutes of hands-on time - a significant timesaving compared to alternate methods. In addition, Nextera technology requires 10-100 times less starting DNA, which enables applications with limited starting material such as tumor biopsies, degraded DNA, or purified RNA. These unique features of Nextera sequencing library prep kits are all critical to advancing the evolution of next-generation sequencing.

The combined company will be uniquely positioned to offer an end-to-end solution for next-generation sequencing, microarray, and real time PCR applications. Epicentre's unique capabilities in enzyme engineering and sample preparation reagent development will complement Illumina's core platform expertise to comprehensively address the needs of researchers across their entire genetic analysis workflow.

About Illumina

Illumina (www.illumina.com) is a leading developer, manufacturer, and marketer of life science tools and integrated systems for large-scale analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA, and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare.

Forward-Looking Statements

This release contains forward-looking statements that involve risks and uncertainties. Important factors that could cause actual results to differ materially from those in any forward-looking statements include challenges inherent in integrating Epicentre with our existing operations and the other factors that are detailed in our filings with the Securities and Exchange Commission, including our most recent filings on Forms 10-K and 10-Q, or in information disclosed in public conference calls, the date and time of which are released beforehand. We do not intend to update any forward-looking statements after the date of this release.

SOURCE: Illumina, Inc.

Illumina, Inc.
Peter J. Fromen
Sr. Director, Investor Relations
Wilson Grabill
Sr. Manager, Public Relations

Monday, January 10, 2011

Visit Epicentre at the PAG XIX Conference

Epicentre will be attending the International Plant and Animal Genome (PAG) XIX Conference, to be held from January 15-19 in San Diego, CA. Stop by Booth #331 to learn more about our products for DNA- and RNA-Seq library preparation, and to receive special discounts on a variety of Epicentre products.

In addition, we will be presenting the following posters:
  • Nextera™ Technology for Directional and Nondirectional RNA-Seq Expression Analysis on the Illumina Platform
  • Improved Technologies for Ribosomal RNA Removal and Directional RNA-Seq Library Preparation
  • Enhanced Methods To Capture the Entire Small-RNA Transcriptome for RNA-Seq
We hope to see you at the conference! If you're not attending, and would like more information about the products highlighted at the conference, please contact us by e-mail or call 1 (800) 284-8474 within the US.

Thursday, January 6, 2011

Enhanced mapping of the C. elegans transcriptome through multiple RNA-Seq techniques

In a recent publication, Lamm et al. demonstrated the use of Epicentre’s CircLigase ssDNA Ligase for template generation in high-throughput RNA-Seq applications. The authors used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of Caenorhabditis elegans. The CircLigase method relies on RNA fragmentation, poly(A) tailing, and oligo(dT)-based hybrid capture to generate a cDNA that can be recircularized and PCR-amplified for high-throughput sequencing. The other two methods involved single-strand RNA ligation, and double-stranded cDNA linker ligation.

The authors found that each RNA-Seq approach shows specific limitations and biases, and the use of multiple methods provided a more complete map than was obtained from any single method. They also note the advantages of CircLigase-based and ssRNA-based capture for locating and sequencing the exact 5’ ends of the RNAs, which were extremely difficult to capture using the double-stranded cDNA capture method.

ResearchBlogging.orgLamm, A. et al. (2010). Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome Genome Research DOI: 10.1101/gr.108845.110