Issue 6: February 2010              IN THE NEWS    PUBLICATIONS    RESEARCHER SPOTLIGHT     Enabling Personalized Medicine Ignite Institute acquires 100 SOLiD™ 4 Systems as it partners with Life Technologies to create largest next generation genomic sequencing facility in North America. Advancing Translational Research Life Techologies and the University of Cambridge announced the formation of a collaboration to advance translational research studies in key disease areas such as cancer, diabetes, and neurological disorders. Accelerating Cancer Research Using Life Tachnologies next-generation sequencing products, scientists from the Wellcome Trust Sanger Institute publish an article in the journal Nature, which demonstrates the power of next-generation DNA sequencing used to identify the mutational burden associated with tobacco smoking. Advancing Autism Research University of Miami Miller School of Medicine's John P. Hussman Institute for Human Genomics collaborates with Life Technologies to begin one of the first large-scale sequencing projects of its kind.   U87MG decoded: The genomic sequence of a cytogenically aberrant human cancer cell line. Clark M, Homer N, O'Connor B et al. PLoS Genetics (2010). Archiving next generation sequencing data. Shumway M, Cochrane G, Sugawara H Nucleic Acids Research p1078 (2009). A novel mechanism of epigenetic regulation: Nucleosome-space occupancy. Cui P, Lingfang Z, Qiang L et al. Biochem Biophys Res Commun 391(1):884–889 (2009). Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing. Chen W, Ullman R, Langnick C et al. European Journal of Human Genetics doi:10.1038/ejhg.2009.211 (2009). Maternal plasma DNA analysis with massively parallel sequencing by ligation for noninvasive prenatal diagnosis of Trisomy 21. Chiu R, Sun H, Akolekar R et al. Clinical Chemistry 136507 (2009). ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. Markljung E, Jiang L, Jaffe J et al. PLoS Biol 7(12):e1000256 (2009). Sequencing technologies—the next generation. Metzker ML, Nature Reviews Genetics, doi:10.1038/nrg2626 (2009). A small-cell lung cancer genome with complex signatures of tobacco exposure. Pleasance ED, Stephens PJ, O’Meara S et al. Nature Online 463:184–190 (2009). PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Chen Y, Souaiaia T, Chen T Bioinformatics 25(19):2514–2521 (2009). Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq. Motallebipour M, Ameur A, Bysani MSR et al. Genome Biology 10:R129 (2009). Variation in the large-scale organization of gene expression levels in the hippocampus relates to stable epigenetic variability in behavior. Alter MD, Rubin DB, Ramsey K et al. Bioinformatics 25(19):2615–2616 (2009).   William Farmerie, PhD Associate Director of the Interdisciplinary Center for Biotechnology Research (ICBR) We had the opportunity to talk with Dr. Bill Farmerie, ICBR's Associate Director, about how the Center is using the SOLiD™ System to help researchers find new ways to ask questions and interpret data. Learn more >               Welcome to the February 2010 issue of The SOLID Read, the e-newsletter dedicated to delivering you the latest scientific and technical advances made with the SOLiD™ System. Highlights in this issue include the SOLiD™ 4 and EZ Bead™ Systems, a webinar featuring InteRNA Genomics™, and upcoming events featuring the SOLiD™ System.   PRODUCT UPDATES          SOLiD™ 4 System The SOLiD™ 4 System enables researchers to obtain higher-quality genomes at lower costs. With Life Technologies, researchers experience peace of mind, knowing that they can upgrade without the purchase of a new instrument. Continually pushing technological boundaries, the SOLiD™ 4 System delivers: $6,000 genome with 100 GB of mappable data Increases in accuracy and coverage uniformity Sample prep automation Multiplexing of up to 96 samples to accelerate scientific discovery Learn more about the SOLiD™ System.  SOLiD™ Transcriptome Multiplexing Kit The SOLiD™ Transcriptome Multiplexing Kit enables you to increase the power of your studies by cost-effectively increasing the numbers of samples analyzed. Each of the 16 individual 3' PCR primers contains a unique bar code sequence that generates a bar-coded library, which can be multiplexed in the emulsion PCR. Learn more about the SOLiD™ Transcriptome Multiplexing Kit.  Automate your workflow with the new SOLiD™ EZ Bead™ System The SOLiD™ EZ Bead™ System reduces your hands-on time by 80%, providing an automated solution for reproducible templated bead preparation in less than 1 hour of hands-on time. The system modularity and quality control checkpoints provide greater experimental control. Additional support for multiplexed libraries further maximizes time and cost savings. Contact your Account Manager for more information. Learn more about the SOLiD™ EZ Bead™ System.         SOFTWARE DEVELOPMENT COMMUNITY UPDATES          NEW SOLiD™ Accuracy Enhancement Tool The new SOLiD™ Accuracy Enhancement Tool (SAET) continues the SOLiD™ System's unsurpassed accuracy and throughput by correcting miscalls within reads prior to mapping or contig assembly. Benefits include: Accurate results—SAET has demonstrated significant improvements in mapping and SNP calling and delivers increases in contig lengths in de novo assembly by up to 3 times Unsurpassed performance and scalability—SAET can scale with linear performance on various data sets, including a large spectrum of genome sizes and complexities as well as coverages and read lengths Data reliability—SAET increases the accuracy of the reads up to 5 times without overcorrecting true SNPs Access the SOLiD™ Accuracy Enhancement Tool from the SOLiD™ Software Community site.  New Software Tools GejiGeji—Java software to create and view images for depth or coverage PerM—PerM is a software package designed to perform highly efficient genome-scale alignments for hundreds of millions of short reads produced by the SOLiD™ System Register here to receive updates and new software release announcements.         SOFTWARE PARTNER SPOTLIGHT          You are invited to view the latest Applied Biosystems online seminar, “Profiling of small RNAs with the SOLiD™ System and miR-Intess™ from InteRNA Genomics™," in a continuing series that highlights the wealth of data analysis solutions for the SOLiD™ System platform. View here >         EVENTS          Americas: Ocean Sciences Meeting Feb 22–26, 2010, Portland, OR AGBT Feb 24–27, 2010, Marco Island, FL Aquaculture 2010 International Triennial Meeting of the World Aquaculture Society March 1–5, 2010, San Diego, CA XGen Congress March 15–19, 2010, San Diego, CA CHI Quantitative PCR March 17–19, 2010, San Diego, CA Cancer Vaccine Consortium March 18–20, 2010, Washington, DC ABRF March 20–23, 2010, Sacramento, CA SNP Workshop III March 22–24, 2010, Seattle, WA 2nd International Conference on Bioinformatics and Computational Biology BICoB March 24–26, 2010, Honolulu, HI    Europe: EMEA SOLiD™ System Users Meeting March 9–11, 2010, Antwerp, Belgium Analytica 2010 March 23–26, 2010, Munich, Germany Translational Cancer Medicine 2010 - Europe March 21–24, 2010, Amsterdam, The Netherlands  APAC: Lorne Cancer Conference February 11–13, 2010, Lorne, Australia Lorne Genome Conference February 14–16, 2010, Lorne, Australia         850 Lincoln Centre Drive Foster City, CA 94404 USA www.appliedbiosystems.com FOR RESEARCH USE ONLY. NOT INTENDED FOR ANY ANIMAL OR HUMAN THERAPEUTIC OR DIAGNOSTIC USE, UNLESS OTHERWISE STATED. © 2010 Life Technologies Corporation. All rights reserved. The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners. In compliance with federal regulations, we hereby disclose that this email communication is for commercial purposes. View the Applied Biosystems privacy policy.