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Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF Mags A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS Revolutionize life The Axiom Genotyping Solution — Conquer the next wave of genomic discoveries. Our next-generation genotyping technology allows you to leverage high-value markers from our proprietary data set, public databases, and your scientific collaborations to find new genetic associations. The Axiom™ Genotyping Solution includes array plates with unique genomic content, complete reagent kits, analysis software, and the new GeneTitan™ Instrument for hands-free sample processing. Trust the Axiom Genotyping Solution to provide: Flexible content – optimize your studies with a diverse set of relevant and novel variants Fast results – process more than 750 samples/week—the highest throughput in the industry More power – run more samples within your budget Greater confidence – generate reliable results with end-to-end automated sample processing Conquer the next wave of genomic discoveries: Visit booth #415 or www.axiom.affymetrix.com And attend our seminar: New Microarray Solutions for GWAS and Cytogenetics Wed., Oct. 21, 11:30 A.M.–1:00 P.M., Room 314, Convention Center A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS Contents | Zoom in | Zoom out For navigation instructions please click here Search Issue | Next Page BONUS: TRADITIONAL & DIGITAL GENE EXPRESSION OCTOBER 2009 GEORGE WEINSTOCK, WASHINGTON UNIVERSITY IN ST. LOUIS The Human Microbiome Companion Diagnostics I Gene Expression in the Brain Contents | Zoom in | Zoom out For navigation instructions please click here Search Issue | Next Page A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS New...NimbleGen Human CGH/CNV 3x720K Arrays Catch Copy Number Variants Genome-Wide NimbleGen Human CGH 3x720K Whole-Genome v3.0 Array 35 kb Comprehensively detect CNVs with 720,000 probes per sample and enhanced coverage of low-copy repeat regions of 382 kb Competitor’s 244K array the genome (e.g. segmental duplications). “Normal” CNVs Increase Throughput, Decrease Costs NimbleGen 3x720K arrays enable simultaneous analysis of Segmental Duplications 3 samples on a single slide, providing increased throughput and cost-effective analysis. Known Genes Discover the NimbleGen Difference Analysis of a Complex CNV Region in Chromosome 17 in a Burkitt The proof is in our data. See how NimbleGen Lymphoma Research Sample Referenced against Normal Genomic DNA. An ~382 kb deletion region and an ~35 kb amplification region are Human CGH/CNV 3x720K Arrays easily detected using the NimbleGen Human CGH 3x720K Whole-Genome Tiling v3.0 array and the NimbleGen MS 200 Microarray Scanner at 2 μm compare to your current technology. resolution. The combination of high-density NimbleGen microarrays and the high-resolution scanning of the MS 200 provides sensitivity to comprehensively detect genome-wide CNVs. Catch what you’ve been missing: www.nimblegen.com/cgh3x720k Roche NimbleGen, Inc. Madison, WI USA For life science research only. Not for use in diagnostic procedures. NIMBLEGEN is a trademark of Roche. © 2009 Roche NimbleGen, Inc. All rights reserved. A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS OCTOBER 2009 Contents “We just don’t know that much about our relationship between our human cells and our microbial cells.” Julia Segre, Page 42 Gene PGx Sequencing Expression Companion Humans as Host Diagnostics Take Off Participants are calling the New Tools in Pharma is realizing that it Human Microbiome Project Neuroscience needs to collaborate with a second Human Genome A brain atlas was once on the diagnostic companies to Project. The massive global order of a coffee table book, stratify patients and to make effort aims to get to the known for its large, glossy safer, more effective drugs. bottom of the relationship illustrations. Today’s brain But obstacles remain in the between microorganism and atlases — led largely by the path to full flight. host, and disease and health. Allen Institute for Brain Sci- BY JEANENE SWANSON BY CIARA CURTIN ence — capitalize on localized gene expression and other data to truly revolutionize the field of neuroscience. BY MEREDITH W. SALISBURY 33 38 30 On The Cover 38 The Human Microbiome 33 Companion Diagnostics 30 Gene Expression in the Brain PHOTOGRAPH BY BOB BOSTON FOR GENOME TECHNOLOGY OCTOBER 2009 GENOME TECHNOLOGY 3 A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS _____________________ A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS OCTOBER 2009 Contents 10 20 53 Markers In every issue Upstream NIH .......................................................10 PRIMER .................................................7 PROTEOMICS ................................... 45 Collins steps into new directorship We all have our bugs Grant supports proteomics with goals at the ready; funding synchrotron work stability a priority WHERE ARE THEY NOW? .................9 Kathy Hudson, next-gen SEQUENCING....................................47 NANOMEDICINE................................11 sequencing on the rise, Centers of Complete Genomics raises Jamey Marth to direct new nano Excellence in Genomic Sciences, $45 million in Series D center at UC-Santa Barbara, and more Burnham RNAI.................................................... 49 ZEITGEIST...........................................16 UMass, Whitehead fire new salvo in SEQUENCING.................................... 12 A blog around the world Tuschl IP suit UW group sequences exomes from 12 people, confirms gene for rare CAREERS............................................19 MICROARRAYS................................. 50 disease The journal perspective Affy inks deal with Beckman for custom tools SYNTHETIC GENOMICS. ................ 13 LAB REUNION .................................. 20 Venter Institute team demonstrates ‘A community of scholars’ BIOINFORMATICS ............................ 51 successful cross-species genome Pharma calls for a pre-competitive UNDER ONE ROOF. ......................... 22 approach METHYLATION.................................. 14 A grassroots institute Markowitz, Vogelstein lead development of novel detection MYTAKE............................................. 25 Downstream technique Project annotation PGX ..................................................... 52 STRUCTURAL VARIATION.............. 14 BRUTE FORCE...................................27 Celera hones panel for non-small New BreakDancer algorithm Personal supercomputers? cell lung cancer performs high-res mapping of Q&A..................................................... 53 indels, more UPCOMING EVENTS....................... 56 Innovation through imaging BLUNT END....................................... 58 PCR ...................................................... 15 CASE STUDY..................................... 55 CDC evaluates rapid flu tests versus The peptide blockade rRT-PCR for detecting novel strain of H1N1 influenza OCTOBER 2009 GENOME TECHNOLOGY 5 A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS ___________________ _____________ A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS A Genome Technology Previous Page | Contents | Zoom in | Zoom out | Front Cover | Search Issue | Next Page BEF MaGS FROM THE EDITOR Primer ISSUE NO. 95 125 Maiden Lane, Second Floor New York, NY 10038 We All Have Our Bugs Tel +1 212 269 4747 Fax +1 212 269 3686 ____________GENOMEWEB.COM t was several years ago that I first heard about a major study of EDITORIAL DIRECTOR the human microbiome — it was from Washington University’s Meredith W. Salisbury [email protected]_______________ Jeff Gordon, presenting at a Marco Island conference some of SENIOR EDITOR the earliest genomics-based research into the microbial content Ciara Curtin [email protected]_____________ SENIOR WRITERS of our bodies. At the time, many attendees were surprised to Matthew Dublin [email protected] Ihear that microbial cells outnumber human cells 10 to one in the Jeanene Swanson [email protected]______________ ART DIRECTOR average human. Rarely have so many scientists been sent scrambling Therese Shechter [email protected]_______________ for hand sanitizer — but, it seems, they also scrambled to participate GENOMEWEB DAILY NEWS in the nascent microbiome field. Ed Winnick, Editorial Director [email protected]______________ By 2007, NHGRI launched its large-scale Human Microbiome Matt Jones,
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