Hot off the presses! Jan 01 Nat Biotech

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Latest Articles Include:

• Similarity trials
  - Nat Biotech 29(1):1 (2011)
  Nature Biotechnology | Editorial Similarity trials Journal name:Nature BiotechnologyVolume: 29,Page:1Year published:(2011)DOI:doi:10.1038/nbt.1760Published online10 January 2011 A European guideline on biosimilar monoclonal antibodies suggests smaller trials with homogeneous, younger patient groups may suffice for marketing authorization. View full text Additional data
• Pfizer reaches out to academia—again
  - Nat Biotech 29(1):3-4 (2011)
  Nature Biotechnology | News Pfizer reaches out to academia—again * Mark Ratner1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Pages:3–4Year published:(2011)DOI:doi:10.1038/nbt0111-3Published online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Pfizer's first Center for Therapeutic Innovation will sit on UCSF's Mission Bay campus (pictured), already home to several dozen biotech start-ups and an incubator network. Pfizer is rolling out a grand plan to draw out drug-development-ready research from academia through a series of collaborations with leading medical centers worldwide. The first collaboration, announced in November, is with the University of California, San Francisco (UCSF), to which the pharma giant will commit $85 million. Coincidentally, London-based GlaxoSmithKline, is launching a similar outreach program, but with a very different approach. Like Pfizer, it wants to access leading academic researchers with targets ripe for translation into the clinic. Its scope, however, is more modest and targeted, focused on individual scientists. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * Cambridge, Massachusetts * Mark Ratner
• Amgen's bone-metastasis win
  - Nat Biotech 29(1):4 (2011)
  Nature Biotechnology | News Amgen's bone-metastasis win * Suzanne Elvidge Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:4Year published:(2011)DOI:doi:10.1038/nbt0111-4Published online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Amgen Xgeva for mets View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Junior and Senior Scientists * Medical University of South Carolina * Charleston, SC * Post a free job * More science jobs Related content Articles * Bone health and prostate cancer Prostate Cancer and Prostatic Diseases 10 Nov 2009 * The effect of novel anti-myeloma agents on bone metabolism of patients with multiple myeloma Leukemia 05 Jul 2007 * Therapy Insight: the risks and benefits of bisphosphonates for the treatment of tumor-induced bone disease Nature Clinical Practice Oncology 01 Jan 2007 * Treatment strategies for bone disease Bone Marrow Transplantation 06 Aug 2007 * Metastasis: Metastasis to bone: causes, consequences and therapeutic opportunities Nature Reviews Cancer 01 Aug 2002 View all Open innovation challenges * Thresholds for Perception of Color Differences Deadline:Jan 17 2011Reward:$10,000 USD Physical appearance (color) is a critical attribute for pharmaceutical product quality. While color… * Statistical Analysis of Genomic Variants Deadline:Feb 01 2011Reward:$25,000 USD The Seeker is searching for the best method of associating genetic variants and clinical variables w… * Powered by: * More challenges Top content Emailed * Whole-genome molecular haplotyping of single cells Nature Biotechnology 19 Dec 2010 * Large-scale in silico modeling of metabolic interactions between cell types in the human brain Nature Biotechnology 21 Nov 2010 * Genomics tools for unraveling chromosome architecture Nature Biotechnology 13 Oct 2010 * Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry Nature Biotechnology 01 Feb 2002 * Spatially addressed combinatorial protein libraries for recombinant antibody discovery and optimization Nature Biotechnology 24 Oct 2010 View all Downloaded * Antibody-based nanoprobe for measurement of a fluorescent analyte in a single cell Nature Biotechnology 01 Jul 2000 * Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips Nature Biotechnology 28 Nov 2010 * Whole-genome molecular haplotyping of single cells Nature Biotechnology 19 Dec 2010 * Haplotype-resolved genome sequencing of a Gujarati Indian individual Nature Biotechnology 19 Dec 2010 * A TALE nuclease architecture for efficient genome editing Nature Biotechnology 22 Dec 2010 View all Blogged * Risk assessment of meat and milk from cloned animals Nature Biotechnology 08 Jan 2007 View all * Nature Biotechnology * ISSN: 1087-0156 * EISSN: 1546-1696 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Boehringer splashes out on bispecific antibody platforms
  - Nat Biotech 29(1):5-6 (2011)
  Nature Biotechnology | News Boehringer splashes out on bispecific antibody platforms * Nuala Moran1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Pages:5–6Year published:(2011)DOI:doi:10.1038/nbt0111-5Published online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. A $2.2 billion deal in October between Macrogenics and Boehringer Ingelheim, followed the next month by another eye-catching $1.7-billion research collaboration between f-star and the German pharma are the latest in a string of blockbuster transactions in which big pharma has accessed exotic antibody platforms. The pharmaceutical industry, which has long since embraced traditional monoclonal antibody (mAb) therapies, is now looking to the next generation of therapeutics—conjugates, fragments or other derivatives (Fig. 1). Over the course of 2010, a raft of collaborations has put the wind into platform-companies' sails. But as the flow of investment into new technologies continues unabated, questions arise over how much value each antibody-modifying technology can add. Figure 1: A cornucopia of different antibody fragments are currently in development. (Adapted from Nat. Biotechnol., 1126–1136, 2005.) View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * London * Nuala Moran * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Junior and Senior Scientists * Medical University of South Carolina * Charleston, SC * Post a free job * More science jobs Related content Articles * Generation of chimeric bispecific G250/anti-CD3 monoclonal antibody, a tool to combat renal cell carcinoma British Journal of Cancer 01 Sep 1996 * Therapeutic antibodies for autoimmunity and inflammation Nature Reviews Immunology 01 May 2010 * A bispecific monoclonal antibody against methotrexate and a human tumour associated antigen augments cytotoxicity of methotrexate-carrier conjugate British Journal of Cancer 01 Apr 1990 * Therapeutic IgG4 antibodies engage in Fab-arm exchange with endogenous human IgG4 in vivo Nature Biotechnology 20 Jul 2009 * Novel antibodies as anticancer agents Oncogene 28 May 2007 View all Open innovation challenges * Statistical Analysis of Genomic Variants Deadline:Feb 01 2011Reward:$25,000 USD The Seeker is searching for the best method of associating genetic variants and clinical variables w… * Low-Volume Liquid Dispersion Mechanism Deadline:Feb 20 2011Reward:$25,000 USD The Seeker is looking for mechanisms to enable dispersion of a fluid sample of 40 nanoliters (nl) ov… * Powered by: * More challenges Top content Emailed * Whole-genome molecular haplotyping of single cells Nature Biotechnology 19 Dec 2010 * Large-scale in silico modeling of metabolic interactions between cell types in the human brain Nature Biotechnology 21 Nov 2010 * Genomics tools for unraveling chromosome architecture Nature Biotechnology 13 Oct 2010 * Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry Nature Biotechnology 01 Feb 2002 * Spatially addressed combinatorial protein libraries for recombinant antibody discovery and optimization Nature Biotechnology 24 Oct 2010 View all Downloaded * Antibody-based nanoprobe for measurement of a fluorescent analyte in a single cell Nature Biotechnology 01 Jul 2000 * Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips Nature Biotechnology 28 Nov 2010 * Whole-genome molecular haplotyping of single cells Nature Biotechnology 19 Dec 2010 * Haplotype-resolved genome sequencing of a Gujarati Indian individual Nature Biotechnology 19 Dec 2010 * A TALE nuclease architecture for efficient genome editing Nature Biotechnology 22 Dec 2010 View all Blogged * Risk assessment of meat and milk from cloned animals Nature Biotechnology 08 Jan 2007 View all * Nature Biotechnology * ISSN: 1087-0156 * EISSN: 1546-1696 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Biogen Idec restructures, sharpens neurology focus
  - Nat Biotech 29(1):7-8 (2011)
  Nature Biotechnology | News Biogen Idec restructures, sharpens neurology focus * Peter Mitchell1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Pages:7–8Year published:(2011)DOI:doi:10.1038/nbt0111-7Published online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Bloomberg via Getty Images George Scangos, Biogen Idec's new chief executive. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * London * Peter Mitchell * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Junior and Senior Scientists * Medical University of South Carolina * Charleston, SC * Post a free job * More science jobs Related content Articles * Biogen Idec goes on the auction block Nature Biotechnology 01 Dec 2007 * PML problems loom for Rituxan Nature Biotechnology 01 Feb 2010 * What's fueling the biotech engine—2007 Nature Biotechnology 01 Nov 2008 * Abbott outbids Biogen for Facet's multiple sclerosis antibody Nature Biotechnology 01 May 2010 * Lymphoma Mabs rivalry continues Nature Biotechnology 01 Nov 1998 View all Open innovation challenges * Chordoma Cancer Cell Lines Needed to Save Lives! Deadline:Mar 13 2011Reward:$10,000 USD The Chordoma Foundation requests cell lines or animal models that can be used for research into chor… * Low-Volume Liquid Dispersion Mechanism Deadline:Feb 20 2011Reward:$25,000 USD The Seeker is looking for mechanisms to enable dispersion of a fluid sample of 40 nanoliters (nl) ov… * Powered by: * More challenges Top content Emailed * Whole-genome molecular haplotyping of single cells Nature Biotechnology 19 Dec 2010 * Large-scale in silico modeling of metabolic interactions between cell types in the human brain Nature Biotechnology 21 Nov 2010 * Genomics tools for unraveling chromosome architecture Nature Biotechnology 13 Oct 2010 * Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry Nature Biotechnology 01 Feb 2002 * Spatially addressed combinatorial protein libraries for recombinant antibody discovery and optimization Nature Biotechnology 24 Oct 2010 View all Downloaded * Antibody-based nanoprobe for measurement of a fluorescent analyte in a single cell Nature Biotechnology 01 Jul 2000 * Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips Nature Biotechnology 28 Nov 2010 * Whole-genome molecular haplotyping of single cells Nature Biotechnology 19 Dec 2010 * Haplotype-resolved genome sequencing of a Gujarati Indian individual Nature Biotechnology 19 Dec 2010 * A TALE nuclease architecture for efficient genome editing Nature Biotechnology 22 Dec 2010 View all Blogged * Risk assessment of meat and milk from cloned animals Nature Biotechnology 08 Jan 2007 View all * Nature Biotechnology * ISSN: 1087-0156 * EISSN: 1546-1696 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Roche cuts Genentech jobs
  - Nat Biotech 29(1):8 (2011)
  Nature Biotechnology | News Roche cuts Genentech jobs * Laura DeFrancesco Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:8Year published:(2011)DOI:doi:10.1038/nbt0111-8aPublished online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. In November, Roche revealed sweeping cuts in its workforce as part of its so-called Operational Excellence Program to reduce costs. Over 4,800 people, 6% of its workforce, will lose their jobs and another 700 will be affected by outsourcing, all of which will save the Basel-based company an estimated CHF2.4 ($2.43) billion annually. But the news isn't all bad. Only 600 of the job cuts are in R&D, with most jobs losses in sales and manufacturing, and none at the US flagship Genentech, according to Robin Snyder spokesperson for the S. San Francisco–based biotech. The cuts in R&D include shuttering RNA interference programs in Kulmbach, Germany; Nutley, New Jersey; and Madison, Wisconsin. And there may be a silver lining to these moves, as projects cast off by Roche may create opportunities for startups that could revitalize the Swiss biotech industry. Indeed Basel-based biotechs Actelion and Basilea were set up to develop programs axed by Roche. In California, somewhat ironi! cally, the reshuffling, which will cause the loss of over 800 local manufacturing jobs, was announced two weeks after the election in which a state-wide proposition rescinding corporate tax credits was defeated. Opponents of the measure, which included Genentech, the biggest contributor to the 'no' campaign, with over $1.6 million in donations, argued that rescinding the tax credits would result in job losses. Snyder claims that the timing of the announcement of cuts in the California workforce was unrelated to the election. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Company Bridge Awards
  - Nat Biotech 29(1):8 (2011)
  Nature Biotechnology | News Company Bridge Awards * Nidhi Subbaraman Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:8Year published:(2011)DOI:doi:10.1038/nbt0111-8bPublished online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. The National Cancer Institute has awarded $9.9 million to four companies developing diagnostics for cancer therapies. The new Small Business Innovation Research (SBIR) Phase II Bridge Awards are designed to support previously funded companies to develop and commercialize their products further (Nat. Biotechnol27, 678, 2009). Phase II recipients are Advanced Cell Diagnostics, 20/20 GeneSystems, AmberGen and Praevium Research; each company receives up to $3 million over three years. Advanced Cell Diagnostics of Hayward, California, is developing a CTCscope system to assess molecular profiles in circulating tumor cells (CTCs) that have the potential to metastasize in other parts of the body. 20/20 GeneSystems of Rockville, Maryland, is focusing on 'PredicTOR' as a companion diagnostic for therapies targeting the mTOR pathway. AmberGen, of Watertown, Massachusetts, will advance a gene expression–based test to predict colorectal cancer recurrence, and its response to treatment.! Praevium Research of Santa Barbara, California, received funding for a miniaturized optoelectronic device, which could allow clinicians to image cancer tissue in real time, without the need for tissue excision and biopsies. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Science snipes at Oxitec transgenic-mosquito trial
  - Nat Biotech 29(1):9-11 (2011)
  Nature Biotechnology | News Science snipes at Oxitec transgenic-mosquito trial * Nidhi Subbaraman1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Pages:9–11Year published:(2011)DOI:doi:10.1038/nbt0111-9aPublished online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Oxitec released 3.3 milion sterile male transgenic Aedes aegypti mosquitoes in a field trial aimed at reducing wild mosquito populations to control dengue. Early in November, at the annual meeting of the American Society of Tropical Medicine and Hygiene (ASTMH) in Atlanta, researchers from the British company Oxitec disclosed results from the world's first genetically modified (GM) mosquito field trials aimed at controlling the carrier for dengue fever. After the presentation at the meeting, Science (, 1030–1031, 2010) published a news story claiming the trials had "strained ties" with Oxitec's collaborator, the Bill and Melinda Gates Foundation. Anthony James, the lead investigator on the Gates team, was also quoted as saying he would "never release GM mosquitoes the way Oxitec has now done in Grand Cayman." Although some concerns have been raised as to how information about the trial was disseminated, it seems that controversy over the environmental release of a GM organism has been overblown. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * New York * Nidhi Subbaraman
• Temporary ban on clones
  - Nat Biotech 29(1):9 (2011)
  Nature Biotechnology | News Temporary ban on clones * Anna Meldolesi Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:9Year published:(2011)DOI:doi:10.1038/nbt0111-9bPublished online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Food from cloned animals is under fire in Europe with the European Commission (EC) calling in October for a temporary commercial suspension. John Dalli, European commissioner for health and consumer policy, describes the proposal as "a realistic and feasible solution to respond to the present welfare concerns." A formal proposal for a five-year ban on the technology will be presented in the first half of 2011. Although sweeping, the proposed exclusion may not carry much weight in practice, because farmers mostly use cloning technology for their prized breeding stock, not to raise animals for food. EU breeders would be forbidden under the proposed ban to clone their best head of cattle in member states. Cloned embryos and semen of clones, however, could still be imported following a proposed traceability scheme. The offspring of clones, sired conventionally, would not be bound by these restrictions, EC spokesperson Frédéric Vincent points out, and consequently their mea! t and milk would not be banned. This decision avoids unleashing trade wars with the US but is likely to be opposed by the European Parliament. A public outcry followed a document release in August by the British Food Standards Agency that three bulls descending from embryos cloned in the US from an undisclosed company entered the food chain in the UK and Belgium. According to Vincent these occurrences are legal under current regulations, but probably uncommon. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Filipinos back GM eggplant
  - Nat Biotech 29(1):9 (2011)
  Nature Biotechnology | News Filipinos back GM eggplant * Nidhi Subbaraman Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:9Year published:(2011)DOI:doi:10.1038/nbt0111-9cPublished online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Filipino farmers clamoring for the adoption of genetically modified (GM) eggplants in October passed a resolution to support multi-location field trials of the biotech crop. GM crop farmers and agriculture representatives from across the country endorsed a set of resolutions to support the advancement of biotech crops in the country including the pest-resistant eggplant. "When we consulted them, [farmers] asked, 'Are the seeds available already? Why is it taking so long?'" says Reynaldo Cabanao, president of the Asian Farmers Regional Network (ASFARNET). The GM eggplant was developed by the Agricultural Biotechnology Support Project II (ABSPII), a global public-private collaboration based at Cornell University in Ithaca, New York. It was engineered with the Cry1Ac gene from the bacterium Bacillus thuringiensis (Bt) to fend off the fruit and shoot borer, which can destroy up to 50% of the region's number-one food crop. Farmers who have witnessed the success of Bt corn are! eager for Bt eggplant to be available, says Desiree Hautea, ABSPII coordinator for South East Asia, at the University of the Philippines, Los Baños. The GM eggplant is currently undergoing confined field tests adhering to biosafety regulations set by the Philippines Department of Agriculture, Bureau of Plant Industry. Multiple-site trials will follow, though commercialization plans remain undefined. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• European R&D buoyant
  - Nat Biotech 29(1):10 (2011)
  Nature Biotechnology | News European R&D buoyant * Emma Dorey Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:10Year published:(2011)DOI:doi:10.1038/nbt0111-10aPublished online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. The economic downturn had less effect than expected on biopharma companies in Europe, according to the newly released EU Industrial R&D investment Scorecard published by the European Commission. The report, which included data on industrial research spending for fiscal year 2009, ranked 400 EU-based companies and 1,000 firms based elsewhere. Many cash-strapped firms scaled back research in 2009, with R&D investments across all sectors worldwide down 1.9%. The biopharma group, however, consolidated its position as top R&D investor, with a 5.3% increase in 2008 in global R&D spending and a 2% hike in Europe alone. Swiss drug giant Roche of Basel ranked second among all sectors for R&D investment. John Shortmoor, pharma analyst at Datamonitor, is not surprised at the findings. "To sustain a presence—especially in a time when a significant number of marketed products are losing patent protection—requires constant product innovation and continued R&D investment." For biot! ech in particular, European firms increased their investment budget by 7.9% in 2009, outperforming their US counterparts, whose R&D spending dropped by 1.6%. "We cannot afford not to invest in R&D and risk losing our market position," says Nickie Inger Spile, vice president at Danish biotech Novozymes. The Bagsvaerd-based firm ranked number 10 for R&D spending among global biotechs. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• EU mAb biosimilars path
  - Nat Biotech 29(1):10 (2011)
  Nature Biotechnology | News EU mAb biosimilars path * Gunjan Sinha Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:10Year published:(2011)DOI:doi:10.1038/nbt0111-10bPublished online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. European regulators laid out the rules for copying biotech's blockbuster monoclonal antibody (mAb) therapies, paving the way for biosimilars developers to access the $36.4 billion market. The draft guidelines, published by the European Medicines Agency (EMA) in November, outline the process biosimilars developers must follow to gain approval for a mAb once a patent on the pioneer drug has expired. The studies and tests needed for approval are "less demanding than expected," comments Huub Schellekens at the departments of Pharmaceutical Sciences and Innovation Studies at Utrecht University, The Netherlands. The EMA will require in vitro pharmacokinetic and phamacodynamic studies to demonstrate that a biosimilar mAb is functionally equivalent to a reference mAb. In some cases, in vivo nonclinical studies may also be necessary. "The need for these studies should be decided on a case-by case basis," the guideline states. Factors that may warrant the need for such studies! are, for instance, processing and formulation differences or insufficient evidence that a biosimilar is as safe and effective as the branded product. The EMA is willing to accept a drug's adverse event profile as proof of biosimilarity, and data from one clinical trial could be sufficient for approval in two different indications if the mechanism of action is the same. "This really opens the door [to biosimilars]," Schellekens points out. The guideline is available for public comment until May 31. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Vatican panel backs GMOs
  - Nat Biotech 29(1):11 (2011)
  Nature Biotechnology | News Vatican panel backs GMOs * Anna Meldolesi1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:11Year published:(2011)DOI:doi:10.1038/nbt0111-11Published online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. The Vatican's Pontifical Academy of Sciences, headquartered at Casina Pio IV shown here, holds a membership roster of the most respected names in 20th century science. A panel of scientists convened by the Pontifical Academy of Sciences (PAS) has made a passionate endorsement of genetically modified organisms (GMOs) for global food security and development. The statement, published in 16 languages in the 30 November issue of the journal New Biotechnology (http://www.ask-force.org/web/Vatican-PAS-Statement-FPT-PDF/PAS-Statement-English-FPT.pdf) is the result of a workshop held in the Vatican in May 2009, involving 7 members of the PAS and 33 outside experts. It states that "there is a moral imperative" to make the benefits of genetic engineering technology "available on a larger scale to poor and vulnerable populations who want them," urging opponents to consider the harm that withholding this technology will inflict on those who need it most. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * Rome * Anna Meldolesi
• Newsmaker: Biocentury Transgene
  - Nat Biotech 29(1):12 (2011)
  Nature Biotechnology | News Newsmaker: Biocentury Transgene * Hepeng Jia1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:12Year published:(2011)DOI:doi:10.1038/nbt0111-12Published online10 January 2011 Biocentury Transgene is not only going head-to-head against Monsanto in China; it's also poised to conquer markets in developing countries. View full text Additional data Affiliations * Beijing * Hepeng Jia
• Can cancer clinical trials be fixed?
  - Nat Biotech 29(1):13-15 (2011)
  Nature Biotechnology | News | News Feature Can cancer clinical trials be fixed? * Malorye Allison1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Pages:13–15Year published:(2011)DOI:doi:10.1038/nbt.1746Published online10 January 2011 As oncology drug after oncology drug fails to achieve accelerated approval, sponsors are seeking other ways to speed trials. Malorye Allison investigates. View full text Additional data Affiliations * Acton, Massachusetts * Malorye Allison
• Breaking the mold
  - Nat Biotech 29(1):16-18 (2011)
  Nature Biotechnology | News | News Feature Breaking the mold * Daniel Grushkin1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Pages:16–18Year published:(2011)DOI:doi:10.1038/nbt.1744Published online10 January 2011 With the construction of two new manufacturing plants, the bioplastics market emerges. Daniel Grushkin reports. View full text Additional data Affiliations * Brooklyn, New York * Daniel Grushkin
• Battling infringement
  - Nat Biotech 29(1):19-21 (2011)
  
• Essential information for synthetic DNA sequences
  - Nat Biotech 29(1):22 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence Essential information for synthetic DNA sequences * Jean Peccoud1 Contact Jean Peccoud Search for this author in: * NPG journals * PubMed * Google Scholar * J Christopher Anderson2 Search for this author in: * NPG journals * PubMed * Google Scholar * Deepak Chandran3 Search for this author in: * NPG journals * PubMed * Google Scholar * Douglas Densmore4 Search for this author in: * NPG journals * PubMed * Google Scholar * Michal Galdzicki5 Search for this author in: * NPG journals * PubMed * Google Scholar * Matthew W Lux1 Search for this author in: * NPG journals * PubMed * Google Scholar * Cesar A Rodriguez6 Search for this author in: * NPG journals * PubMed * Google Scholar * Guy-Bart Stan7 Search for this author in: * NPG journals * PubMed * Google Scholar * Herbert M Sauro3 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Page:22Year published:(2011)DOI:doi:10.1038/nbt.1753Published online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. To the Editor: Following a discussion by the workgroup for Data Standards in Synthetic Biology, which met in June 2010 during the Second Workshop on Biodesign Automation in Anaheim, California, we wish to highlight a problem relating to the reproducibility of the synthetic biology literature. In particular, we have noted the very small number of articles reporting synthetic gene networks that disclose the complete sequence of all the constructs they describe. View full text Accession codes * Accession codes * Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Referenced accessions Entrez Nucleotide * CP002027 Author information * Accession codes * Author information Affiliations * Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA. * Jean Peccoud & * Matthew W Lux * Department of Bioengineering, QB3: California Institute for Quantitative Biological Research, University of California, Berkeley, California, USA. * J Christopher Anderson * Department of Bioengineering, University of Washington, Seattle, Washington, USA. * Deepak Chandran & * Herbert M Sauro * Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, USA. * Douglas Densmore * Biomedical and Health Informatics, University of Washington, Seattle, Washington, USA. * Michal Galdzicki * BIOFAB, Emeryville, California, USA. * Cesar A Rodriguez * Department of Bioengineering and Centre for Synthetic Biology and Innovation, Imperial College London, London, UK. * Guy-Bart Stan Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Jean Peccoud Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Reply to Essential information for synthetic DNA sequences
  - Nat Biotech 29(1):22-23 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence Reply to Essential information for synthetic DNA sequences Journal name:Nature BiotechnologyVolume: 29,Pages:22–23Year published:(2011)DOI:doi:10.1038/nbt0111-22bPublished online10 January 2011Updated online10 January 2010 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Nature Biotechnology replies: Kemmer et al.1 have now lodged the sequences of the constructs used in their paper with GenBank HQ644133, HQ644134, HQ644135, HQ644136 and HQ644137. Nature Biotechnology and other Nature research journals currently require disclosure only of the sequences of genomes, deep sequencing and short-read data, short stretches of novel sequence information (e.g., epitopes, functional domains, genetic markers or haplotypes) and their surrounding sequence information as well as any RNA interference, antisense or morpholino probes used in a paper (http://www.nature.com/authors/editorial_policies/availability.html); there is no consensus as yet that the sequence of every plasmid used in every paper should be lodged with GenBank or that such a policy would be beneficial to the wider community. Even so, as Peccoud et al. point out, full sequence information is often essential to reproduce the findings reported in papers in the area of synthetic biology. As such, on a case-by-case basis, N! ature Biotechnology will encourage authors of such papers to lodge the sequences of the constructs used in a paper in GenBank together with the corresponding accession numbers. View full text Accession codes * Accession codes * Change history Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Referenced accessions GenBank * HQ644133 * HQ644134 * HQ644135 * HQ644136 * HQ644137 Change history * Accession codes * Change historyUpdated online 10 January 2010Editor's Note: Because of a delay at Genbank, the accession numbers printed in this correspondence are not yet live. Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Is transgenic maize what Mexico really needs?
  - Nat Biotech 29(1):23-24 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence Is transgenic maize what Mexico really needs? * Francisca Acevedo1 Contact Francisca Acevedo Search for this author in: * NPG journals * PubMed * Google Scholar * Elleli Huerta1 Search for this author in: * NPG journals * PubMed * Google Scholar * Caroline Burgeff1 Search for this author in: * NPG journals * PubMed * Google Scholar * Patricia Koleff1 Search for this author in: * NPG journals * PubMed * Google Scholar * José Sarukhán1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:23–24Year published:(2011)DOI:doi:10.1038/nbt.1752Published online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. To the Editor: In the past three years, substantial progress has been made in updating knowledge on the present diversity of maize landraces and where these are still being grown within the Mexican territory. Here, we summarize some of these findings and briefly discuss their implications in relation to maize production and use in Mexico. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, México D.F., México. * Francisca Acevedo, * Elleli Huerta, * Caroline Burgeff, * Patricia Koleff & * José Sarukhán Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Francisca Acevedo Disclaimer The manuscript reflects only the opinion of the authors and not the institution they represent. Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Integrative genomics viewer
  - Nat Biotech 29(1):24-26 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence Integrative genomics viewer * James T Robinson1 Contact James T Robinson Search for this author in: * NPG journals * PubMed * Google Scholar * Helga Thorvaldsdóttir1 Search for this author in: * NPG journals * PubMed * Google Scholar * Wendy Winckler1 Search for this author in: * NPG journals * PubMed * Google Scholar * Mitchell Guttman1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Eric S Lander1, 2, 3 Search for this author in: * NPG journals * PubMed * Google Scholar * Gad Getz1 Search for this author in: * NPG journals * PubMed * Google Scholar * Jill P Mesirov1 Contact Jill P Mesirov Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:24–26Year published:(2011)DOI:doi:10.1038/nbt.1754Published online10 January 2011 To the Editor: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools. View full text Figures at a glance * Figure 1: Copy number, expression and mutation data grouped by tumor subtype. This figure illustrates an integrated, multi-modal view of 202 glioblastoma multiforme samples from The Cancer Genome Atlas (TCGA). Copy number data are segmented values from Affymetrix (Santa Clara, CA, USA) SNP6.0 arrays. Expression data are limited to genes represented on all TCGA-employed platforms and displayed across the entire gene locus. Red shading indicates relative upregulation of a gene and the degree of copy gain of a region; blue shading indicates relative downregulation and copy loss. Small black squares indicate the position of point missense mutations. Samples are grouped by tumor subtype (2nd annotation column) and data type (1st sample annotation column) and sorted by copy number of the EGFR locus. Linking by sample attributes ensures that the order of sample tracks is consistent across data types within their respective tumor subtypes. * Figure 2: View of aligned reads at 20-kb resolution. Coverage plot and alignments from paired-end reads for a matched tumor/normal pair. Sequencing was performed on an Illumina (San Diego, CA) GA2 platform and aligned with Maq (http://maq.sourceforge.net/). Alignments are represented as gray polygons with reads mismatching the reference indicated by color. Loci with a large percentage of mismatches relative to the reference are flagged in the coverage plot as color-coded bars. Alignments with unexpected inferred insert sizes are indicated by color. There is evidence for a ~10-kb deletion (removing two exons of AIDA) in the tumor sample not present in the normal. Author information * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. * James T Robinson, * Helga Thorvaldsdóttir, * Wendy Winckler, * Mitchell Guttman, * Eric S Lander, * Gad Getz & * Jill P Mesirov * Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. * Mitchell Guttman & * Eric S Lander * Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. * Eric S Lander Competing financial interests The authors declare no competing financial interests. Corresponding authors Correspondence to: * Jill P Mesirov or * James T Robinson Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (8.5M) Supplementary Figs. 1–9, Supplementary Table 1 and Supplementary Notes Additional data
• The problems with today's pharmaceutical business—an outsider's view
  - Nat Biotech 29(1):27-33 (2011)
  Nature Biotechnology | Opinion and Comment | Commentary The problems with today's pharmaceutical business—an outsider's view * Mark Kessel1 Contact Mark Kessel Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Pages:27–33Year published:(2011)DOI:doi:10.1038/nbt.1748Published online10 January 2011 The pharmaceutical industry must devote greater resources, investment and effort to address its anemic drug pipeline in the long term, rather than focusing on its bottom line in the near term. View full text Figures at a glance * Figure 1: The number of big pharma deals with biotech have fallen in all stages. Source: Burrill & Co. (San Francisco); 2010 year to date (YTD) is through September 30. * Figure 2: The number and value of biotech acquisitions by pharma have fallen. Source: Burrill; 2010 year to date (YTD) is through September 30. * Figure 3: Licensing volumes and payments are declining as big pharma shifts priorities. Source: Burrill & Co.; 2010 year to date (YTD) is through September 30. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Mark Kessel is partner at Symphony Capital, New York, New York, USA. Competing financial interests The author declares no competing financial interests. Corresponding author Correspondence to: * Mark Kessel Additional data
• Patent term extensions for biologic innovators in Japan
  - Nat Biotech 29(1):34-37 (2011)
  Nature Biotechnology | Feature | Patents Patent term extensions for biologic innovators in Japan * John A Tessensohn1 Contact John A Tessensohn Search for this author in: * NPG journals * PubMed * Google Scholar * Shusaku Yamamoto1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:34–37Year published:(2011)DOI:doi:10.1038/nbt.1743Published online10 January 2011 The Japanese Intellectual Property High Court recently issued two decisions that bolster the market exclusivity period for brand biologic manufacturers. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * John A. Tessensohn & Shusaku Yamamoto are at Shusaku Yamamoto Patents, Chuo-Ku, Osaka, Japan. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * John A Tessensohn Additional data
• The next phase in human genetics
  - Nat Biotech 29(1):38-39 (2011)
  Nature Biotechnology | News and Views The next phase in human genetics * Vikas Bansal1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Ryan Tewhey2 Search for this author in: * NPG journals * PubMed * Google Scholar * Eric J Topol1, 2, 3 Search for this author in: * NPG journals * PubMed * Google Scholar * Nicholas J Schork1, 2, 3 Contact Nicholas J Schork Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:38–39Year published:(2011)DOI:doi:10.1038/nbt.1757Published online10 January 2011 Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Experimental haplotyping of whole genomes is now feasible, enabling new studies aimed at linking sequence variation to human phenotypes and disease susceptibility. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Vikas Bansal, Eric J. Topol & Nicholas J. Schork are at Scripps Health, La Jolla, California, USA. * Vikas Bansal, Ryan Tewhey, Eric J. Topol & Nicholas J. Schork are at The Scripps Translational Science Institute, La Jolla, California, USA. * Eric J. Topol & Nicholas J. Schork are in The Department of Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Nicholas J Schork Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Crafting rat genomes with zinc fingers
  - Nat Biotech 29(1):39-41 (2011)
  Nature Biotechnology | News and Views Crafting rat genomes with zinc fingers * Meng Amy Li1 Search for this author in: * NPG journals * PubMed * Google Scholar * Allan Bradley1 Contact Allan Bradley Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:39–41Year published:(2011)DOI:doi:10.1038/nbt.1749Published online10 January 2011 Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Expressing zinc-finger nucleases in zygotes enables targeted transgene integration in the mouse and rat genomes. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Meng Amy Li & Allan Bradley are at Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Allan Bradley Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Out of harm's way
  - Nat Biotech 29(1):41-42 (2011)
  Nature Biotechnology | News and Views Out of harm's way * David A Williams1 Contact David A Williams Search for this author in: * NPG journals * PubMed * Google Scholar * Adrian J Thrasher2 Contact Adrian J Thrasher Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:41–42Year published:(2011)DOI:doi:10.1038/nbt.1750Published online10 January 2011 Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Screening for safe harbor sites in the genome may improve the safety of gene therapy. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * David A. Williams is at Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. * Adrian J. Thrasher is at the Centre for Immunodeficiency, Molecular Immunology Unit, Institute of Child Health, London, UK. Competing financial interests The authors declare no competing financial interests. Corresponding authors Correspondence to: * David A Williams or * Adrian J Thrasher Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Research highlights
  - Nat Biotech 29(1):43 (2011)
  Nature Biotechnology | Research Highlights Research highlights Journal name:Nature BiotechnologyVolume: 29,Page:43Year published:(2011)DOI:doi:10.1038/nbt.1761Published online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Aptamer-based proteomics arrays Progress in the use of high-throughput proteomic analysis for biomarker discovery and diagnostics has been stymied by the challenge of quantifying tens of thousands of proteins whose abundance spans approximately twelve orders of magnitude. The use of mass spectrometry still poses technical difficulties and the inherent cross-reactivity of antibodies has limited the utility of antibody arrays. Gold et al. couple the use of slow off-rate modified aptamers (SOMAmers)—oligonucleotides containing functionalities that mimic amino acid side chains to enhance their specificity for targets—with the robustness of nucleotide arrays to provide an assay that can measure >800 human proteins in ~15 μl of human blood with low limits of detection (1 pM median) over a dynamic range from ~100 fM to 1 μM. First, proteins to be assayed (pink) bind tightly to their cognate SOMAmer, which is modified with biotin (B) and a fluorescent label (L), and bound protein-SOMAmer complexes are trappe! d on beads coated with streptavidin (SA). Then, as depicted, unbound proteins are washed away, and biotin-tagged bound proteins are released by exposure to UV light (hν). After a subsequent recovery step on SA-coated beads, the SOMAmers are eluted from their targets and quantified by hybridization to a customized DNA microarray. The fluorescent intensity of each probe spot is proportional to the amount of its target protein in the original sample, with the SOMAmers acting as both the binding agent and the quantifiable species. Gold et al. use this approach to identify 58 potential markers for chronic kidney disease. Ostroff et al. use the assay to analyze archived samples from >1,300 human subjects. From 44 candidate biomarkers, they identify a 12-protein panel with strong potential to diagnose non-small cell lung cancer. (PLoS One, e15003, e15004, 2010) PH Sequence-specific DNA-binding TALEs Recent studies have mapped the relationships between the amino-acid sequences and DNA-binding specificities of transcription activator–like effector (TALE)-type transcription factors from the pathogenic plant genus Xanthomonas. Morbitzer et al. demonstrate that knowledge of this code allows the design of sequence-specific transcription factors that activate user-defined endogenous genes in vivo in plants. The researchers create custom TALEs that target a 19-bp sequence in the tomato promoter Bs4S or 19-bp sequences in the promoters of the Arabidopsis thaliana genes EGL3 and KNAT1. Moreover, they show that TALEs targeting a 23-bp sequence have enhanced target specificity as compared to those targeting 19-bp sequences. Additional experiments enabled Morbitzer et al. to identify particular repeat units in TALE proteins that target G nucleotides specifically, an aspect of the binding code that had not been described previously. These results suggest that designer TALEs may rep! resent an alternative to sequence-specific DNA targeting using zinc-finger domains. (Proc. Natl. Acad. Sci. USA, 21617–21622, 2010) CM View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Trends in computational biology—2010
  - Nat Biotech 29(1):45 (2011)
  Nature Biotechnology | Computational Biology | Feature Trends in computational biology—2010 * H Craig Mak1 Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Page:45Year published:(2011)DOI:doi:10.1038/nbt.1747Published online10 January 2011 Interviews with leading scientists highlight several notable breakthroughs in computational biology from the past year and suggest areas where computation may drive biological discovery. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * H. Craig Mak is Associate Editor, Nature Biotechnology Additional data
• Whole-genome molecular haplotyping of single cells
  - Nat Biotech 29(1):51-57 (2011)
  Nature Biotechnology | Research | Article Whole-genome molecular haplotyping of single cells * H Christina Fan1 Search for this author in: * NPG journals * PubMed * Google Scholar * Jianbin Wang1 Search for this author in: * NPG journals * PubMed * Google Scholar * Anastasia Potanina2 Search for this author in: * NPG journals * PubMed * Google Scholar * Stephen R Quake1, 2, 3 Contact Stephen R Quake Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:51–57Year published:(2011)DOI:doi:10.1038/nbt.1739Received05 October 2010Accepted24 November 2010Published online19 December 2010 Abstract * Abstract * Accession codes * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Conventional experimental methods of studying the human genome are limited by the inability to independently study the combination of alleles, or haplotype, on each of the homologous copies of the chromosomes. We developed a microfluidic device capable of separating and amplifying homologous copies of each chromosome from a single human metaphase cell. Single-nucleotide polymorphism (SNP) array analysis of amplified DNA enabled us to achieve completely deterministic, whole-genome, personal haplotypes of four individuals, including a HapMap trio with European ancestry (CEU) and an unrelated European individual. The phases of alleles were determined at ~99.8% accuracy for up to ~96% of all assayed SNPs. We demonstrate several practical applications, including direct observation of recombination events in a family trio, deterministic phasing of deletions in individuals and direct measurement of the human leukocyte antigen haplotypes of an individual. Our approach has potential ! applications in personal genomics, single-cell genomics and statistical genetics. View full text Figures at a glance * Figure 1: Microfluidic device designed for the amplification of metaphase chromosomes from a single cell. A single metaphase cell is recognized microscopically and captured in region 1. Protease (pepsin at low pH) is introduced to generate chromosome suspension in region 2. Chromosome suspension is partitioned into 48 units (region 3). Content in each partition is individually amplified (region 4). Specifically, chromosomes at low pH are first neutralized and treated with trypsin to digest chromosomal proteins. Chromosomes are denatured with alkali and subsequently neutralized for multiple strand displacement amplification to take place. As reagents are introduced sequentially into each air-filled chamber, enabled by the gas permeability of the device's material, chromosomes are pushed into one chamber after the next and finally arrive in the amplification chamber. Amplified materials are retrieved at the collection ports (region 5). In the overview image of the device, control channels are filled with green dye. Flow channels in the cell-sorting region and amplification region ! are filled with red and blue dyes, respectively. * Figure 2: Whole-genome haplotyping. () Determining the chromosomal origin of amplification products in a microfluidic device using 46-loci PCR. This table represents results from an experiment using a single metaphase cell of P0's cultured whole blood. A row represents the content inside a chamber on the microfluidic device, and a column represents a locus, with specified chromosome and coordinate (NCBI Build 36.1). Each locus, except those on chromosomes 17 and 20, was found in two chambers. The two alleles of a SNP are highlighted in red and green. Heterozygous loci are labeled in blue. Chamber numbers labeled yellow were pooled together and genotyped on one HumanOmni1-Quad array, and chamber numbers labeled orange were pooled together and genotyped on another array. Genomic DNA extracted from cultured whole blood was also tested with the same 46-loci PCR. () Statistics of whole-genome haplotyping. The fraction of SNPs present on the array phased for each chromosome of each individual (GM12891, GM12892, GM12! 878 and a European individual 'P0') is shown as a colored bar. () Fraction of SNPs phased as a function of the number of pairs of homologous chromosomes assayed. This is based on the results from four single-cell experiments of P0. Each point represents the coverage of an autosome. The error bars represent s.e.m. * Figure 3: Comparison of statistically determined phases with experimentally determined phases. () Comparison of experimentally determined phases of ~160,000 heterozygous SNPs of GM12878 (child of the trio) and those determined by phase III of the HapMap project. Unambiguous SNPs refer to those that are homozygous for at least one parent and are deterministically phased using family data in HapMap. This comparison shows the accuracy of DDP. Ambiguous SNPs refer to those that are heterozygous for all members of the trio and statistical phasing is used in HapMap. This comparison provides an evaluation of statistical phasing. () Comparison of experimentally determined phases of P0 and those determined by PHASE. Seventy-six regions on the autosomal chromosomes were randomly selected and statistically phased three times. Each region carried 100 heterozygous SNPs and spanned an average of ~2 Mb. Switch error rate was calculated as the proportion of heterozygous SNPs with different phases relative to the SNP immediately upstream. Single-site error rate was calculated as the p! roportion of heterozygous SNPs with incorrect phase. A SNP was considered correctly phased if it had the dominant phase. For each region, the average values from the three runs were reported. Presented here are the average switch error and single-site error per region. The deterministic phases measured by DDP are taken as the ground truth. * Figure 4: Direct observation of recombination events and deterministic phasing of heterozygous deletions in the family trio. Each allele with DDP data available for the child and the parent is represented by a colored line (blue, alleles transmitted to the child from the father; red, alleles transmitted to the child from the mother; black, untransmitted alleles). Centromeres and regions of heterochromatin are not assayed by genotyping arrays and are thus in white. Heterozygous deletions in the parents are represented as triangles along each homologous chromosome. A solid triangle represents one copy and a hollow triangle represents a null copy. The phases of deletions are determined for each parent independently. The triangles are color coded according to the state of transmittance as determined by the location of the deletion relative to spots of recombination. The phases of the deletions in the child are determined independent of the parents and are shown on top of the parental chromosomes. The integers on the left are the IDs of each region given by HapMap phase III. The numbers on the right ar! e the copy number of a region in the child as determined by HapMap. Chromosomes are plotted with the same length. * Figure 5: HLA haplotypes of P0 determined using DDP. At each of the six classical HLA loci, the experimentally phased SNP haplotypes of P0 and 176 phased SNP haplotypes of CEU trios available from HapMap phase III were placed on a neighbor-joining tree. The two haplotypes of P0 are labeled in red and blue. For haplotypes in the CEU panel with HLA typing data, the four-digit HLA allele is presented next to the sample label. Most of each tree is compressed. Each compressed subtree is labeled with the HLA allele associated with members inside the subtree, if HLA allele information is available. The allelic identities of HLA-B and HLA-C on haplotype 1 were not determined with DDP because CEU individuals with similar SNP haplotypes as P0's SNP haplotypes did not have HLA typing data at these loci but could be inferred from the results of direct HLA typing of genomic DNA (first row of table). HLA-DQA1 was not directly typed. Accession codes * Abstract * Accession codes * Author information * Supplementary information Referenced accessions Sequence Read Archive * SRA026722 Author information * Abstract * Accession codes * Author information * Supplementary information Affiliations * Department of Bioengineering, Stanford University, Stanford, California, USA. * H Christina Fan, * Jianbin Wang & * Stephen R Quake * Howard Hughes Medical Institute, Stanford University, Stanford, California, USA. * Anastasia Potanina & * Stephen R Quake * Department of Applied Physics, Stanford University, Stanford, California, USA. * Stephen R Quake Contributions H.C.F. and S.R.Q. conceived the experiments. H.C.F. designed the microfluidic device. A.P. developed protocols for device fabrication. H.C.F. and J.W. performed the experiments. H.C.F., J.W. and S.R.Q. analyzed the data and wrote the manuscript. Competing financial interests S.R.Q. is a founder, consultant and shareholder of Fluidigm Corporation and Helicos Biosciences Corporation, and a consultant and shareholder of Artemis Health. H.C.F. was previously employed at Fluidigm Corporation. All other authors declare no conflict of interest. Corresponding author Correspondence to: * Stephen R Quake Supplementary information * Abstract * Accession codes * Author information * Supplementary information Text files * Supplementary Data Set 1 (21M) Haplotypes 1 GM12891 haplotypes.txt * Supplementary Data Set 2 (20M) Haplotypes 2 GM12892 haplotypes.txt * Supplementary Data Set 3 (21M) Haplotypes 3 GM12878 haplotypes.txt * Supplementary Data Set 4 (31M) P0 Omni1S * Supplementary Data Set 5 (16M) P0 Omni1Quad PDF files * Supplementary Text and Figures (980K) Supplementary Tables 1–6 and Supplementary Figs. 1–4 Additional data
• Haplotype-resolved genome sequencing of a Gujarati Indian individual
  - Nat Biotech 29(1):59-63 (2011)
  Nature Biotechnology | Research | Letter Haplotype-resolved genome sequencing of a Gujarati Indian individual * Jacob O Kitzman1 Contact Jacob O Kitzman Search for this author in: * NPG journals * PubMed * Google Scholar * Alexandra P MacKenzie1 Search for this author in: * NPG journals * PubMed * Google Scholar * Andrew Adey1 Search for this author in: * NPG journals * PubMed * Google Scholar * Joseph B Hiatt1 Search for this author in: * NPG journals * PubMed * Google Scholar * Rupali P Patwardhan1 Search for this author in: * NPG journals * PubMed * Google Scholar * Peter H Sudmant1 Search for this author in: * NPG journals * PubMed * Google Scholar * Sarah B Ng1 Search for this author in: * NPG journals * PubMed * Google Scholar * Can Alkan1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Ruolan Qiu1 Search for this author in: * NPG journals * PubMed * Google Scholar * Evan E Eichler1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Jay Shendure1 Contact Jay Shendure Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:59–63Year published:(2011)DOI:doi:10.1038/nbt.1740Received26 October 2010Accepted29 November 2010Published online19 December 2010 Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Haplotype information is essential to the complete description and interpretation of genomes1, genetic diversity2 and genetic ancestry3. Although individual human genome sequencing is increasingly routine4, nearly all such genomes are unresolved with respect to haplotype. Here we combine the throughput of massively parallel sequencing5 with the contiguity information provided by large-insert cloning6 to experimentally determine the haplotype-resolved genome of a South Asian individual. A single fosmid library was split into a modest number of pools, each providing ~3% physical coverage of the diploid genome. Sequencing of each pool yielded reads overwhelmingly derived from only one homologous chromosome at any given location. These data were combined with whole-genome shotgun sequence to directly phase 94% of ascertained heterozygous single nucleotide polymorphisms (SNPs) into long haplotype blocks (N50 of 386 kilobases (kbp)). This method also facilitates the analysis of st! ructural variation, for example, to anchor novel insertions7, 8 to specific locations and haplotypes. View full text Figures at a glance * Figure 1: Haplotype-resolved genome sequencing. (,) A single, highly complex fosmid library was constructed () and split into 115 pools (), each representing ~3% physical coverage of the diploid human genome. Barcoded shotgun libraries from each pool were constructed, then combined and sequenced. As expected, reads from each library map to ~5,000 × ~37 kbp blocks, minimally redundant within each library. () Whole-genome shotgun sequencing of the same individual generated unphased variant calls. () Unphased variant calls were combined with haploid genotype calls to assemble haplotype blocks using a maximum parsimony approach19 (reference allele in black, nonreference allele in red). * Figure 2: Haplotype assembly results. () Size distribution of blocks within the haplotype assembly up to a maximum block size of 2.79 Mbp. Half of the assembly comprised blocks longer than 386 kbp (N50). () Comparison of experimental phasing with HapMap population-based inference2 for NA20847, with agreement of pairwise haplotype predictions as a function of physical distance and linkage disequilibrium. () Agreement of pairwise haplotype predictions as a function of physical distance and minor allele frequency (defined as the lower allele frequency of the pair in GIH). Key is the same as for . * Figure 3: Enrichment of novel variants on 'GIH-like' haplotypes. () Haplotypes were scored and rank ordered within sliding windows of 20 HapMap variants2 for greater similarity to GIH or CEU on the basis of population allele frequencies (left on x axis: more similar to GIH). Plotted is the fraction of novel variants (not in dbSNP v130) in rank-ordered groups of haplotype windows, demonstrating that the most 'GIH-like' haplotype windows are enriched for novel variants. Values from trio-phased14 CEU individual NA12891 are shown for comparison (red). () Scores calculated in for haplotype windows were compared between homologous chromosomes, and haplotypes were ranked based on the extent to which they scored as 'GIH-like' relative to their homolog. Plotted is the fraction of novel variants found on the more 'GIH-like' haplotype in rank-ordered groups of homologous haplotype windows. As above, the analysis was also performed for individual NA12891 using the rank ordering from individual NA20847. Haplotype blocks that are most differentiated re! lative to their homolog (higher ranked) with respect to GIH versus CEU similarity are enriched for novel variants relative to their homolog, consistent with the pattern observed in . * Figure 4: Insertion anchoring and structural variation detection. () Homozygous deletion (top), hemizygous deletion (middle) and inversion (bottom) with fosmid clone support. Deletion calls were made using read depth and paired-read discordance. Inversions were called by paired-read discordance. SNPs within hemizygous deletions appear as stretches of hemizygosity by whole-genome shotgun sequencing. Purple connections indicate the additional support of strand discordance of read pairs spanning genomic DNA and the vector backbone. () Novel contigs not present in the reference assembly (red) but detected among clone pool–derived reads (light blue, purple, yellow) are anchored by searching for positions in the reference common to those pools but missing from most or all other pools. This approach anchors 1,733 recently reported insertion sequences7, 8 including contig GU268019. Accession codes * Accession codes * Author information * Supplementary information Referenced accessions Sequence Read Archive * 026360 Author information * Accession codes * Author information * Supplementary information Affiliations * Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. * Jacob O Kitzman, * Alexandra P MacKenzie, * Andrew Adey, * Joseph B Hiatt, * Rupali P Patwardhan, * Peter H Sudmant, * Sarah B Ng, * Can Alkan, * Ruolan Qiu, * Evan E Eichler & * Jay Shendure * Howard Hughes Medical Institute, Seattle, Washington, USA. * Can Alkan & * Evan E Eichler Contributions The project was conceived and experiments planned by J.O.K., E.E.E. and J.S. J.O.K., A.P.M. and R.Q. carried out all experiments. J.O.K., A.A., J.B.H., R.P.P., P.H.S., S.B.N. and C.A. performed data analysis. J.O.K., A.P.M., A.A., J.B.H., R.P.P. and J.S. wrote the manuscript, and all authors reviewed it. All aspects of the study were supervised by J.S. Competing financial interests J.S. is a member of the science advisory boards of Tandem Technologies, Stratos Genomics, Good Start Genetics and Adaptive TCR. E.E.E. is on the scientific advisory board for Pacific Biosciences. Corresponding authors Correspondence to: * Jay Shendure or * Jacob O Kitzman Supplementary information * Accession codes * Author information * Supplementary information Excel files * Supplementary Table 4 (1M) Pan-genome and novel sequence anchoring. PDF files * Supplementary Text and Figures (2M) Supplementary Tables 1–3,5, Supplementary Methods and Supplementary Figs. 1–7 Additional data
• Targeted integration in rat and mouse embryos with zinc-finger nucleases
  - Nat Biotech 29(1):64-67 (2011)
  Nature Biotechnology | Research | Letter Targeted integration in rat and mouse embryos with zinc-finger nucleases * Xiaoxia Cui1 Contact Xiaoxia Cui Search for this author in: * NPG journals * PubMed * Google Scholar * Diana Ji1 Search for this author in: * NPG journals * PubMed * Google Scholar * Daniel A Fisher1 Search for this author in: * NPG journals * PubMed * Google Scholar * Yumei Wu1 Search for this author in: * NPG journals * PubMed * Google Scholar * David M Briner1 Search for this author in: * NPG journals * PubMed * Google Scholar * Edward J Weinstein1 Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:64–67Year published:(2011)DOI:doi:10.1038/nbt.1731Received09 April 2010Accepted10 November 2010Published online12 December 2010 Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Gene targeting is indispensible for reverse genetics and the generation of animal models of disease. The mouse has become the most commonly used animal model system owing to the success of embryonic stem cell–based targeting technology1, whereas other mammalian species lack convenient tools for genome modification. Recently, microinjection of engineered zinc-finger nucleases (ZFNs) in embryos was used to generate gene knockouts in the rat2, 3 and the mouse4 by introducing nonhomologous end joining (NHEJ)-mediated deletions or insertions at the target site. Here we use ZFN technology in embryos to introduce sequence-specific modifications (knock-ins) by means of homologous recombination in Sprague Dawley and Long-Evans hooded rats and FVB mice. This approach enables precise genome engineering to generate modifications such as point mutations, accurate insertions and deletions, and conditional knockouts and knock-ins. The same strategy can potentially be applied to many othe! r species for which genetic engineering tools are needed. View full text Figures at a glance * Figure 1: Targeted integration of NotI restriction site. () Schematic of donor and target site. Donors contain a NotI site inserted between the ZFN binding sequences (squares) with two flanking 800 bp homologous arms. F and R, forward and reverse primers (short bar) that sit outside of the homology. H, boundary of homology. DSB, double-strand break. () One pup (arrowhead) with NotI insertion was identified in each target using PCR with specific F and R primers followed by NotI digestion. * Figure 2: Targeted integration of a GFP cassette. () Schematic of target site (square) and GFP integration at Mdr1a and PXR loci. F, R and H, same as in Figure 1a. GF and GR, forward and reverse primers in GFP cassette. PvuII and PciI are restriction enzymes used in Southern blot analysis; neither cuts the 1.5-kb GFP insert, which inserts in the opposite orientation of transcription in both donors. Probes used in Southern blot analysis (thick bars) are marked at corresponding positions. () PCR analysis of GFP integration in selected Mdr1a and PXR rat pups. Pup IDs are labeled under the primers used. () Southern blot analysis of pups for GFP integration. GFP, GFP probe; Mdr1a and PXR, respective flanking probes. wt, wild-type Sprague Dawley genomic DNA. () GFP expression was visualized under UV light in the eyes of Mdr1a founder no. 3. Full-length blots are presented in Supplementary Figure 9. * Figure 3: Germline transmission of site-specific GFP integration. Integration-positive offspring of Mdr1a founder no. 3 (F1 and F2 pups identified by PCR as in Supplementary Fig. 7a and not shown) and PXR founder no. 4 (F1 pups identified by PCR as in Supplementary Fig. 7b) were further confirmed with Southern blot analysis. GFP, GFP probe; Mdr1a and PXR, respective target probes. wt, wild-type Sprague Dawley genomic DNA. () Mdr1a heterozygotes. () Mdr1a F2 homozygotes. Wild-type and an F1 heterozygote are included as controls. () PXR F1 heterozygotes. Arrowheads indicate F1 animals in which targeted integration allele of PXR was segregated from the extra GFP locus. Full-length blots are presented in Supplementary Figure 9. Author information * Author information * Supplementary information Affiliations * Sigma Advanced Genetic Engineering (SAGE) Labs, Sigma-Aldrich Biotechnology, St. Louis, Missouri, USA. * Xiaoxia Cui, * Diana Ji, * Daniel A Fisher, * Yumei Wu, * David M Briner & * Edward J Weinstein Contributions X.C. designed the project, built donor constructs and carried out some of the diagnostic PCRs; D.J. built donor constructs and performed most of the PCR diagnosis; D.A.F. performed Southern blot analysis; Y.W. microinjected the rat samples; D.M.B. assembled ZFNs; X.C., D.J., D.A.F. and E.J.W. wrote the manuscript. Competing financial interests All authors are full-time employees of Sigma-Aldrich Biotechnology. Corresponding author Correspondence to: * Xiaoxia Cui Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (4M) Supplementary Tables 1–4, Supplementary Methods and Supplementary Figs. 1–9 Additional data
• Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
  - Nat Biotech 29(1):68-72 (2011)
  Nature Biotechnology | Research | Letter Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine * Chun-Xiao Song1 Search for this author in: * NPG journals * PubMed * Google Scholar * Keith E Szulwach2 Search for this author in: * NPG journals * PubMed * Google Scholar * Ye Fu1 Search for this author in: * NPG journals * PubMed * Google Scholar * Qing Dai3 Search for this author in: * NPG journals * PubMed * Google Scholar * Chengqi Yi1 Search for this author in: * NPG journals * PubMed * Google Scholar * Xuekun Li2 Search for this author in: * NPG journals * PubMed * Google Scholar * Yujing Li2 Search for this author in: * NPG journals * PubMed * Google Scholar * Chih-Hsin Chen4 Search for this author in: * NPG journals * PubMed * Google Scholar * Wen Zhang1 Search for this author in: * NPG journals * PubMed * Google Scholar * Xing Jian1 Search for this author in: * NPG journals * PubMed * Google Scholar * Jing Wang1 Search for this author in: * NPG journals * PubMed * Google Scholar * Li Zhang4 Search for this author in: * NPG journals * PubMed * Google Scholar * Timothy J Looney4 Search for this author in: * NPG journals * PubMed * Google Scholar * Baichen Zhang5 Search for this author in: * NPG journals * PubMed * Google Scholar * Lucy A Godley6 Search for this author in: * NPG journals * PubMed * Google Scholar * Leslie M Hicks5 Search for this author in: * NPG journals * PubMed * Google Scholar * Bruce T Lahn4 Search for this author in: * NPG journals * PubMed * Google Scholar * Peng Jin2 Contact Peng Jin Search for this author in: * NPG journals * PubMed * Google Scholar * Chuan He1 Contact Chuan He Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:68–72Year published:(2011)DOI:doi:10.1038/nbt.1732Received25 August 2010Accepted15 November 2010Published online12 December 2010 Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg In contrast to 5-methylcytosine (5-mC), which has been studied extensively1, 2, 3, little is known about 5-hydroxymethylcytosine (5-hmC), a recently identified epigenetic modification present in substantial amounts in certain mammalian cell types4, 5. Here we present a method for determining the genome-wide distribution of 5-hmC. We use the T4 bacteriophage β-glucosyltransferase to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5-hmC. The azide group can be chemically modified with biotin for detection, affinity enrichment and sequencing of 5-hmC–containing DNA fragments in mammalian genomes. Using this method, we demonstrate that 5-hmC is present in human cell lines beyond those previously recognized4. We also find a gene expression level–dependent enrichment of intragenic 5-hmC in mouse cerebellum and an age-dependent acquisition of this modification in specific gene bodies linked to neurodegenerative disorders. View full text Figures at a glance * Figure 1: Selective labeling of 5-hmC in genomic DNA. () The hydroxyl group of 5-hmC in duplex DNA can be glucosylated by β-GT to form β-glucosyl-5-hydroxymethylcytosine (5-gmC) using UDP-Glu as a co-factor. () An azide group can be installed onto 5-hmC using chemically modified UDP-Glu (UDP-6-N3-Glu), which in turn can be labeled with a biotin moiety using click chemistry for subsequent detection, affinity purification and sequencing. * Figure 2: MS characterization of 5-hmC-, N3-5-gmC- and biotin-N3-5-gmC-containing 11-mer DNA in a model experiment. () MALDI-TOF of 5-hmC-, N3-5-gmC- and biotin-N3-5-gmC-containing 11-mer DNA, respectively, with the calculated molecular weight and observed molecular weight indicated. () Corresponding reactions of the β-GT–catalyzed formation of N3-5-gmC and the subsequent copper-free click chemistry to yield biotin-N3-5-gmC in duplex DNA. Reactions were performed in duplex DNA with the complementary strand; however, MS monitored the single-stranded DNA containing the modification. * Figure 3: Quantification of 5-hmC in various cell lines and tissues. () Dot-blot assay of avidin-HRP detection and quantification of mouse cerebellum genomic DNA containing biotin-N3-5-gmC. Top row: 40 ng of biotin-labeled samples using UDP-6-N3-Glu. Bottom row: 40 ng of control samples using regular UDP-Glu without biotin label. The exact same procedures were followed for experiments in both rows. P7, P14 and P21 represent postnatal day 7, 14 and 21, respectively. () Amounts of 5-hmC are shown in percentage of total nucleotides of mouse genome. *, P < 0.05, Student's t-test; means ± s.e.m. for n = 4 experiments. () Dot-blot assay of avidin-HRP detection and quantification of genomic DNA samples from four cell lines (from same blot as in ), except that each dot contains 700 ng DNA. () Amounts of 5-hmC are shown in percentage of total nucleotides of the genome; means ± s.e.m. for n = 4 experiments. The dashed line indicates the limit of detection (~0.004%). * Figure 4: Genome-wide distribution of 5-hmC in adult mouse cerebellum and gene-specific acquisition of intragenic 5-hmC during mouse cerebellum development. () Genome-scale reproducibility of 5-hmC profiles and enrichment relative to genomic DNA and control-treated DNA in adult mouse cerebellum. Heatmap representations of read densities have been equally scaled and then normalized based on the total number of mapped reads per sample. Data are derived from a single lane of sequence from each condition. Control, UDP-Glu treated without biotin; Input, genomic DNA; 5-hmC, UDP-6-N3-Glu treated with biotin incorporated. () Metagene profiles of 5-hmC and input genomic DNA reads mapped relative to RefSeq transcripts expressed at different levels in adult mouse cerebellum. RefSeq transcripts were divided into four equally sized bins based on gene expression level and 5-hmC or input genomic DNA reads falling in 10-bp bins centered on transcription start sites or end sites. The reads were summed and normalized based on the total number of aligned reads (in millions). Input genomic DNA reads were mapped to each of the four gene expression l! evel bins and are plotted here in black. The profiles completely overlap and so are collectively referred to as 'Input'. () Proximal and intragenic enrichment of 5-hmC relative to surrounding regions in adult and P7 mouse cerebellum. Reads from 5-hmC-captured samples and input genomic DNA were summed in 10-bp intervals centered on either TSS or txEnds and normalized to the total number of aligned reads from each sample (in millions). () Enrichment of pathways associated with age-related neurodegenerative diseases in genes acquiring intragenic 5-hmC in adult mice relative to P7 mice. Shown are the number of genes that acquired 5-hmC in adult cerebellum and the number of genes expected based on the total number of genes associated with that pathway in mouse. **, P < 10−10; *, P < 10−5. Accession codes * Accession codes * Author information * Supplementary information Referenced accessions Gene Expression Omnibus * GSE25398 Author information * Accession codes * Author information * Supplementary information Affiliations * Department of Chemistry and Institute for Biophysical Dynamics, the University of Chicago, Chicago, Illinois, USA. * Chun-Xiao Song, * Ye Fu, * Chengqi Yi, * Wen Zhang, * Xing Jian, * Jing Wang & * Chuan He * Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA. * Keith E Szulwach, * Xuekun Li, * Yujing Li & * Peng Jin * Department of Biochemistry and Molecular Biology, the University of Chicago, Chicago, Illinois, USA. * Qing Dai * Department of Human Genetics and Howard Hughes Medical Institute, the University of Chicago, Chicago, Illinois, USA. * Chih-Hsin Chen, * Li Zhang, * Timothy J Looney & * Bruce T Lahn * Donald Danforth Plant Science Center, St. Louis, Missouri, USA. * Baichen Zhang & * Leslie M Hicks * Section of Hematology/Oncology, the University of Chicago, Chicago, Illinois, USA. * Lucy A Godley Contributions C.H., C.-X.S. and P.J. designed the experiments with help from Y.F. and B.T.L. Experiments were performed by C.-X.S., K.E.S., Y.F., C.Y. and Q.D. with the help of W.Z. and X.J.; Q.D. and J.W. carried out the chemical synthesis; K.E.S., X.L., Y.L. and P.J. provided the mouse cerebellum, mouse aNSC and fly samples, and performed deep sequencing; C.-H.C., L.Z., T.J.L. and L.A.G. helped with the mouse ESC, human HeLa, human HEK and related samples; B.Z. and L.M.H. performed the mass spectrometry analysis from HeLa cells. C.H., C.-X.S. and P.J. wrote the paper. All authors discussed the results and commented on the manuscript. Competing financial interests A patent application has been filed for the technology disclosed in this publication. Corresponding authors Correspondence to: * Chuan He or * Peng Jin Supplementary information * Accession codes * Author information * Supplementary information PDF files * Supplementary Text and Figures (6M) Supplementary Tables 1–5, Supplementary Methods and Supplementary Figs. 1–12 Additional data
• Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells
  - Nat Biotech 29(1):73-78 (2011)
  Nature Biotechnology | Research | Letter Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells * Eirini P Papapetrou1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Gabsang Lee3 Search for this author in: * NPG journals * PubMed * Google Scholar * Nirav Malani4 Search for this author in: * NPG journals * PubMed * Google Scholar * Manu Setty5 Search for this author in: * NPG journals * PubMed * Google Scholar * Isabelle Riviere1, 2, 6 Search for this author in: * NPG journals * PubMed * Google Scholar * Laxmi M S Tirunagari1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Kyuichi Kadota1, 7 Search for this author in: * NPG journals * PubMed * Google Scholar * Shoshannah L Roth4 Search for this author in: * NPG journals * PubMed * Google Scholar * Patricia Giardina8 Search for this author in: * NPG journals * PubMed * Google Scholar * Agnes Viale9 Search for this author in: * NPG journals * PubMed * Google Scholar * Christina Leslie5 Search for this author in: * NPG journals * PubMed * Google Scholar * Frederic D Bushman4 Search for this author in: * NPG journals * PubMed * Google Scholar * Lorenz Studer1, 3 Search for this author in: * NPG journals * PubMed * Google Scholar * Michel Sadelain1, 2 Contact Michel Sadelain Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:73–78Year published:(2011)DOI:doi:10.1038/nbt.1717Received24 September 2010Accepted26 October 2010Published online12 December 2010 Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Realizing the therapeutic potential of human induced pluripotent stem (iPS) cells will require robust, precise and safe strategies for genetic modification, as cell therapies that rely on randomly integrated transgenes pose oncogenic risks. Here we describe a strategy to genetically modify human iPS cells at 'safe harbor' sites in the genome, which fulfill five criteria based on their position relative to contiguous coding genes, microRNAs and ultraconserved regions. We demonstrate that ~10% of integrations of a lentivirally encoded β-globin transgene in β-thalassemia-patient iPS cell clones meet our safe harbor criteria and permit high-level β-globin expression upon erythroid differentiation without perturbation of neighboring gene expression. This approach, combining bioinformatics and functional analyses, should be broadly applicable to introducing therapeutic or suicide genes into patient-specific iPS cells for use in cell therapy. View full text Figures at a glance * Figure 1: Safe harbor selection strategy and characterization of thal-iPS cell lines. () Following the establishment of patient-specific iPS cell lines, which in this study were generated from skin fibroblasts or bone marrow mesenchymal stem cells (BM MSCs) from β-thalassemia major patients, with an excisable single polycistronic vector co-expressing OCT4, KLF4, cMYC and SOX2 (illustrated in Supplementary Fig. 10a), the genetic rescue strategy is as follows: thal-iPS cells are transduced with a lentiviral vector expressing β-globin and an excisable Neo-eGFP selection cassette and subcloned into single cells, and single-vector-copy integrants are selected according to vector chromosomal position. The levels of β-globin expression afforded by the vector integrated at different genomic positions are analyzed in the erythroid progeny of each selected clone. Microarray analysis is used to examine perturbation of endogenous gene expression by the integrated provirus. The reprogramming vector can be efficiently excised before globin gene transfer or after—toget! her with the Neo-eGFP selection cassette of the globin vector—through transient expression of Cre (Supplementary Fig. 10). () MSCs from β-thalassemia major patient 1. () Thal1.52 iPS cell line. () Expression of pluripotency markers in iPS cell lines thal1.52, thal2.1, thal5.10 and thal5.11. Thal1 MSCs: MSCs from β-thalassemia major patient 1; H1 hES: hES cell line H1. () NANOG expression in iPS cell lines. () Immunohistochemical analysis of a teratoma derived from line thal1.52. Upper panel: cytokeratin (CK) 20-positive intestine-like epithelium (endoderm); middle panel: vimentin-positive fibroblastic spindle cells (mesoderm); lower panel: S-100–positive peripheral nerve (ectoderm). () Bisulfite sequencing analysis of the OCT4 promoter in the indicated thal-iPS cell lines and the MSCs from which they were derived. Each horizontal row of circles represents an individual sequencing reaction with white circles representing unmethylated CpG dinucleotides and black circles! representing methylated CpG dinucleotides. The numbers indica! te the CpG position relative to the transcriptional start site (TSS). () Karyotype analysis of thal2.1 iPS cell line. Scale bars, 50 μm. * Figure 2: Single-vector copy, clonality and mapping of the integration site. (,) Upper panel: schematic representation of the TNS9.3/fNG lentiviral vector. An asterisk depicts a 4-bp insertion in the 5′ untranslated region (UTR) of the β-globin gene, which allows discrimination of the longer vector-encoded transcript from the endogenous β-globin transcript. TNS9.3/fNG also contains the human phosphoglycerate kinase (hPGK) promoter-driven neomycin phosphoryltransferase (Neo) and enhanced green fluorescent protein (eGFP) genes flanked by loxP sites. LTR: long terminal repeat; RRE: rev-responsive element; cPPT: central polypurine tract; HS: DNAse I hypersensitive site. Lower panels: Southern blot analysis to ascertain single integrations of the TNS9.3/fNG vector and clonality. Genomic DNA was digested with EcoRI () or XbaI (). The probe used in is eGFP (shown in the upper panel). The probe in spans exons 1 and 2 of the β-globin gene (shown in the upper panel). The parental thal-iPS cell lines thal1.52, thal2.1, thal5.10 and thal5.11 and the clone n! umber are depicted above the lanes. UT: untransduced. Arrowheads in indicate bands corresponding to the reprogramming vectors pLM-GO, pLM-YS and pLM-CM (Supplementary Fig. 8d) present in the thal1.52 line and the clones derived from it. Arrowheads in indicate endogenous bands (corresponding to the endogenous β-globin locus). Asterisks depict unique vector integration bands. (–) Examples of chromosome ideograms (upper panels) and graphics (lower panels) depicting 300 kb of human genome on both sides of the globin vector integration site in iPS clones thal1.52-10 (), thal2.1-49 (), thal1.52-17 () and the safe harbor clone thal5.10-2 (). A vertical red line depicts the position of the vector insertion. Numbers depict positions in the corresponding human chromosome. All RefSeq genes present in the genomic region spanning 600 kb illustrated in the graphic are shown in blue. Genes implicated in cancer (Supplementary Table 1) are shown in red. Chromosome ideograms and graphics ! were generated with the UCSC Genome Graphs tool. * Figure 3: β-globin expression in the erythroid progeny of single-vector-copy thal-iPS cell clones. () Expression of erythroid cell markers CD71 and glycophorin A (GPA) in the erythroid progeny of thal-iPS cell line 1.52. () β-globin expression in the erythroid progeny of 13 single-vector-copy thal-iPS cell clones assessed by qRT-PCR. Expression levels are expressed per gene copy, relative to the average endogenous β-globin expressed in the in vitro differentiated erythroid progeny of peripheral blood CD34+ cells from four healthy individuals and normalized to endogenous α-globin expression. hES: erythroid progeny of hES cell line H1, wt iPS: erythroid progeny of iPS cell line FDCT, derived from fibroblasts of an 11-year-old healthy individual30. Numbers below graphs depict thal-iPS clone numbers derived from lines thal1.52, thal2.1, thal5.10 and thal5.11. n: number of independent differentiations for each clone. UT: untransduced. Error bars denote s.e.m. () β-globin expression in the erythroid progeny of a subset of single-vector-copy thal-iPS cell clones and controls! assessed by quantitative primer extension. βE: endogenous β-globin (80 bp); αE: endogenous α-globin (60 bp); βV: vector-encoded β-globin (84 bp). PB CD34+: erythroid cell derivatives of in vitro differentiated peripheral blood (PB) CD34+ cells from a normal donor; H1 hES: erythroid cell derivatives of the H1 hES line; wt iPS: erythroid cell derivatives of iPS cell line FDCT, derived from fibroblasts of a healthy individual; thal1.52 UT, thal2.1 UT: erythroid cell derivatives of untransduced lines thal1.52 and thal2.1, respectively; thal1.52-17, thal2.1-67, thal1.52-10, thal1.52-16, thal1.52-38, thal2.1-49, thal2.1-48, thal2.1-55, thal5.11-32, thal5.10-2: erythroid cell derivatives of the respective single-vector-copy thal-iPS clones. () Chromatograms of HPLC analysis of α- and β-globin expression in the erythroid progeny of clones thal5.10-2 and thal5.11-28. Cord blood, H1 hES and untransduced (UT) thal1.52 cells were used as controls. For quantification of these d! ata, see Supplementary Table 7. Accession codes * Accession codes * Author information * Supplementary information Referenced accessions Gene Expression Omnibus * GSE24901 Author information * Accession codes * Author information * Supplementary information Affiliations * Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. * Eirini P Papapetrou, * Isabelle Riviere, * Laxmi M S Tirunagari, * Kyuichi Kadota, * Lorenz Studer & * Michel Sadelain * Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. * Eirini P Papapetrou, * Isabelle Riviere, * Laxmi M S Tirunagari & * Michel Sadelain * Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. * Gabsang Lee & * Lorenz Studer * Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. * Nirav Malani, * Shoshannah L Roth & * Frederic D Bushman * Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. * Manu Setty & * Christina Leslie * Cell Therapy and Cell Engineering Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. * Isabelle Riviere * Thoracic Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. * Kyuichi Kadota * Thalassemia Program, Pediatric Hematology/Oncology Division, Weill Cornell Medical College, New York, New York, USA. * Patricia Giardina * Genomics Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. * Agnes Viale Contributions E.P.P. conceived and designed the study, designed and performed experiments, analyzed data and wrote the manuscript; G.L. performed iPS cell differentiation experiments; N.M. performed bioinformatics analyses; M.S. and C.L. analyzed microarray data; L.M.S.T. provided technical assistance; K.K. performed histological analyses of teratomas; S.L.R. generated and analyzed integration site data; P.G. provided skin biopsy samples from β-thalassemia patients; A.V. generated microarray data; I.R., F.D.B. and L.S. analyzed data; M.S. conceived and designed the study, analyzed data and wrote the manuscript. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Michel Sadelain Supplementary information * Accession codes * Author information * Supplementary information Movies * Supplementary Movie 1 (20M) Beating putative cardiomyocytes derived from iPS cell line thal1.52. PDF files * Supplementary Text and Figures (3M) Supplementary Tables 1–9 and Supplementary Figs. 1–20 Additional data
• Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNAi
  - Nat Biotech 29(1):79-83 (2011)
  Nature Biotechnology | Research | Letter Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNAi * Johannes Zuber1, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * Katherine McJunkin1, 2, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * Christof Fellmann1, 4 Search for this author in: * NPG journals * PubMed * Google Scholar * Lukas E Dow1 Search for this author in: * NPG journals * PubMed * Google Scholar * Meredith J Taylor1 Search for this author in: * NPG journals * PubMed * Google Scholar * Gregory J Hannon1, 2, 3 Search for this author in: * NPG journals * PubMed * Google Scholar * Scott W Lowe1, 2, 3 Contact Scott W Lowe Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:79–83Year published:(2011)DOI:doi:10.1038/nbt.1720Received01 July 2010Accepted03 November 2010Published online05 December 2010 Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Short hairpin RNAs (shRNAs) are versatile tools for analyzing loss-of-function phenotypes in vitro and in vivo1. However, their use for studying genes involved in proliferation and survival, which are potential therapeutic targets in cancer and other diseases, is confounded by the strong selective advantage of cells in which shRNA expression is inefficient. We therefore developed a toolkit that combines Tet-regulated miR30-shRNA technology, robust transactivator expression and two fluorescent reporters to track and isolate cells with potent target knockdown. We demonstrated that this system improves the study of essential genes and was sufficiently robust to eradicate aggressive cancer in mice by suppressing a single gene. Further, we applied this system for in vivo negative-selection screening with pooled shRNAs and propose a streamlined, inexpensive workflow that will facilitate the use of RNA interference (RNAi) for the identification and evaluation of essential therapeut! ic targets. View full text Figures at a glance * Figure 1: Dual-color TRMPV vectors enable Tet-regulated shRNA expression for suppression of genes involved in cell proliferation and survival. () Vector schematic of TRMPV, which was constructed in the pQCXIX self-inactivating (SIN) retroviral backbone. Ψ+, extended retroviral packaging signal. () Western blot of immortalized Rosa26-rtTA-M2 MEFs transduced with TRMPV harboring different Rpa3 shRNAs (numbered by start position) or a Renilla luciferase (Ren) shRNA. After selection, cells were cultured in the presence or absence of doxycycline for 4 d before collection. β-actin served as loading control. Uncropped blots are shown in Supplementary Figure 2d. () Representative flow cytometry plots of Rosa26-rtTA-M2 MEFs transduced with TRMPV.shRen.713 and TRMPV.shRpa3.455 in competitive proliferation assays. Cells selected for TRMPV were mixed with untransduced cells and passaged in doxycycline for 16 d. () Quantification of fluorescent cells in representative competitive proliferation assays. Each series of bars is a time course from left to right: day 0, 4, 8, 12, 16, 20. In all series, day 0 bar represents percenta! ge Venus-positive cells before doxycycline treatment. In the presence of doxycycline, transduced cells were gated either on Venus or on both Venus and dsRed. () Vector schematic of TRMPVIR showing constitutive and inducible transcripts produced by the vector. IRES-dependent rtTA3 expression from the inducible transcript creates a positive feedback loop of TRE induction. () Representative flow cytometry plots of Eμ-myc;Trp53−/− lymphoma cells transduced with TRMPVIR.shRen.713 and TRMPVIR.shRpa3.455 in competitive proliferation assays over 10 d. Cells were incompletely transduced with TRMPVIR before day 0 (rather than selected and admixed with untransduced cells). () Quantification of fluorescent cells in representative competitive proliferation assays. Each series of bars is a time course from left to right: day 0, 2, 4, 6, 8, 10; see for details. * Figure 2: TRMPV enables RNAi-based evaluation of genes involved in tumor maintenance in vivo. () Schematic of the generation and application of a Tet-On-competent mouse model of leukemia. Hematopoietic stem and progenitor cells (HSPC, Cd45.2+) are transduced with retroviruses that coexpress oncogenes, rtTA3 and firefly luciferase and subsequently transplanted into recipient mice. Resulting Tet-On leukemias are collected, transduced with TRMPV, selected and retransplanted into secondary Cd45.1+ recipients. After leukemia onset, shRNAs are induced by doxycycline and effects analyzed using different readouts. () Representative bioluminescence imaging of recipient mice transplanted with TRMPV-transduced AML cells. Mice were treated with doxycycline at disease onset (day 0). () Kaplan-Meier survival curve of recipient mice of AML cells transduced with indicated TRMPV shRNAs. Mice were treated with doxycycline at disease onset as assayed by imaging (7 d after transplantation). () Representative flow cytometry plots of donor-derived (Cd45.2+) cells in bone marrow of moribun! d doxycycline-treated mice in . () Quantification of Venus+dsRed+ cells in Cd45.2+ bone marrow cells collected from doxycycline-treated recipient mice (n = 4) at a terminal disease stage. Mean and s.e.m. are plotted. * Figure 3: TRMPV-induced suppression of Rpa3 cures clonal MLL-AF9;NrasG12D AML. () Bioluminescence imaging of recipient mice of clonal MLL-AF9;NrasG12D AML harboring TRMPV.shRpa3.455. After leukemia onset as assayed by imaging (day 0) mice were either left untreated (no dox), treated with doxycycline (early dox) or treated at a more advanced disease stage (late dox). () Bone marrow and liver histology of untreated and doxycycline-treated mice 4 d after leukemia onset. Scale bars: 20 μm for bone marrow, 100 μm for liver. () Kaplan-Meier survival curve of recipient mice of clonal TRMPV.shRpa3.455 or TRMPV.shRen.713 leukemias. After disease onset as assayed by bioluminescent imaging (day 7 after transplantation), mice were either left untreated (off dox) or treated with doxycycline for 40 d (on dox). * Figure 4: Pooled negative selection RNAi screening in vivo detects shRpa3 depletion in MLL-AF9;NrasG12D AML. () Scatter plot illustrating the correlation of normalized reads per shRNA between the plasmid library and transduced selected leukemia cells before transplantation (T0); r, nonparametric (Spearman) correlation coefficient. () Scatter plot of normalized reads per shRNA in T0 cells compared to an untreated leukemic recipient mouse. () Scatter plot of normalized reads per shRNA in T0 cells compared to average reads in three untreated recipient mice. () Relative abundance of Rpa3 and Renilla luciferase shRNAs in leukemias isolated from untreated (off dox) and doxycycline-treated (on dox) recipient mice, each compared to the initial representation before transplantation (T0). Leukemias from doxycycline-treated mice were analyzed both without and with purification of shRNA-expressing cells (Venus+dsRed+) before DNA isolation. () Relative abundance of all 824 shRNAs in Venus+dsRed+-sorted leukemia cells from doxycycline-treated mice compared to T0 cells. The mean of normalized rea! ds in doxycycline-treated mice (n = 3) was divided by normalized reads in T0 cells; shRNAs are plotted according to the resulting ratios in ascending order. All three shRNAs targeting Rpa3 were among the 25 most depleted shRNAs, whereas neutral shRen.713 was not altered. Author information * Author information * Supplementary information Primary authors * These authors contributed equally to this work. * Johannes Zuber & * Katherine McJunkin Affiliations * Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. * Johannes Zuber, * Katherine McJunkin, * Christof Fellmann, * Lukas E Dow, * Meredith J Taylor, * Gregory J Hannon & * Scott W Lowe * Watson School of Biological Sciences, Cold Spring Harbor, New York, USA. * Katherine McJunkin, * Gregory J Hannon & * Scott W Lowe * Howard Hughes Medical Institute, Cold Spring Harbor, New York, USA. * Gregory J Hannon & * Scott W Lowe * Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. * Christof Fellmann Contributions J.Z. and K.M. designed and performed experiments. C.F. and L.E.D. contributed new reagents and performed experiments. M.J.T. managed mouse monitoring and husbandry. G.J.H. and S.W.L. supervised this project. J.Z., K.M. and S.W.L. wrote the paper. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Scott W Lowe Supplementary information * Author information * Supplementary information Excel files * Supplementary Table 1 (210K) PDF files * Supplementary Text and Figures (3.5M) Supplementary Table 2 and Supplementary Figs. 1–8 Additional data
• Pay for executives at private life sciences companies continues to steadily increase
  - Nat Biotech 29(1):85-86 (2011)
  Nature Biotechnology | Careers and Recruitment Pay for executives at private life sciences companies continues to steadily increase * Bruce Rychlik1 Contact Bruce Rychlik Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature BiotechnologyVolume: 29,Pages:85–86Year published:(2011)DOI:doi:10.1038/nbt.1751Published online10 January 2011 In 2010, compensation targets for top life sciences executives once again moved upwards at a faster rate than those of their technology-sector peers. View full text Figures at a glance * Figure 1: Cash compensation for life sciences nonfounders. * Figure 2: A sample CompStudy Company Scorecard. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bruce Rychlik is at J. Robert Scott, Boston, Massachusetts, USA. Competing financial interests The author declares no competing financial interests. Corresponding author Correspondence to: * Bruce Rychlik Additional data
• People
  - Nat Biotech 29(1):88 (2011)
  Nature Biotechnology | Careers and Recruitment | People People Journal name:Nature BiotechnologyVolume: 29,Page:88Year published:(2011)DOI:doi:10.1038/nbt.1758Published online10 January 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. The Ontario Genomics Institute (Toronto) has announced the appointment of (below, right) as president and CEO, replacing . Poznansky has served on the OGI board of directors since 2004 and has been chairman since 2008. He was previously president, CEO and scientific director of the Robarts Research Institute in London, Ontario, and also served as president and CEO of Viron Therapeutics. For the past two years, he has managed his own consultancy for clients in government, hospitals, universities and the private sector. "Dr. Poznansky brings a wealth of experience to OGI, in genomics, in business development and in government affairs," says Mark Lievonen, acting chair of the board of directors. "His knowledge of life sciences and in running institutes and businesses will serve OGI well as it continues its plans to aid the growth of the life sciences sector in Ontario and increase the province's reputation as a world leader in genomics research." View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data