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Invitrogen, Applied Biosystems, Life Technologies, Complete Genomics, Isilon, DNAStar, Memorial Sloan-Kettering Cancer Center, RainDance Technologies, J. Craig Venter Institute, National Science Foundation, Genome British Columbia, Myriad Genetics, Geneti

Invitrogen, ABI to be Named Life Technologies Post-Merger
Following the merger of Invitrogen and Applied Biosystems, which is expected to close this month, the company will be called Life Technologies, according to an internal memo from Invitrogen Chairman and CEO Greg Lucier to employees obtained by In Sequence.
When the $6.7 billion deal was announced in June, the firms said that the merged entity would operate under the Applied Biosystems name. However, in a memo sent to employees this week, Lucier said that as the leadership teams of the two firms were “working together to define the identity and vision of our combined organization … one word became prominent in our discussions. That word was ‘life’ — a word that we believe truly symbolizes the promise of our combined company.”
He said the leadership team had chosen Life Technologies as the new name for the firm after the merger is closed.
Life Technologies also was the name of the Rockville, Md.-based provider of molecular biology and cell culture supplies that Invitrogen merged with back in July 2000.
Lucier said in the memo that the combined entity is “not losing the Invitrogen or Applied Biosystems brands, which will continue to be prominently positioned as part of our brand strategy.”
Invitrogen officials confirmed the planned name change.

Complete Genomics Taps Isilon for Data Storage
Complete Genomics is using Seattle-based Isilon Systems’ data storage services in its effort to sequence 100 human genomes in 2009, Isilon said this week.
The company said Complete Genomics is using its IQ clustered storage system to store over 700 terabytes of data to help power its DNA sequencing effort.
Complete Genomics said a month ago that it is working with the Institute for Systems Biology to sequence 100 genomes in 2009, and 2,000 genomes in 2010, as it aims to dramatically lower the cost of whole-genome sequencing (see In Sequence 10/7/2008).
The company plans to offer a sequencing service, rather than selling its next-generation sequencing instruments. This business model will necessitate a storage solution that can handle more data cheaply, according to Isilon.

DNAStar Extends Site License for Memorial Sloan-Kettering Cancer Center
Bioinformatics firm DNAStar said this week that it has extended a site license agreement with Memorial Sloan-Kettering Cancer Center for its Lasergene sequence analysis software.
Under the terms of the three-year license, Lasergene will continue to be available to all researchers at the institute’s New York City location. MSKCC originally licensed the software from DNAStar, which is based in Madison, Wis., in 2000.
Researchers use Lasergene primarily for the assembly and analysis of DNA and protein sequences. The software offers a broad range of analysis tools that can be used with both traditional and next-generation sequencing data.

RainDance Signs JCVI as Early Access Partner for Sequence-Enrichment Technology
RainDance Technologies said last week that it has signed the J. Craig Venter Institute as an early-access partner for its microfluidics-based sequence-enrichment technology for next-generation sequencing.
Under the terms of the agreement, JCVI will have access to the company’s RDT 1000 instrument and sequence enrichment application, which are based on RainDance's RainStorm droplet-based technology platform.
The RDT 1000 generates picoliter-volume PCR reactions at a rate of 10 million reactions per hour, and the sequence enrichment application uses a library of PCR primers in droplets to amplify hundreds to thousands of genomic loci in a single tube, the company said.
Bob Strausberg, deputy director and group leader in genomic medicine at JCVI, said in a statement that the institute’s scientists will use the RainDance technology in “various large-scale targeted sequencing studies.”
RainDance expects to launch the system commercially in the first quarter of 2009.

NSF Grants Nearly $60M for Plant Genome Research Program Awards
The National Science Foundation has injected $57.3 million into plant genomics studies across the country, and to several international recipients, covering a wide variety of plant life, such as legumes, soil microbes, flower nectar, mutant plants, and other crops.
This round of Plant Genome Research Program grants, in the eleventh year of the program, range from $350,000 to $6.8 million, and vary from two to five years in duration.
These grants will support tool development to advance genomics studies, and the studies will use sequence and functional genomics resources to investigate gene function and interactions between genomes and the environment. They will emphasize studies of crop plants that are economically useful such as corn, soybean, wheat, and rice, NSF said.
These awards will be spread out among a total of 45 institutions in 28 states, and they will support international scientists in Asia, Australia, Europe, and South America. The grants are focused on funding research partnerships between two or more institutions, such as the following:
The University of California, Davis, Cold Spring Harbor Laboratory, and Kansas State University will use $6.8 million to conduct physical mapping of the Wheat D genome.
The J. Craig Venter Institute and the University of Wisconsin-Madison will receive $3.8 million to curate the genome of the Medicago truncatula, a legume from the Mediterranean regions commonly used in biology.
The University of Southern California and the University of California, Davis, will study the same legume, and will receive $3.2 million to conduct community genomics research into local adaptation of the plant.
The University of Arizona and the University of Missouri, Columbia, will use $4.3 million to study comparative functional genomic and proteomic analysis of rhizome specificity across the plant kingdom.
A complete list of the NSF’s PGCSP funding recipients for 2008, and previous years, is available here.

Genome BC Awards $2M to Regional Genomics Projects
Genome British Columbia has invested C$2.3 million ($1.9 million) in a number of short-term genomics research projects in the Vancouver area, Genome BC last week.
The nine Genome BC awards under the Science Opportunities Fund are one-time grants that range from between C$68,000 and C$609,950. The goal of these competitive awards is to increase access to emerging genomics technologies, to foster partnerships with national and international stakeholders, and to help develop new means of interacting with industry and the genomics sciences community.
These research programs are aimed at generating results that can impact important sectors of British Columbia’s economy and environment.
The Vancouver Island University and Fisheries and Oceans Canada have won a C$400,000 award to develop “a sensitive genomic tool” for marine mussels that can be used to assess the health of coastal zones.
The University of British Columbia was awarded C$85,000 to fund studies of the symbiotic association between fungus and plant roots in order to understand cedar and hemlock seedlings during forest regeneration.
The University of Victoria will use C$140,000 to study Sablefish genomics to develop a suite of genomic tools that can provide important information for both aquaculture and managing fish stocks.
The University of British Columbia Okanagan will receive C$156,000 to identify traits that lavender farmers can manipulate to improve yield and quality.
Other programs include studies of the conifer genome that could help in future breeding, research into the wild bullfrog, which could serve as an indicator of environmental quality, and the BC BioLibrary, which supports developing better bioinformatics that can generate more accurate data.
A complete list of winners of these Genome BC awards is available here.

Molecular Diagnostics Sales Propel Strong Q1 Results for Myriad Genetics
Myriad Genetics reported 53 percent revenue growth this week and a swing from a net loss to a profit for its first quarter, which ended Sept. 30.
The Salt Lake City-based firm brought in total revenues of $73.6 million for the quarter, compared to $48.3 million for the comparable period of 2007. Its molecular diagnostics sales jumped 52 percent, to $70 million, from $46.1 million, and its research and other revenue increased 68 percent, to $3.7 million, from $2.2 million.
“All five of our molecular diagnostic products exceeded the company’s 45-percent annual compound growth rate, and patient sample flow continues to be very strong, despite the current economic environment,” Myriad President and CEO Peter Meldrum said in a statement.
Myriad posted a profit of $14.5 million, or $.30 per share, for the quarter, compared to a net loss of $8 million, or $.18 per share, for the first quarter of 2007.
The firm’s R&D spending dropped 34 percent year over year, to $17.1 million, from $26 million, while its SG&A expenses increased 26 percent, to $33.4 million, from $26.5 million. Myriad attributed the increase in SG&A costs to “significant expenditures” for its direct-to-consumer marketing campaign.
The company also noted that its women’s healthcare sales force has increased to 100 representatives, while its total sales force in the US is around 250 representatives.
Myriad finished its first quarter with $442.6 million in cash, cash equivalents, and marketable investment securities.

Policy Center to Use NHGRI Funds to Study Direct-to-Consumer Genetic Testing
To get a sharper picture of the state of the new direct-to-consumer genetic testing industry, the National Human Genome Research Institute has funded the Genetics and Public Policy Center at Johns Hopkins University with almost $600,000 to conduct studies.
Under the funding, the GPPC will study issues related particularly to the ways in which offering genotyping tests and services directly to customers — as companies such as Navigenics, Decode Genetics, and 23andMe do — differs from genetic testing offered by healthcare providers.
"There is a lot of hype and a lot of angst about how personal genome testing will play out in healthcare," GPPC’s Law and Policy Director Gail Javitt said in a statement. "Ensuring that the public has information adequate to making informed choices about genetic testing is a prerequisite to realizing the public health benefits that have been promised from genetic medicine.”
She added, "What's missing are hard facts about this industry and its consumers, and what the public's motivations for, and experiences with, these tests have been."
The GPPC plans to analyze the current regulations that cover marketing, advertising, and selling of genetic testing directly to consumers, and it will attempt to study the validity of the claims sellers make in their advertising by comparing them to scientific literature.
“We seek to get at what are consumers’ motivations for using these tests, and then what they feel they have gotten after using these tests,” Javitt told In Sequence’s sister publication GenomeWeb Daily News.
Another question is how the utility of a DTC test can be measured. Javitt said that it is important to “give credence to consumers’ interest,” and to understand “both the potential benefits and the potential harms from this mode of test delivery.”
This is a question that has been brought up by federal and state regulators who have begun to consider whether or not tests and services that show the presence of a genetic mutation that have been linked with levels of risk or predisposition toward an illness are usable.
The researchers at GPPC also will look at how state laws attempting to cover this very new field allow “some incoherence and lack of uniformity.” The center also will conduct some legal analysis that supports coordinated efforts to protect consumers, Javitt explained.
GPPC is currently drafting how these studies will be structured, and their work will not be complete until late 2010.
— By Matt Jones; originally published on GenomeWeb Daily News

NIDA Seeks Collaborator for Center for Genetic Studies
The National Institute on Drug Abuse is looking for a partner to start a center to handle the data from its genomic and molecular biology studies of drug addiction, abuse, and related psychiatric causes and implications, according to the National Institutes of Health.
NIDA seeks applicants to maintain a NIDA Center for Genetic Studies, which will generate, process, and distribute high-quality data files, documentation, and biological materials including DNA, RNA, cell lines, and serum. These data and materials will be collected from individuals with drug abuse and addiction-related disorders and their relatives.
NIDA seeks a contractor with experience in biospecimen processing, extraction, and dissemination, as well as in preparing pedigree files and files used in statistical genetic analysis. The collaborator will be expected to work interactively with grantees funded by NIDA.
NIDA expects to fund a three-year contract with options for two additional years.
Applicants should be able to store over 35,000 existing samples and around 15,000 new samples, have an informatics component with a public, queriable interface, and must have personnel with expertise in psychiatric diseases.
Responses to the RFP will be due Dec. 22. More information is available here.

Enzymatics Expects ISO Certification This Month
Reagent provider Enzymatics of Beverly, Mass., said last week that it expects to obtain certification for two ISO standards this month.
The company, which provides enzymes for DNA sequencing, diagnostics, and other purposes, said it has already implemented ISO 13485:2003, which relates to quality management system for medical devices. In addition, it is adhering to ISO 9001:2000.
The company provides enzymes and buffer solutions for the Polonator, a low-cost sequencing system developed by George Church’s group at Harvard Medical School and sold by the Dover unit of Danaher-Motion.

Alpine Mummy Mitochondrial Genome Yields Clues About Human Evolution
Researchers reported last week that they have sequenced the complete human mitochondrial genome of the Tyrolean Iceman, whose mummified carcass was discovered in the Eastern Alps nearly two decades ago.
In a paper appearing online last week in Current Biology, researchers from the UK and Italy sequenced the mitochondrial genome of an individual, nicknamed “Ötzi,” who lived more than five millennia ago during the Late Neolithic-Copper Age. Based on phylogenetic analysis of the mitochondrial sequence, the team found that Ötzi belonged to the so-called K1 haplogroup, still relatively common in Europe. But the Iceman does not appear to be closely related to any known European populations.
“The frequency of genetic lineages tends to change over time, due to random variations in the number of children people have — a process known as ‘genetic drift’ — and as a result, some variants die out,” co-author Martin Richards, an archeo-geneticist at the University of Leeds, said in a statement. “Our results suggest that Ötzi’s lineage may indeed have become extinct.”
Ötzi’s mummified corpse was discovered in the Alps near the Austrian-Italian border in 1991. Subsequent research suggests Ötzi died when he was about 46 years old, after being wounded by an arrow and receiving a blow to the head. The body, which has been displayed at the South Tyrol Museum of Archeology in Bolzano, Italy, since 1998, was almost completely preserved over 5,100 to 5,350 years by a process akin to freeze-drying.
Researchers have been dabbling in Ötzi’s genetics for nearly a decade. In the mid- to late-1990’s research teams from Munich and Oxford sequenced the first hypervariable segment of Ötzi’s mitochondrial DNA, revealing that the mummy belonged to a west Eurasian haplogroup K, which includes the sub-groups K1 and K2.
Then in 2000, researchers defrosted the mummy for the first time, looking at his intestinal contents. Along with genetic material from plants and animals that Ötzi consumed, researchers also found some human DNA, which appears to have come from cells in Ötzi’s intestines. Over the past six years, the team has been delving into mitochondrial DNA from the intestinal sample.
For this paper, the researchers used a combination of Sanger sequencing and Roche 454 sequencing of 235 short, pooled PCR amplification products with a FLX Genome Sequencer. They then compared Ötzi’s mitochondrial genome to those of 115 living individuals in the K haplogroup for whom complete mitochondrial sequences were available.
In the future, researchers say, similar techniques could aid research efforts on ancient samples, including studies of animal domestication. For their part, the team plans to try analyzing Ötzi's Y-chromosome. But, they say, this may prove difficult given that DNA from the Y-chromosome is less abundant than mitochondrial DNA. The researchers are also interested in determining whether they can find others who share Ötzi’s genetic lineage.

Cave Bear Mitochondrial Genome Sequenced, Provides Clues to Bear Evolution
Cave bears belonged to a sister group to modern day polar bears and brown (grizzly) bears, according to phylogenetic analyses of the newly sequenced cave bear mitochondrial genome.
A team of researchers from France and the Netherlands sequenced ancient mitochondrial DNA extracted from skeletal fragments of an extinct cave bear, Ursus spelaeus, found in a cave in southern France. The work, appearing online last week in the Proceedings of the National Academy of Sciences, suggests that cave bears' ancestors diverged from those of brown bears and polar bears some 1.6 million years ago. It also highlights the feasibility of analyzing cave bear DNA — a task that has proven challenging in the past.
Short cave bear mitochondrial sequences have been amplified in the past. For this paper, though, the researcher set out to sequence the cave bear’s entire mitochondrial genome from 32,000-year-old bone fragments found in the Chauvet-Pont d’Arc cave in southern France.
Despite the constant temperature and absence of damaging UV light, the researchers noted, analyzing the cave bear DNA was demanding since the samples were not as well maintained as those from ancient animals — notably the woolly mammoth — that have been exceptionally well-preserved in permafrost.
The researchers used PCR amplification and sequencing of overlapping fragments to reconstruct the 16,8-kilobase pair cave bear mitochondrial genome. After using nearly 250 primer pairs to amplify 150 to 180 base-pair bits of mitochondrial DNA at a time, they confirmed their initial sequence results by having collaborators at another institute repeat the analysis.
Their phylogenetic and gene-by-gene analyses suggested that cave bears belong to a sister group to polar bears and brown bears, with the ancestors of each diverging some 1.6 million years ago during the Early Quaternary period — long before the polar-brown bear lineage diversified. Eastern and western brown bears seem to have diverged just 550,000 years ago with the polar-western brown bear split occurring about 350,000 years ago.
To put this in perspective, the giant panda lineage appears to have diverged from Ursidae species about 12 million years ago, whereas the precursor to South American spectacled bears diverged from other bear species around 6.3 million years ago. Meanwhile, the group to which most modern bears belong appears to have undergone extensive radiation within the past two to three million years.
With the cave bear mitochondrial genome sequence in hand, researchers say, it should be possible to tease apart even more precise information about the timing and nature of bear evolution. And, researchers say, it illustrates the potential of studying ancient DNA from the Chauvet-Pont d’Arc cave and similar environments.

Spartan Bioscience, NorDiag to Combine Technologies in New DNA Analysis Platform
Canadian molecular diagnostics firm Spartan Bioscience said last week that it will collaborate with Norwegian firm NorDiag on the development of an end-to-end DNA sample preparation and analysis system.
The firms intend to combine NorDiag’s Arrow DNA isolation device with the Spartan DX-12 DNA Analyzer. The instruments will be offered to customers separately and as a combined offering, and are expected to cost less than $15,000 each.

“Each device is designed to complete its processing of 12 samples in 30 minutes or less making the entire workflow possible in less than an hour,” Mark Kershey, VP of corporate development of Spartan, said in a statement. “This capability and its affordability will open DNA analysis to labs around the world.”

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.