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Illumina, Avantome, Roche, 454 Life Sciences, Applied Biosystems, InteRNA Genomics, Biotique Systems, Genomatix Software, BioTeam, Invitrogen, Active Motif, Genetic Technologies, LabCorp, 23andMe, Oxford Biomedical Research Centre, International Genomics

Illumina to Acquire Sequencing Startup Avantome for up to $60M

Illumina said this week that it will acquire Avantome, a start-up company developing a low-cost, long-read sequencing technology that Illumina said will complement its Genome Analyzer platform.

As part of the deal, Illumina will make an up-front payment of $25 million and contingent payments of up to $35 million.

Avantome’s principal founders, Mostafa Ronaghi and Helmy Eltoukhy, will join Illumina. Ronaghi will become senior vice president and chief technical officer, and Eltoukhy will join as director of Advantome sequencing development.

The acquisition is expected to close in the next few weeks.

Ronaghi, a senior research associate at the Stanford Genome Technology Center, has been developing a miniaturized pyrosequencer under a three-year, $1.8 million Advanced Sequencing Technology award in 2004 from the National Human Genome Research Institute (see In Sequence's sister publication GenomeWeb Daily News, 1/2/2007).

Earlier this year, he told In Sequence that he and his team have developed a scaleable and sensitive detection chip for the system (see In Sequence 3/4/2008). He said they had integrated different parts of the platform into a “small box” and were preparing for large genome sequencing applications. At the time, he said Stanford University had not yet licensed the technology to a company.

In collaboration with Microchip Biotechnologies, Ronaghi has also been developing an automated sample-prep system for high-throughput pyrosequencing.

Roche's 454 Sequencing Product Sales ‘More than Double’ in First Half of 2008
Roche reported this week that its applied science revenues, which include revenues from its 454 Life Sciences unit, rose 21 percent for the first half of 2008.
Sales for Roche Applied Science totaled 367 million Swiss francs ($358 million), with growth driven by the firm’s Genome Sequencer FLX, LightCycler 480, and microarrays.
Roche noted that its sequencing product sales more than doubled for the first half of the year, even though there has been increased pressure from competitors. The company did not disclose its sequencing revenues.
Overall, the diagnostics division, which houses both the molecular diagnostics and applied science businesses, reported revenue growth of 11 percent to 4.7 billion Swiss francs for the first half.
The Roche Group had total first-half revenues of 22 billion Swiss francs, up 4 percent in local currencies. Its net income was 5.7 billion Swiss francs.
Sales for Roche’s pharmaceutical division, which includes Roche Pharmaceuticals, Genentech, and Chugai, were 17.3 billion Swiss francs for the first six months of 2008, up 3 percent.
The firm made an offer this week to acquire the 44.1 percent of Genentech that it doesn’t already own for $89 per share, or $43.7 billion.

Four Companies Join ABI’s SOLiD Software Development Community
Applied Biosystems said this week that InteRNA Genomics, Biotique Systems, Genomatix Software, and the Bioteam have joined its SOLiD software development community. The company also said it has released new software tools for the SOLiD platform (see New Products in this issue).
InteRNA Genomics’ miR-Intess software converts large sets of raw sequence data into interpretable formats, enabling researchers to integrate the information with existing data resources. The software, which ABI will co-market for the SOLiD platform, is designed for the analysis of high-throughput small RNA sequencing data, with a focus on discovery and expression profiling of miRNAs and for the classification and annotation of sequence reads according to knowledge in the small RNA field. Analysis includes alignment and annotation of SOLiD reads to a reference genome as well as prediction of novel miRNA candidate genes.
Biotique Systems’ High-Throughput HT-BLIS software enables researchers to process large amounts of sequence data generated by high-throughput instruments. The system can store and manipulate sequence data in real time as it is generated by platforms like the SOLiD system.
ABI’s software development program supports scientists in the development and potential commercialization of informatics applications for the SOLiD platform and has made sample data sets and data analysis tools and resources available for download.
The group “is expected to help drive innovation and speed the development of bioinformatics solutions that will enable researchers to realize the full potential of ultra-high- throughput genomic analysis,” according to ABI.
Existing members of the program are Geospiza and GenomeQuest (see In Sequence 2/12/2008).

Invitrogen, Active Motif to Collaborate on FPGA-Based Analysis of Next-Gen Sequencing Data
Invitrogen and Active Motif said this week that they will collaborate in exploring the use of field programmable gate array technology for analyzing next-generation sequencing data.
Active Motif markets TimeLogic's biocomputing systems, which couple an FPGA accelerator with optimized genomics algorithms to rapidly compare novel sequences to databases of well-characterized genes.
The alliance is aimed at exploring “ways in which [Active Motif’s] technology can speed the processing of data directly from next-generation sequencing instruments, and to assess the physical requirements — such as power consumption, cooling, data transfer, and space constraints — that an optimal computational solution for research and clinical teams would require,” Joe Fernandez, CEO of Carlsbad, Calif.-based Active Motif, said in a statement.

Genetic Technologies to Enforce BRCA Test Rights in Australia, New Zealand
Australian firm Genetic Technologies recently announced that it would enforce its patent rights covering diagnostic testing for BRCA1 and BRCA2 genes in Australia and New Zealand, reversing its earlier strategy of allowing other labs to offer the tests.
The firm holds an exclusive license from Myriad Genetics covering the Utah-based firm’s patents for breast and ovarian cancer testing based on the BRCA markers. Genetic Technologies publicly announced in May 2003 that it would not enforce its patent rights to prevent other service providers from performing BRCA tests.
However, after spending several million dollars on creating a high-throughput molecular diagnostics lab and paying Myriad ongoing fees for the BRCA license, Genetic Technologies has decided to enforce its rights in Australia and New Zealand. The firm noted that it is now able to offer a four-week turnaround on test results compared to the average turnaround time of 11 months from certain other labs.
“Going forward, the company hopes to engage with the relevant stakeholders to affect a smooth transition that ensures patient needs are met and ultimately enhanced,” Genetic Technologies said in a statement.

LabCorp Takes Over as 23andMe's Genotyping Service Provider
Laboratory Corporation of America is providing genotyping services for 23andMe, In Sequence’s sister publication GenomeWeb Daily News has learned.
“I can confirm that we are doing lab work for 23andMe,” Eric Lindblom, LabCorp’s senior vice president for investor and media relations, said last week.
Lindblom also noted that LabCorp is CLIA-licensed in California and New York, the two states that recently warned 23andMe, along with several other personal genomics firms, to stop marketing genetic tests directly to consumers. One of the reasons cited by regulators was that the consumer genomics firms were not licensed in these states to provide laboratory services.
Perhaps due to these regulatory difficulties, 23andMe had not been forthcoming about its relationship with LabCorp since cutting ties with Illumina, which was not CLIA-licensed, in February. 23andMe, however, continues to use Illumina's genotyping chips.
Illumina had received one of the cease-and-desist letters from New York health regulators, but not from California authorities.
23andMe expressed its apprehensions about the uncertain regulatory environment for consumer genomics in April on its blog, The Spittoon, apologizing to customers for delays in delivering test results. At the time, 23andMe attributed the delays to a change in laboratory.
“Because 23andMe is creating an entirely new kind of business in delivering personal genetic information, the regulatory requirements we face are both complicated and uncertain,” 23andMe co-founder Anne Wojcicki said in the blog post. “Because of the way these requirements are evolving, we recently changed the laboratory where our customers’ saliva samples are processed.”
Although Wojcicki described the new contract laboratory as a “‘high complexity’ laboratory [certified] under the federal Clinical Laboratories Improvement Act of 1988,” she did not name the laboratory.
LabCorp also has partnerships with several firms across the country that conduct genotyping services, including the National Genetics Institute, which is based in Los Angeles and has CLIA certification in the state.
However, when asked why LabCorp decided to move into the controversial DTC space, when the bulk of the company’s tests are marketed to physicians, Lindblom was quick to answer that LabCorp is not a DTC genomics company.
“We are not DTC, as we are the lab for 23andMe and they are the DTC,” Lindblom said. “This is a ‘client’ just like other client arrangements we have, [including] hospitals, pharma companies for clinical trials, and employers for drug testing.”
— By Turna Ray, originally published on GenomeWeb Daily News

Oxford Center to Use 454 Sequencing, NimbleGen Arrays in Genetic Disease Studies
Roche Diagnostics will support the Oxford Biomedical Research Centre to develop genetic and cytogenetic tests using its 454 sequencing and NimbleGen array platforms, the company said last week.
OxBRC, a partnership between Oxford Radcliffe Hospitals NHS Trust and the University of Oxford, will install several 454 GS FLX sequencing instruments and will use them, as well as NimbleGen arrays, to “work on improved solutions for the analysis of genetic diseases.”
The researchers will sequence several genes in disease samples for private familial mutations using the 454 platform, they will conduct mutation screening in a large number of genes using both the 454 and NimbleGen capture arrays, and they will seek to identify genes and regions with genomic imbalances using NimbleGen CGH arrays.

IGC Taps LabVantage for Lab Software for Cancer Genome Atlas
The International Genomics Consortium will use LabVantage’s Sapphire lab information management software to handle biobanking needs for the Cancer Genome Atlas pilot project, the company said last week.
IGC, a Phoenix, Ariz.-based non-profit, is running the biobank for CGA’s Human Cancer Biospecimen Core Resource component. TCGA is a joint project of the National Cancer Institute and the National Human Genome Research Institute.
The Sapphire solution is used in all the steps of biorepository management including informed consent, clinical data collection, sample and data collection, pathology review, and biomolecule extraction and distribution.

NHGRI to Fund Human Microbiome Technologies
The National Human Genome Research Institute will grant up to $2 million this year to several investigators studying new technologies for obtaining microbe samples for use in sequencing programs in the Human Microbiome Project.
With funding from the National Institutes of Health’s Roadmap Initiative, the NHGRI will support between four and ten programs for up to three years to support the HMP’s efforts to expand the number of microbial genome sequences.
NIH listed a number of potential strategies that these R01 and R21 grants might support, including methods to isolate single microbial cells that are useful in analyzing the large number of species in the human microbiota, and development of methods for culturing additional species.
These new approaches could include ways to obtain pure cultures or mixed cultures of small numbers of species that could be used in genomic analysis studies of the human microbiota.
Investigators could propose methods to isolate, amplify, or clone DNA of whole genomes from individual cells, or could develop methods to “normalize” the complexities of populations at the cellular or DNA level. These methods could facilitate the ability to isolate single cells that are rare within a population, or to perform bioinformatics analysis on metagenomic sequences.
These programs also could include methods that disaggregate cells from the complex mixtures of microbial cells, human cells, and extracellular material.

USDA Awards $4.1M Grant for Honeybee Disorder Studies
Scientists at the University of Georgia will study honeybee genomics and other aspects of honeybee biology under a $4.1 million grant from the US Department of Agriculture in attempts to understand what is causing honeybee colony collapse disorder.
This disorder has caused the loss of between 30 percent and 90 percent of the hives of as many as 25 percent of beekeepers since late 2006.
The Protection of Managed Bees Coordinated Agricultural Project, which is to be funded over four years by the USDA’s Cooperative State Research, Education, and Extension Service, aims to improve the health of managed bee populations in agricultural systems.
The research will involve studies of honeybee genes, breeding, pathology, immunology, and applied ecology that can help explain the disorder that is affecting the colonies.

NIH to Fund Epigenomics of Disease Studies with $8M in FY 2009
The National Institutes of Health will invest $8 million in fiscal 2009 to support researchers studying epigenetics and human disease, which is the fifth part of the Roadmap Epigenomics Program.
Under the “Epigenetics of Human Health and Disease” grants program, the NIH will support between 12 and 16 projects over five years under the R01 mechanism. The goal of these studies is to “transform our understanding of the epigenetic contributions to human disease,” NIH said in the program announcement.
The research will characterize epigenome-wide features and their interactions in cells and tissues that represent human disease states, conditions, or processes.
“Unbiased epigenome-wide (global) mapping approaches must be used to identify marks in diseased, aged, or environmentally compromised human primary cells or tissues,” NIH said in the announcement.
The research should focus on human samples, but other mammalian animal models are allowed in rare exceptions.
Studies also could include follow-up epigenetic approaches that would reveal the function or significance of genomic regions that are identified through the mapping process.
Scientists should propose studies that focus on compromised, abnormal, or diseased states in humans. Examples of these areas could include perturbation caused by exposure to dietary, chemical, social, or behavioral factors, abnormal regulation of fundamental processes during critical stages of life, and dysregulation of processes such as inflammation, apoptosis, and oxidative stress.
Letters of intent for the grants are due Sept. 28, with anticipated start dates in July 2009.

NHGRI Awards Four Groups $31M to Study Role of Genetic Variation in Human Disease
The National Human Genome Research Institute said last week that it plans to award around $31 million over the next four years to four research projects that will explore the link between human disease and genetic variants that have been identified in genome-wide association studies.
NHGRI said in a statement that the rise of GWAS research over the last several years has unearthed more than 300 novel genetic variants associated with common diseases, but these discoveries are only “the first step in the challenging process of piecing together the complex biological picture of common diseases.”
The new program will support new research in existing large epidemiology studies with the goal of linking genetic variants to biological and physical characteristics, such as weight, cholesterol levels, blood sugar levels, or bone density. In addition, researchers funded under the program will investigate how non-genetic factors, such as diet, medications, and smoking, might interact with genetic factors to influence health outcomes, NHGRI said.
"By drawing on the combined strengths of genomics and epidemiology, this innovative program will create a much-needed research resource,” NHGRI Director Francis Collins said in a statement. ”The data it generates will save researchers around the world considerable time and energy, accelerating our ongoing efforts to translate genetic findings into new strategies for improving human health."
Data from the studies will be released through the National Center for Biotechnology Information’s dbGaP database.
Teri Manolio, director of the NHGRI Office of Population Genomics, said that the investigators funded under the program will “collaborate to establish criteria and prioritize specific variants to test within their populations.”
She said that NHGRI’s goal is to investigate about 100 genetic variants in 10,000 participants each year for four years.
The grantees, along with their estimated funding levels over four years and the cohorts involved, are Dana Crawford of Vanderbilt University, who will receive $7 million for the National Health and Nutrition Examination Survey; Gerardo Heiss of the University of North Carolina, Chapel Hill, who will receive $7 million for the CALiCo Consortium, which involves the Atherosclerosis Risk in Communities study, the Coronary Artery Risk in Young Adults study, the Cardiovascular Heart Study, the Hispanic Community Health Study, the Strong Heart Cohort Study, and the Strong Heart Family Study; Loîc Le Marchand of the University of Hawaii Cancer Research Center, who will receive $6.7 million for the Multiethnic Cohort; and Charles Kooperberg of the Fred Hutchinson Cancer Research Center, who will receive $7.6 million for the Women's Health Initiative. 
NHGRI will also fund a data-coordination center for the project, which will be led by Tara Matise of Rutgers University. The center will receive around $3.1 million over four years. The data-coordinating center will be co-funded by the National Institute of Mental Health, which will contribute approximately $1.2 million over four years.

US Genomics Receives $9.1M to Develop Pathogen Detection Tool
The US Department of Homeland Security has awarded US Genomics a contract for $9.1 million to continue to develop its DNA mapping technology for use in detecting airborne pathogens, the company said last week.
The contract was delivered through the Bioagent Autonomous Networked Detectors Program under the DHS Science and Technology Directorate.
"The resources provided under the contract will allow us to perform extensive operational testing and to advance the capabilities of our prototype systems,” said US Genomics CEO John Canepa.
The company said its single molecule approach can be used to rapidly detect multiple bacterial pathogens, toxins, and viruses simultaneously in an environmental sample using a single reagent set.
This technology potentially could be used to detect genetically modified species as well, including “those that may have been deliberately engineered to elude traditional detection methods,” the company said.
DHS awarded US Genomics an $8.6 million contract in May of last year to develop the same technology.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.