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Sequenom to Complete Proof-of-Concept Study for Optical Nanopore Sequencing This Year; Aims for Commercial Application As Early As 2010
Sequenom said this week that it plans to complete a proof-of-concept study for its optical nanopore sequencing technology in the last quarter of this year. Depending on the success of the study, it aims to develop a commercial application of the technology “potentially as early as 2010.”
Sequenom made the remarks in a prospectus it filed this week with the US Securities and Exchange Commission to sell 5.5 million shares of common stock through the open market.
The company licensed the sequencing technology from Harvard University and Boston University last year (see In Sequence 10/2/2007). Sequenom said it believes the technology, which has been developed by Amit Meller at Boston University, “may potentially provide whole-genome sequencing for less than $1,000.”
The San Diego-based firm said that it expects to realize net proceeds of around $73.4 million from the sale of its shares, assuming an offering price of $14.25 per share, which was its closing price on the Nasdaq on Friday.
The underwriters of the offering have an option to purchase an additional 825,000 shares. If that option is exercised, Sequenom expects net proceeds of roughly $84.5 million.
Joint book-running managers for the offering are Lehman Brothers and UBS, while co-managers for the offering are Leerink Swann, Lazard Capital Markets, Oppenheimer, and Rodman & Renshaw.
Sequenom said that it will use funds raised in the offering to develop diagnostic tests for use on its MassArray system and other platforms, as well as for general corporate purposes. The firm also said it may use proceeds to acquire or invest in other businesses, “although we have no current plans, commitments, or agreements with respect to any acquisition,” as of this week.
The MassArray is currently used for fine-mapping genotyping and quantitative gene expression applications, and Sequenom has been developing molecular diagnostic products for the platform as well. According to the prospectus, the firm will be targeting several new applications for MassArray this year.
It plans to launch this month its iSEQ Pathogen Typer for rapidly identifying and typing microbes, viruses, and other haploid organisms. During the third quarter of this year, Sequenom also intends to launch a new application for identifying copy number variations and an epigenomics application for the MassArray.
Later this year, the firm expects to launch its Onco-Gene Mutation Panel for identifying patterns of genes that are associated with the development of specific cancers.

Children's Oncology Group and Helicos Collaborate on Sarcoma Study
The Children’s Oncology Group, a pediatric cancer research cooperative funded by the US National Cancer Institute, is collaborating with Helicos Biosciences to study genomic variation in sarcoma, a bone or soft tissue cancer that generally occurs in children and young adults, the company said this week.
The study, which is funded by the NCI and the Department of Defense, will use Helicos’ sequencing technology and is “aimed at demonstrating the power and versatility” of the platform for DNA sequencing, methylation state analysis, and mRNA expression analysis of normal, primary, and metastatic cell states, according to Helicos.
The scientists will study several samples collected from a single patient, including a normal bone marrow sample and tumor cell lines derived from a Ewing's sarcoma primary tumor biopsy, and metastases obtained after two cycles of chemotherapy.
They hope that a comparison of genomic DNA sequence and RNA expression levels between the normal tissue, primary tumor, and treatment resistant metastases will reveal structural and functional genomic changes associated with clinical aggressiveness and treatment resistance.
The work will be led by Greg Reaman, a professor of pediatrics at George Washington University School of Medicine and Health Sciences, and chairman of COG, and by Timothy Triche, who is chair of pathology at the Children’s Hospital, Los Angeles, and vice chair of translational research at COG.
"We hope to exploit the next-generation capability of Helicos technology to identify rare mutations, polymorphisms, copy number variants, true whole-genome RNA transcriptional activity, and global methylation patterns to identify structural and functional alterations associated with aggressive and treatment-resistant childhood cancer," Triche said in a statement.

ImaGenes to Offer Fasteris Solexa Sequencing Services in Germany and Austria
Genomic service firm ImaGenes will offer next-generation sequencing services provided by Fasteris in Germany and Austria, the companies said this week.
Under the terms of the agreement, ImaGenes of Berlin, Germany, will act as a local distributor for Fasteris’ sequencing services in Germany and Austria. ImaGenes, founded in 2007 as a spin-off from the German Resource Center for Genome Research, specializes in microarray-based genomic and bioinformatics services and harbors a large clone collection.
Fasteris, based in Geneva, Switzerland, offers a range of sequencing services on the Illumina Genome Analyzer platform, including small RNA sequencing, ChIP-Seq, and transcriptome analysis; gene expression profiling; de novo sequencing; and whole-genome or targeted re-sequencing for the detection of genetic variants.
Fasteris said that it has developed barcoding protocols for preparing genomic, small RNA, or gene expression samples and has installed a paired-end module for the Illumina system.
Steffen Hennig, director of bioinformatics and services at ImaGenes, said in a statement that the addition of Fasteris' sequencing technology to its offerings will provide the firm with new genomic or transcriptome sequence information that it can use to design new microarrays.
He added that the company also plans to offer SAGE and CAGE analyses on Fasteris’ Illumina sequencer, “adding a new dimension to studies of transcript regulation.”

Fluidigm Sues Applied Biosystems over Nucleic Acid Amplification Patent
South San Francisco, Calif.-based Fluidigm has filed a lawsuit against Applera and its Applied Biosystems unit in which it is seeking a declaration from the court that it is not infringing an Applera patent relating to DNA amplification.
Fluidigm has not filed a patent infringement suit against ABI, but rather filed the suit in response to a letter it recently received from ABI, demanding the firm “immediately cease and desist from the manufacture, importation, use, sale, and offer of sale of [Fluidigm’s] BioMark System for Genetic Analysis” in jurisdictions in which ABI’s patent is valid.
The patent at issue, US No. 6,814,934, is entitled “Instrument for Monitoring Nucleic Acid Amplification” and was issued to ABI in November 2004. After it was issued, ABI filed patent-infringement suits against Bio-Rad Laboratories, MJ Research, and Stratagene, but the company has since settled all litigation surrounding the patent.
Fluidigm said in its complaint, filed on June 9 in the US District Court for the Southern District of New York, that it believes “the danger that Applera will sue Fluidigm for infringement is real and imminent.”
Fluidigm is seeking a declaratory judgment of non-infringement of the ‘934 patent and a judgment that the ‘934 patent is invalid because it fails to satisfy the conditions and requirements for patentability.
The BioMark system is used for gene expression analysis, genotyping, and digital PCR applications.

NIGMS Sets Aside $7M in FY 2009 to Create Two National Systems Biology Centers
The National Institute of General Medical Sciences has set aside $7 million in fiscal year 2009 to create two National Centers for Systems Biology.
According to a request for applications issued last week, the centers will conduct studies in a variety of areas of systems biology. Applicants for the program may request up to $2 million per year in direct costs for up to five years.
In the RFA, NIGMS defined systems biology as “an integrated experimental, informational, and computational science” that has “benefited from advances in genomics, proteomics, metabolomics, and other high-throughput technologies and is driven by innovations in computational analysis and simulation.”
NIGMS said that systems biology provides a wealth of new knowledge in many areas of biomedical research, but there are “significant conceptual, technological, and cultural challenges to the realization of the systems biology goals.”
The purpose of the program, NIGMS said, is “to promote innovative responses to these challenges.”
NIGMS expects the centers to promote communication, collaboration, and technology and data sharing, and to develop continuous communication and feedback between experimental and theoretical researchers.
The systems biology centers will study synthetic biology systems, multi-scale modeling approaches, signaling, genetic, and metabolic networks, and genetic variations in relation to complex phenotypes.  

Celera Registration Statement Declared Effective; Split with ABI Expected on July 1
Celera’s registration statement with the US Securities and Exchange Commission was declared effective by the regulatory body last week, clearing the way for Celera’s formal separation from sister company Applied Biosystems and parent firm Applera.
The split will take place at 12:01 a.m. EDT, on July 1, subject to certain conditions, including receipt of certain contents and listing of Celera’s stock on the Nasdaq, according to an Applera statement.
Celera had filed for the split in April. Under terms of the separation, shareholders of the Applera Group-Celera Group tracking stock will receive one share of new Celera Corporation shares for each share of the tracking stock they currently own. Upon completion of the deal, Celera will become an independent, publicly traded company.
Celera will trade on the Nasdaq under its current ticker symbol, CRA, and its current tracking stock will be delisted from the New York Stock Exchange.

California Letters to Consumer Genomics Firms Cite Lab Certification, Physician Oversight
Lab certification and physician oversight are the two primary issues that the State of California has with consumer genomics firms, which it believes are running afoul of state law.
Earlier this month, the California Department of Public Health sent warning letters to thirteen consumer genetics companies telling them to stop offering their tests to the state’s residents. Two firms that have confirmed that they have received letters from the CDPH are DNATraits and Navigenics.
Houston, Texas-based DNATraits specializes in genetic testing to identify susceptibility to inherited diseases and characteristics. The letter it received from the CDPH, posted yesterday on the website of the magazine Wired, stated that by offering its service to California residents over the Internet, DNATraits is violating state Business and Professions codes concerning clinical licensing and physician oversight.
Navigenics, which is based in California, said that it believes its service is in compliance with the law. The firm sends its tests to Affymetrix's CLIA lab for processing.
In order to be licensed in California, the letter states, the company “must provide satisfactory validation documentation to verify the test performance specifications of all genetic tests.”
According to California law, which was cited by the CDPH, “No clinical laboratory license shall be issued by the department unless the clinical laboratory and its personnel meet the CLIA requirements for laboratories performing tests or examinations classified as of moderate or high complexity, or both."
The letter also said the companies are violating a code that prohibits the offering of a clinical laboratory test directly to consumers without a doctor’s order, except in special cases.
The state also requires that tests that are not subject to US Food and Drug Administration clearance meet certain performance specifications for accuracy, analytical sensitivity and specificity, and precision, among others.
Until companies offering these genetic tests apply for and obtain licenses for performing such services in California, they must include a clause in their advertising saying that their services are prohibited for California residents.
DNATraits and the CDPH did not return calls or e-mails as of press time.
Navigenics e-mailed a statement to In Sequence’s sister publication GenomeWeb Daily News saying that it would work with the CDPH to resolve the department's concerns.
“We are confident that our approach, which incorporates physicians, genetic counselors, and a CLIA-certified lab, is evidence of our commitment to quality and compliance while providing consumers with a valuable health and wellness service,” Mari Baker, president and CEO of Navigenics, said in the statement.

UK Insurance Group Extends Ban on Requiring Genetic Test Information
A UK insurance industry group will extend a rule through the year 2014 that keeps insurance customers from having to disclose genetic information from predictive tests.
The Association of British Insurers agreed on June 13 to extend a moratorium that was initiated in 2001 on insurance companies requiring results from customers.
The extension on the moratorium “means people can insure themselves and their families, even if they have had an adverse result from a predictive genetic test,” ABI Director General Stephen Haddrill said in a statement. He said it “has proved effective since its introduction” and that it “works well for consumers.”
The agreement to extend the moratorium through 2014 came after a scheduled review of the policy, and the next review will take place in 2011.
The moratorium covers policies worth up to £500,000 ($987,000) for life insurance and £300,000 for critical illness insurance.
Above these levels, the group said, its member insurers have agreed not to use predictive genetic tests unless the test has been approved by the government.
According to ABI, the only genetic test approved so far by the Genetics and Insurance Committee is for Huntington’s Disease and is for life insurance policies valued over £500,000.

Industry Survey Shows 'Upscale' Consumers Wary of Genetic Tests
Americans are still very much in the toe-dipping phase when it comes to taking genetic tests, and are concerned about privacy and learning something frightening about themselves, according to a newly released survey from Burrill & Company and ChangeWage Research.
In a survey the two firms conducted of 550 “upscale business professionals” in late May about attitudes regarding several health-related issues, including personal genetic tests, respondents said that “doctors are still the most important source of information for consumers on genetic testing,” Burrill & Co. CEO Steven Burrill said in a statement.
"While consumers are taking a more active role in their own healthcare, doctors remain the gatekeepers. Consumers are turning to them for guidance on genetic tests," Burrill added.
The surveyors found that only five percent of consumers said that they were “very likely” to take a disease-specific genetic test in the next few years, and 15 percent said they would be “likely” to take one.
A total of 35 percent said that they would not submit to genetic tests, with 14 percent citing concerns about privacy, 5 percent saying they would not want to know about the results of their tests, and 16 percent saying both reasons would compel them to avoid genetic tests.
Although more than 50 percent of those who responded said that they are concerned about getting cancer or heart disease, only 4 percent of those said they had taken a genetic test for a particular disease. Two-thirds of those who did have a genetic test were advised to do so by a doctor.
The respondents had about the same comfort level of sharing genetic information with their spouses or partners as with their doctors, 72 percent and 71 percent, respectively.
Only 22 percent of those who responded were comfortable with sharing results from genetic tests with institutions for research purposes. Very few would give up that information to health insurance companies (3 percent), and even fewer to employers (2 percent) and prospective employers (1 percent).
From these findings, Burrill & Co. concluded that “makers of these tests might have more success penetrating the market by working through doctors rather than trying to make the case for their products directly to the consumer.”
The company said “The Personalized Medicine and Wellness Survey” is the first of a three-part study on the subject that will be released sometime this summer.

NC State Researchers Finish Tobacco Genome Mapping Project
Researchers from North Carolina State University have completed the Tobacco Genome Initiative, which sequenced the majority of the gene space of tobacco, Nicotiana tabacum.
The tobacco genome contains around 4.5 billion bases, but only 20 to 25 percent of the plant’s genome is defined as "gene space." Charles Opperman, director of the Center for the Biology of Nematode Parasitism and a co-director of the project, told In Sequence’s sister publication GenomeWeb Daily News via e-mail that researchers did not sequence the entire genome, but used a methyl filtration approach to sequence the majority of the plant’s gene space.
The five-year, $17.6 million project was funded by tobacco firm Philip Morris USA.
In addition to the tobacco plant, researchers did a partial sequence of the genome of N. benthamiana, an amphiploid species with 38 chromosomes that is closely related to tobacco and is an important model host for studying plant-disease interactions, according to NC State.
The tobacco plant is a member of the Solanaceae family, which includes the tomato, eggplant, potato, and pepper plants. Researchers hope that the Tobacco Genome Initiative will benefit studies on these plants as well.
Opperman said that data from the project has been released to public databases, including GenBank.

New Genome Sequence Provides Clues About Vertebrate Evolution
Scientists last week reported that they have sequenced the genome of a small marine invertebrate — a feat that is providing a wealth of information about vertebrate evolution.
In a paper published last week in Nature, an international team of researchers report sequencing the genome of an amphioxus, also called lancelet, species called Branchiostoma floridae. The sequence provided them with information not only about relationships between chordate groups, but also about the characteristics of their shared common ancestor.
Three additional papers appearing online in Genome Research last week include analyses of amphioxus sequence data to answer specific questions about vertebrate evolution.
Amphioxus are small, eel-like invertebrate chordates that live at the bottom of the ocean. Called cephalochordates, amphioxus share a common ancestor with vertebrates and urochordates, such as sea squirts. And, like other chordates, amphioxus have a segmented body plan, a hollow dorsal nerve tube and a notochord, a post-anal tail and gill slits.
“Amphioxus was selected because of its evolutionary relationship to vertebrates,” lead author Nicholas Putnam, a post-doctoral fellow affiliated with the US Department of Energy’s Joint Genome Institute and the University of California at Berkeley, told In Sequence’s sister publication GenomeWeb Daily News. “It’s one of the living relatives to the vertebrate, phylogenetically.”
The amphioxus genome sequence is helping to clarify relationships between the three chordate groups, he noted. At one time it was widely believed that amphioxus was a sister branch to vertebrates. But mounting evidence suggests that they are actually more distantly related than sea squirts and other urochordates.
Indeed, the amphioxus genome sequence supports the idea that amphioxus branched off from the chordate common ancestor before urochordates, diverging from vertebrates some 520 million years ago.
As such, the sequence shines new light on the relationships between living chordates. It also provides clues about the characteristics of their ancient common ancestor. “It gives sort of a starting point for changes that happened on the vertebrate stem,” Putnam said.
Putnam and his co-workers used whole-genome shotgun sequencing to sequence the roughly 520-megabase amphioxus genome, with collaborators at Japan’s RIKEN Genomic Sciences Center sequencing the BAC ends and ESTs.
The genome proved to be highly polymorphic — more so than that of any other organism reported so far — containing an estimated 21,900 protein-coding loci.
Using comparative genomics, the researchers identified genes that were conserved between amphioxus and vertebrates. They found another, somewhat surprising, similarity: non-coding sequences. “We weren’t expecting it, but we did find a number of conserved non-coding sequences,” Putnam said.
The researchers also found evidence that vertebrate genomes have undergone two rounds of whole-genome duplication. That’s consistent with the idea — first proposed by Susumu Ohno in 1970 — that genome duplication and vertebrate evolution go hand-in-hand.
In addition, the researchers wrote, it’s “tempting to speculate” that these genome duplications in ancestral jawed vertebrates paved the way for complex body plans and physiology. Consistent with this notion, they noted, genes linked to processes such as developmental signaling and gene regulation are often present in multiple copies in living vertebrates.
— By Andrea Anderson; originally published on GenomeWeb Daily News

Scientists Use DNA Barcoding to ID Canadian Freshwater Fish
Scientists can accurately identify the majority of Canadian freshwater fish species using DNA “barcodes” that are just a few hundred base pairs long, new research suggests.
Using a newly developed set of barcoding standards, a team of Canadian researchers sequenced a DNA barcode — part of a mitochondrial gene — from 95 percent of the known freshwater fish species in Canada. The work, published in last week’s issue of the journal PLoS ONE, demonstrates that the DNA sequence can accurately and effectively distinguish between more than 90 percent of the species tested. It also exposed sequence divergence between some individuals lumped into the same species — suggesting cryptic species may exist or be in the process of forming.
DNA barcodes are short stretches of DNA that are used as molecular tags by researchers to classify different plant and animal species. Proponents see it as a fast and efficient way to accurately identify organisms at any stage in their life cycle, uncover previously unrecognized species, and aid research on biodiversity, predator-prey relationships, and invasive species.
Even so, the concept of DNA barcoding is somewhat controversial. Some critics have claimed that the proposed benefits of DNA barcoding are overblown, arguing that barcoding is a poor alternative to other classification methods such as morphology and traditional taxonomy.
In the past, barcoding has proven itself highly accurate in marine fish, co-author Robert Hanner, associate director for the Canadian Barcode of Life and biologist at the University of Guelph, told GenomeWeb Daily News last week. But, he added, some believed it would be much more difficult to distinguish between freshwater fish, which live in more changeable freshwater ecosystems or “harbors of speciation.”
“The suspicion was that there’d be more hybridization going on,” Hanner said.
As part of the international Fish Barcoding of Life, or FISH-BOL, initiative, the team set out to test the validity of DNA barcoding as a method for distinguishing between individuals from similar species, specifically freshwater fish. They amplified barcode DNA from 1,360 individual fish representing 190 of Canada’s 203 documented freshwater fish species.
To gauge variability between populations, the team attempted to sample between three and five individuals per site and at least two different sites whenever possible. For each species, they tested between one and 17 different individuals.
They then bi-directionally sequenced about 650 base pairs of “barcode” sequence from the mitochondrial cytochrome c oxidase I, or COI, gene of each individual. Based on their analysis of these barcodes, the investigators reported that the set of barcodes they had were adequate for identifying about 93 percent of the species tested.
For the most part, genetic distances were much higher between species in a genus than they were between individuals belonging to the same species. On average, the researchers found 27 times greater genetic distances between than within species. Just over a dozen species — about seven percent of those tested — had barcodes that were the same as or overlapped with those of other species.
And Hanner noted that DNA barcoding will likely be useful even for species that share sequence because it provides enough information to narrow a Canadian freshwater fish down to two species out of more than 200.
In combination with other types of data, the work may also fuel a re-assessment of freshwater fish taxonomy. The researchers detected both similarities between sister species, but also deep genetic divergence between some individuals assigned to the same species.
“This just reflects the fact that speciation is a process,” Hanner said. “We do have these sort of evolutionary bursts taking place.” But for the most part, he added, the fish species are sufficiently distinct to be distinguished from one another by DNA barcoding.
Data from the freshwater fish barcoding project will be available through the actively curated Barcode of Life Database, called BOLD, which contains raw sequence data and detailed information about specimen taxonomy.
Although there are hundreds of DNA barcoding papers in print, Hanner noted, “This is one of the first to implement barcode standards.” Those standards were developed by the Consortium for the Barcode of Life and denote barcoding data that meets a set of criteria for sequence quality as well as availability of additional information such as when and where specimens were collected, the primers used to amplify the barcode, and so on, Hanner explained.
Barcode sequence data that meets the standards will eventually be available through GenBank and other databases under the reserved keyword “BARCODE.”
The FISH-BOL team is currently expanding their work to include all North American freshwater fish — work that is already underway. Hanner said the consortium has also gathered information about some 5,000 fish species internationally.
— By Andrea Anderson; originally published on GenomeWeb Daily News

The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.