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Venter Institute, EPO, eGene, GATC, DNAStar, University of Bristol, Clinical Data, Broad Institute, PIPRA, Gene-IT, Enzo Biochem, OGT, Sequenom

Venter Institute Publishes ‘Largest Ever’ Marine Metagenomics Dataset From Sorcerer Expedition
Researchers from the J. Craig Venter Institute have published several studies from the Sorcerer II Global Ocean Sampling Expedition in PLoS Biology, in which they describe “millions of new genes, thousands of new protein families,” and characterize thousands of new protein kinases.
According to the Venter Institute, the dataset is 90 times larger than other marine metagenomic datasets, “thus making it the largest-ever released in the public domain,” and almost doubles the number of previously known proteins.
The Sorcerer II Expedition began in 2003 with a pilot project in the Sargasso Sea near Bermuda that identified more than 1 million new genes and hundreds of new photoreceptors. The PLoS publications are a result of ocean water sampling conducted from Halifax, Nova Scotia, to the Eastern Tropical Pacific during a two-year expedition.
The JCVI also launched a new database and computational resource for managing metagenomics data called the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis, or CAMERA.
CAMERA was developed by the UC San Diego Division of the California Institute for Telecommunications and Information Technology in partnership with JCVI and UCSD's Center for Earth Observations and Applications at Scripps Institution of Oceanography.
In addition to the CAMERA database, the GOS data is also being deposited in GenBank.
In one of the PLoS papers, the authors describe the results of metagenomic analysis of 37 samples taken aboard Sorcerer II in 2003 and 2004, combined with seven samples collected during the pilot. The group analyzed a dataset of 7.7 million DNA sequences totaling 6.3 billion base pairs.
In another paper, the authors describe 6.12 million new proteins uncovered from 7.7 million GOS sequences by using a new sequence clustering approach. The researchers found that the GOS dataset covered almost all of the known prokaryote protein families and that there were 1,700 unique protein families in the GOS dataset. The researchers were also able to match 6,000 previously unmatched sequences in current protein databases to proteins in the dataset.

EPO Allows eGene’s Bioseparation Patent Application
EGene said this week that it has received notification that the European Patent Office has allowed its patent application entitled "Optical Detection in a Multi-Channel Bio-Separation System."
The company said that this patent would be its 11th granted worldwide.
EGene develops capillary electrophoresis, liquid handling, and automation technologies for use in microfluidic digital analyzer systems.

GATC Installs 454's FLX in its Sequencing Core Lab
GATC Biotech said last week that it has installed 454 Life Sciences’ Genome Sequencer FLX System in its core lab in Konstanz, Germany.
GATC said in January that it had ordered the FLX together with a Solexa 1G Genetic Analyzer with the goal of increasing its sequencing capacity from 15.6 gigabases to more than 130 gigabases per year [In Sequence 01-09-07]. 
Last week, GATC said it will use the FLX to focus on “in-depth analysis of whole transcriptomes,” but also will provide customers with all available FLX applications, including high-throughput genome sequencing, single-sample sequencing, transcriptomics, and functional analysis.

DNAStar Taps GATC as Exclusive Distributor for Parts of Europe
DNAStar said this week that it has signed a distribution agreement with GATC Biotech under which GATC will serve as the exclusive distributor for DNAStar products in Germany, France, Switzerland, and Austria.
The companies have already worked together for more than 10 years. The new agreement also gives GATC a site license for all DNAStar products that it will use as part of its DNA sequencing services business. 
Additional terms of the agreement were not disclosed. 

… as University of Bristol Licenses Its Lasergene Sequence-Analysis Software
DNAStar said last week that the UK’s University of Bristol has licensed its Lasergene sequence analysis software.
The site license gives scientists at the university access to a current version of the software for a three-year period.
Additional terms of the agreement were not provided.

Clinical Data’s Cogenics Group Installs Protedyne's Robotics System for qPCR and Sequencing Automation
Clinical Data said this week that its Cogenics services business has installed a Radius Automation from Protedyne for use in qPCR and CLIA sequencing services.
Clinical Data's Cogenics unit develops GLP-validated research assays for genotyping, sequencing, qPCR and gene expression research. The group was demarcated as a distinct business unit last year when Clinical Data restructured its operations into three divisions.
Cogenics includes capabilities and infrastructure that Clinical Data picked up in its acquisitions of Genaissance, Lark, and Icoria.
Cogenics will use Protedyne’s robotic benchtop platform in its services business. Robert Bondaryk, Cogenics’ general manager, said the automated system will support Clinical Data’s Familion Long QT tests and new CLIA sequencing tests developed by its PGxHealth Division.
Financial terms of the sale were not disclosed.

Broad Institute Wins $100M Donation to Build Psychiatric GenomicsCenter
The Broad Institute last week said it will use a $100 million donation to create a new center to study the genomics and chemical biology of psychiatric diseases.
The Broad said the gift came from the Stanley Medical Research Institute and will fund the creation of the Stanley Center for Psychiatric Research. The funding will support 10 years of research, the Broad said.
The Stanley Center aims to discover the molecular links between mental illness and genetics. It will focus on “systematic surveys” of the human genome to identify genes contributing to schizophrenia and bipolar disorder, and will use high-throughput chemical screening to seek new treatments.
The center will expand Broad’s Psychiatric Disease Initiative, and will be run by the initiative’s founder, Edward Scolnick.
Broad Institute director Eric Lander said psychiatric disease poses particular problems “because you can’t study it in cell culture, like cancer, or measure it with a blood test like diabetes.”
Yet Lander said these diseases “may be the most important application for genomics,” because it can “help uncover the molecular mechanisms of the disease.”

PIPRA to Use Gene-IT’s GenomeQuest
Gene-IT said last week that the Public Intellectual Property Resource for Agriculture will use its GenomeQuest sequence-search software as part of its work in agricultural IP analysis research.
Cecilia Chi-Ham, director biotechnology resources of PIPRA, said in a statement that GenomeQuest is “a valuable additional resource” for researchers exploring the agricultural intellectual property landscape.
Financial terms of the agreement were not provided.
PIPRA includes 42 member institutions who aim “to enable the broadest commercial and humanitarian applications of existing and emerging agricultural technologies.”

Enzo Biochem Receives Favorable Judgment From USPTO in Nucleic Acid Case
Enzo Biochem last week said that the Board of Patents and Interferences of the US Patent and Trademark Office has judged in favor of its patent application for nucleic acid signal amplification over a pair of patents owned by Princeton University, after Princeton had conceded priority to Enzo.
According to Enzo, in an interference declared by the USPTO in August, Enzo was named the senior party, and Princeton – which owned US Patent Nos. 4,882,269 and 5,424,188 – was named the junior party. Princeton had licensed the ‘269 patent to Chiron, which subsequently licensed it to Bayer Healthcare.
At the same time, the USPTO declared another interference involving the same technology, naming Enzo subsidiary Enzo Life Sciences the senior party against Chiron, the junior party, and Chiron’s US Patent No. 5,124,246, also licensed to Bayer. That interference is still pending, Enzo said.
“We believe this development further clarifies the historic account of which party first invented nucleic acid signal amplification technology,” Elazar Rabbani, Enzo’s chairman and CEO, said in a statement.
The technology in question is the basis for several products in clinical diagnostics and life sciences marketed or licensed by several companies. Among these products are the Versant branched DNA assays sold by the diagnostics division of Bayer Healthcare, which was recently acquired by Siemens Medical Solutions.
Enzo said that its invention uses a “bridging” probe or strand to find a nucleic acid of interest and a “signaling” probe or strand that is hybridized to the bridging probe or strand in order to detect an amplified signal.

OGT Will Use Integrated Genomics' P. pastoris Sequence to Develop Microarray
Oxford Gene Technology will use a gene sequence from the Pichia pastoris yeast genome owned by Integrated Genomics to develop a new microarray, the firms said last week.
Under the agreement, OGT will use the sequence to design and build a 60-mer microarray.
OGT will market the array worldwide and offer sample analysis services at its UK lab.
P. pastoris is a methylotrophic yeast commonly used in recombinant DNA and protein expression projects.

Sequenom's Q4 Revenue Jumps 80 Percent as R&D Spend Rises by One-Third
Sequenom last week said fourth-quarter revenues increased 80 percent as R&D spending rose 33 percent and losses decreased 24 percent.
Total receipts for the three months ended Dec. 31, 2006, increased to $7.9 million from $4.4 million in the fourth quarter of 2005. Sequenom said the revenue growth was primarily driven by sales of its MassArray systems.
R&D spending increased to $4 million from $3 million year over year, due in part to “additional expenses associated with intellectual in-licensing and non-invasive prenatal diagnostic technology,” the company said.
Sequenom said losses declined to $5.3 million from $7 million in the year-ago period.
Sequenom said it had around $26.3 million in cash, cash equivalents, short-term investments, and restricted cash as of Dec. 31.
For 2007, the company said it expects annual revenues to grow to between $37 million and $39 million, or as much as 37 percent, year over year. Projected R&D costs will jump to between $16 million and $17 million, or as much as 42 percent over last year; and net losses are expected to swell to between $23 million and $25 million, or as much as 42 percent compared with 2005.
The company also said it expects to begin selling its non-invasive prenatal test for RhD incompatibility on RT-PCR as a "home brew" test by the end of the second quarter. During the year, the firm expects to announce additional commercialization partnerships with CLIA-certified labs.
Sequenom said it is also currently developing the third version of its iPLEX assay, iPLEX III, which it expects to launch by the end of the year. The company said the platform will “reduce by half or more” the current $.035 cost per genotype for a typical study.
Finally, Sequenom said it expects to deliver by the end of the third quarter a proof-of-concept for intermediate-level fetal DNA enrichment, and a “commercially viable” product for fetal DNA enrichment for quantitative genomic tests such as CFTR or Tay-Sachs.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.