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Pacific Biosciences, Li-Cor Biosciences, Leiden University Medical Center, Eurofins MWG Operon, Affymetrix, Synthetic Genomics, Asiatic Centre for Genome Technology, Roche, Institute of Genomics and Integrative Biology, Oxford Nanopore Technologies, GINA,

Pacific Biosciences Acquires Li-Cor's Single Molecule Sequencing Technology
Pacific Biosciences said this week that it has acquired Li-Cor Biosciences’ single molecule sequencing technology, called “sequencing by incorporation.”
Along with Li-Cor’s technology, Menlo Park, Calif.-based PacBio acquired a number of issued US and foreign patents, as well as pending US applications covering the technology, which broaden PacBio’s existing intellectual property related to its single-molecule real-time sequencing technology.
The company said that Li-Cor, which is based in Lincoln, Neb., has retained rights to intellectual property for sequencing enzymes that were designed for polymerase-based sequencing-by-synthesis. It noted that Li-Cor has an active out-licensing program for those enzymes.
In addition to the acquisition, PacBio said that the agreement includes ongoing opportunities to collaborate with Li-Cor’s scientists on sequencing enzymes.
"Li-Cor's early developments in the field of sequencing by incorporation, as well as their comprehensive intellectual property portfolio surrounding those developments, provide a unique and attractive opportunity for us to combine our resources to build a strong foundation from which to ultimately deliver on the huge advantages of single-molecule real-time sequencing by synthesis," Hugh Martin, Pacific Biosciences chairman and CEO, said in a statement.

Dutch Scientists Use Illumina GA to Generate 8X Coverage of Woman’s Genome
Scientists at the Leiden University Medical Center in the Netherlands have sequenced the genome of a clinical geneticist working at the institute to eight-fold coverage using Illumina’s Genome Analyzer, LUMC said this week.
Marjolein Kriek is the first woman as well as the first European to have her genome sequenced, the institute claims.
After analyzing the genome sequence, the scientists plan to make it publicly available with the exception of “incidental privacy-sensitive findings.”
For their project, they used an Illumina Genome Analyzer that was installed at the Leiden Genome Technology Center, the genomics facility of LUMC and the Center for Medical Systems Biology, in January of 2007.
Within six months, they generated approximately 22 gigabases of sequence data, or almost eight-fold coverage of the genome, at a cost of approximately €40,000 ($63,000), which does not include downstream bioinformatics analysis. The project was run as a “side operation,” filling run time between other projects, and would otherwise have taken 10 weeks, LUMC said.
The institute did not say whether the project involved paired or unpaired sequence reads. The data analysis is estimated to take another six months.

Eurofins Tapped to Help Crack Barley Code
Eurofins MWG Operon will provide DNA sequencing and assembly services to sequence parts of the barley genome, the firm said this week.
The company will provide its services to a project that is part of the International Barley Sequencing Consortium. The project is backed by the German Ministry for Education and Research and involves the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, the Fritz-Lipmann-Institute for Age Research in Jena, the Munich Information Center for Protein Sequences, and the Julius-Kühn-Institute in Quedlinburg.
Eurofins MWG Operon will tackle gene-rich parts of the barley genome by multiplex sequencing BAC pools using its 454 GS FLX system and customized software.
Longer term, the IBSC, which involves institutions in Germany, the US, Australia, Japan, Finland, and Scotland, aims to develop a high-quality reference sequence of the entire genome, which eventually would be used to harness the plant’s genetic diversity to improve its use as a food crop.
Barley, Hordeum vulgare L., was domesticated over 10,000 years ago as one of the first crop species. The barley genome is around 5.3 billion base pairs in size.

Affymetrix Plans to Expand Genetic Analysis Footprint via M&A; May Look Beyond Arrays
Affymetrix is planning to expand its presence in the genetic analysis market through an “aggressive” merger-and-acquisitions strategy that will likely extend beyond the firm’s foothold in the microarray sector, company officials said recently.
Speaking to investors at the recent Baird Growth Stock Conference in Chicago, Affy CFO John Batty said that the company is seeking to “acquire technology that will allow us to compete in the broader genetic-analysis market.”
Batty’s comments follow several statements Affy officials have made about the company’s M&A plans in recent months. During the firm’s fourth-quarter earnings conference call in January, for example, President Kevin King said Affy is “bullish and aggressive about growing our business” and will “do more acquisitions going forward” in order to cast a “pretty broad net across this whole field of genetic analysis.”
At the Baird conference, Batty said that the company has spent the last year and a half developing “a long-range strategic plan” that sets out “a roadmap for the technologies we need to develop internally or acquire from outside sources.”
To date, Affy has typically made acquisitions to bolster the capabilities of its flagship GeneChip microarray platform. In 2000, the company bought Neomorphic for $70 million to gain access to its computational genomics and bioinformatics capabilities. And in 2005, it purchased ParAllele Bioscience for $121 million for its molecular inversion probe technology.
Affy’s $75 million acquisition of USB, which closed in January, was also related to its chip business. The company said it plans to become a direct provider of reagents that were previously manufactured by other companies and bundled together with its GeneChip products. Meanwhile, Affy is developing a sequencing-on-array technology based on enzymes gained through the USB deal (see In Sequence 1/15/2008).
According to Batty, though, the company is now ready to buy technologies that may not necessarily integrate into its array business. “We have pointed out in our discussions with investors that we are really platform agnostic,” he said.
“Our mission is really to be the leader in genetic analysis tools, and that means that we may add additional platforms to the Affymetrix portfolio to really expand the reach of our solutions across the entire workflow, from discovery all the way to validation and routine use,” Batty added.
Affy has not provided any more detail on what kinds of technologies it would buy. The company had $431 million in cash and cash equivalents as of March 31.
— The complete version of this article appeared last week in BioArray News, In Sequence’s sister publication.

Synthetic Genomics, Malaysian Company Sequence Draft of Oil Palm Genome
Synthetic Genomics and a Malaysian genomics company have completed a draft sequence assembly and annotation of the genome of the oil palm, a tree that is used primarily to produce cooking oil but which could be employed for other uses such as biofuel, the companies said last week.
The Asiatic Centre for Genome Technology, a subsidiary of the palm oil plantation company Asiatic Development Berhad, also is working with Synthetic Genomics to sequence and analyze the genome of another oilseed crop, the jatropha, as well as the material of some of the microbes found around these plants, the companies said.
The oil palm genome is roughly 1.8 billion base pairs in size, which is around four times the size of the rice genome and around two thirds that of maize, the companies found. The jatropha genome is roughly the same size as the rice genome, at around 500 million base pairs.
The researchers sequenced a combination of two types of the oil palm to create a seven-fold coverage of the plant’s genome, which they will continue to sequence and analyze in order to create a reference genome.
The companies said that the jatropha crop, which grows well on land that is not good for food production, can be used to produce clean, renewable fuels. They plan to continue to sequence and analyze the jatropha genome to ten-fold coverage.
"The genome sequences of these highly productive oilseed crops will enable the in-depth understanding of genes encoding for plant yield and health and foster the development of improved plant varieties,” Synthetic Genomics CEO J. Craig Venter said in a statement. "Our goal is to harness this knowledge to produce improved feedstocks, renewable fuels, biofertilizers, and disease-control solutions."
The companies said the oil palm genome study has already found useful information about the palm’s genome that could be used to help modify plant yield, oil quality, growth, disease tolerance, and other qualities.
"The completion of the first draft sequence of the oil palm genome and progress on the jatropha genome are significant milestones towards the genetic improvement of these inherently high yielding oil crops,” said ADB Chief Executive Tan Sri Lim Kok Thay. “Unlocking the knowledge encoded in the genomes could further increase our understanding of these important crops which could lead to substantially improved oil yield.”
The companies did not say when they expect to complete the jatropha genome or whether they plan to publish their results.

Roche Places 454 GS FLX at India's IGIB
Roche said last week that it has installed a Genome Sequencer FLX System at the Institute of Genomics and Integrative Biology in Delhi, India.
Roche said that IGIB plans to use the system for a range of applications, “with a special focus on metagenomics and de novo genome sequencing.”
The Centre for Genomic Application, a collaboration between IGIB and the Institute of Molecular Medicine, will use the system to provide sequencing services, Roche said.
Financial terms of the agreement were not disclosed.

Oxford Nanolabs Changes Name to Oxford Nanopore Technologies
Oxford NanoLabs has changed its name to Oxford Nanopore Technologies, the company said last week.
The new name better reflects its ambition to develop nanopore technology into molecular detection and analysis products, according to the firm.
The UK-based company said its nanopore technology is “a revolutionary method” that could be used for DNA sequencing, diagnostics, drug development, and defense applications.
The company, founded by University of Oxford professor Hagan Bayley, raised £10 million ($19.6 million) in private financing earlier this year (see In Sequence 4/8/2008) to speed its R&D program, which is focused on developing a nanopore-based DNA sequencing method.

Bush Signs Genetic Nondiscrimination Bill Into Law
US President George W. Bush signed into law the Genetic Information Nondiscrimination Act last week, making it illegal to discriminate on matters of employment and health insurance in the US based on genetic information.
A law that was more than a decade in the making, GINA was signed last week by the president after passing in Congress with near unanimous support in both houses after legislators managed to reach agreements on certain language that had previously stopped the bill in the Senate.
Before signing GINA in the Oval Office, President Bush said “it protects our citizens from having genetic information misused, and this bill does so without undermining the basic premise of the insurance industry.”
The law was envisioned to protect an individual’s civil rights against discrimination as genetics technologies become more commonplace. That bill was particularly forward-looking over a decade ago when it was proposed by Congresswoman Louise Slaughter (D – NY) and backed by Senator Olympia Snowe (R – Maine).
“This is a tremendous victory for every American not born with perfect genes – which means it’s a victory for every single one us,” Slaughter said in a statement last week, adding that “we are all potential victims of genetic discrimination.”
“Up until now, our laws have not kept pace with emerging technology, and doubts about the misuse of genetic information are preventing Americans from participating in tests that could improve their long-term health,” Snowe said in a statement.
"Americans have been waiting a long time for this bill, but the wait has been worth it," Johns Hopkins University's Genetics and Public Policy Center Director Kathy Hudson said in a statement. "Our challenge now is to make sure that doctors and patients are aware of these new protections so that fear of discrimination never again stands in the way of a decision to take a potentially life-saving genetic test.”
The law will not be implemented immediately. The health insurance protections are expected to begin in about a year and the employment rules are to take full effect in about a year and a half, according to Genetic Alliance.
Sharon Terry, Genetic Alliance’s CEO, said that it “is now our responsibility to make sure the public knows that these new protections are in place.” Terry said that “the promise of genetic testing and disease management and prevention can be realized more fully.”
“Once this legislation has taken effect, clinicians will be able to order genetic tests for patients and their families in a manner that ensures the full realization of the advantages of personalized medicine, while also easing patients’ concerns about the risk of genetic discrimination by insurance companies and employers based on this data,” said Joann Boughman, executive VP of the American Society of Human Genetics.
The law prohibits group health insurance plans and issuers from basing determinations about premiums or contributions on an individual’s genetic information. These companies may not request, require, or buy the results of genetic tests, and they are prohibited from disclosing genetic information.
Those who issue Medigap policies also will not be allowed to make conditions about eligibility based on genetic information.
Under the law, employers will not be allowed to use genetic information in considerations regarding hiring and firing, or in drafting conditions of employment. Like health insurance companies, employers will not be allowed to request, require, or buy an individual’s genetic information, and the law prohibits disclosing private genetic information. The law extends to employment agencies and to labor organizations.

Metagenomics Uncovers New Information About Skin Microbes
A new metagenomic study by National Institutes of Health researchers has revealed the diverse microorganisms residing on human skin — and lays the foundation for larger studies of the skin microbiome.
In a paper published online last week in Genome Research, NIH scientists used 16S rRNA sequencing to survey the microbes on five people’s inner elbows. They identified a common microbiome as well as microorganisms that varied between individuals’ right and left elbows and from person to person. The study, part of the NIH’s Human Microbiome Project, also compared three different sampling methods — an analysis that will inform future projects cataloguing microbial diversity on and within human skin.
The Human Microbiome Project, part of the NIH Roadmap for Medical Research, is intended to explore the role of microorganisms in both health and disease, NIH researcher Julie Segre, the paper’s senior author, told In Sequence’s sister publication GenomeWeb Daily News. By cataloguing the beneficial or harmless microorganisms found on human skin, it may be possible to better understand the changes in the microbial community that are associated with disease states, she said.
Traditionally, studies of skin microbes have depended on culturing bugs in the lab and then identifying them. While that approach is useful, researchers say it misses a great deal of the real microbial diversity on the skin and elsewhere, because some microbes can’t be cultured in the lab or require very specific growth conditions.
To get around that problem, the team took a metagenomic approach, extracting DNA from uncultured microbes. They used conserved primers to amplify 16S rRNA from microbes found on both inner elbows of five individuals using three different sampling methods — swabs, scrapes, or punch biopsies. Overall, the three sampling methods gave very similar results, although more bacterial cells were collected by scraping and punch biopsy than by swabbing.
The researchers sequenced roughly 200 clones from each library using an ABI 3730x1 sequencer. After tossing out chimeric sequences, they performed phylogenetic analysis on nearly 5,400 sequences and classified the bugs in 113 phylotypes or “operational taxonomic units” containing organisms whose sequences were at least 97 percent similar.
About half of the OTUs and some 90 percent of the total sequences represented bacteria in the Proteobacteria group. The majority of these — some 59 percent — belonged to the genus Pseudomonas, although the researchers also found Janthinobacterium, Serratia, and Stenotrophomonas.
“It was actually quite surprising that Proteobacteria was the dominant bacteria,” Segre noted, since culturing studies suggested Staphylococcus epidermidis would be prevalent. As it turned out, S. epidermidis and Propionibacterium acnes — another bug that was thought to be quite common on skin — actually represented less than five percent of the microbes detected.
The researchers also found sequences from the Actinobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Cyanobacteria divisions and from a group of microorganisms that was nearly 94 percent similar to an unknown organism found in agricultural soil samples.
These results overlapped, to a certain extent, with the findings of a 2007 metagenomics paper on forearm microbes published by New York University researchers in the Proceedings of the National Academy of Sciences. But Segre’s team found a distinct microbiome on the inner elbow skin.
Segre suspects the disparate results reflect real differences in the microbial communities at the two skin sites. “The microbiome — the bacterial species and their diversity — are really quite different,” she said, suggesting there is great microbial diversity between skin on different parts of the body.
For the most part, the variation between the five individuals was similar to that detected when the researchers compared the microbial communities on each person’s left inner elbow with their right. But there was an exception: one individual was colonized by Staphylococcus, a bug previously shown to colonize some five to 10 percent of healthy adults without causing clinical symptoms.
Eventually, the researchers hope to tease apart the gene-environment interactions influencing microbial diversity, Segre explained. To begin doing this, they compared the microbes found on human skin with those found on mouse ear skin. The microbiome of mouse ear skin appeared to be remarkably similar to that of the human inner elbow.
In the future, Segre said, the information gained from these early experiments will be applied to help culture and eventually sequence reference genomes for skin microbes. Investigators participating in the Human Microbiome Project also plan to do larger studies, surveying 250 individuals to catalogue the microbes at five sub-sites: the gut, mouth, nose, skin, and vagina.
— By Andrea Anderson; originally published by GenomeWeb Daily News.

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.