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City of Hope, Helicos, MWG, 454, SeqWright, Wellcome Trust, Celera, Applera, International Barley Sequencing Consortium, CLC Bio, DNAStar, Academy of Sciences of the Czech Republic, University of the Mediterranean, Northeastern University, Broad Institute

City of Hope and Helicos Collaborate on Cancer Study
Researchers at the City of Hope research and treatment center in Duarte, Calif., will use Helicos BioSciences’ single-molecule sequencing technology to study known cancer-associated gene variants and potentially discover new mutations within those genes, Helicos said this week.
Under the collaboration, Helicos will provide City of Hope researchers with sequence data from its True Single Molecule sequencing technology.
“Our potential to personalize the treatment of cancer will be directly dependent on our ability to understand the genetic variation among individual patients as well as the genetic heterogeneity of their tumor genomes,” Steve Sommer, director of the department of molecular genetics and director of the department of molecular diagnosis at City of Hope, said in a statement.

MWG Biotech Purchases Second 454 GS FLX
German sequencing service provider MWG Biotech has purchased a 454 Genome Sequencer FLX from Roche, 454 said this week.
This is MWG Biotech’s second GS FLX purchase. The instrument will be used for de novo sequencing and re-sequencing of genomes, metagenomics, RNA analysis, and targeted sequencing of specific DNA regions, 454 said.
MWG decided to add the instrument “in order to meet the demands of a steadily increasing number of sequencing customers across Europe,” according to a company statement.
MWG Biotech bought its first GS FLX in July of last year.

SeqWright Adds 454 GS FLX System to Offering
SeqWright said this week that it has purchased a 454 GS FLX DNA sequencing system from Roche.
The Houston, Texas-based sequencing service provider had previously purchased a SOLiD sequencer from Applied Biosystems.
It said the GS FLX would complement the ABI system and enable it to offer a more diverse array of next-generation services, including de novo sequencing of higher organisms. “For example, utilizing the strengths of the two systems, SeqWright can create a scaffold sequence using the long reads of the GS FLX and subsequently combine that scaffold with the vast amounts of sequence data from SOLiD to build up the genomic coverage,” the company said in a statement.
SeqWright CEO Fei Lu told In Sequence that the new instrument is scheduled to be installed in two weeks. The company will not initially offer the extra-long reads that 454 is currently making available to early-access customers.

Wellcome Trust Expanding Genomic Disease Studies
A new series of genome-wide association studies, driven by the Wellcome Trust and involving up to 60 international institutes, will analyze DNA from approximately 120,000 people, the Wellcome Trust said this week.
The Wellcome Trust Case Control Consortium is using £30 million ($59.5 million) to study genomic contributions to 25 diseases, as well as studying the genetics of learning in children, and individuals’ response to statins, the Wellcome Trust said.
"Breakthroughs in our understanding of the human genome and rapid advances in sequencing technology mean that we are able to do very powerful analysis much faster and on a vastly bigger scale than ever before," said University of Oxford Professor Peter Donnelly, who will chair the consortium.
The Wellcome Trust Sanger Institute in Hinxton, Cambridge, will “devote a large part of its high-throughput genotyping pipeline” to perform DNA testing, and most of the data analysis will be performed by the Wellcome Trust Center for Human Genetics at the University of Oxford.
During the two-year project, the Wellcome Trust and its collaborators will hunt for genes that could be linked to various diseases, including multiple sclerosis, schizophrenia, asthma, and others. The researchers will study between 500,000 and 1 million SNPs per sample and “a comprehensive set of copy number variants,” the Wellcome Trust said.
In February of this year, the Wellcome Trust made public its plan to massively increase spending on biomedical research, saying that it expects to lay out around £4 billion over the next five years to respond to medical needs and to pursue scientific opportunities.
Last year, the Wellcome Trust Case Control Consortium published data from its £9 million study of genetics and disease that involved 17,000 people across the UK.

Celera Takes Next Step in Planned Split from Applera
Celera has filed with the US Securities and Exchange Commission a preliminary prospectus to split off from parent company Applera.
The filing is the latest step in the previously announced plans of Applera to split its two businesses — Celera and Applied Biosystems — which currently trade as tracking stocks, into two independently traded companies.
Applera filed with the SEC in late February to separate the two firms. Under the terms of the separation, shareholders of the Applera Group-Celera Group tracking stock would receive one share of new Celera Corporation shares for each share of the tracking stock they currently own. Upon completion of the deal, Celera would become an independent, publicly traded company.
Celera confirmed in its filing yesterday that it will trade on the Nasdaq under its current ticker symbol, CRA, and its current tracking stock would be delisted from the New York Stock Exchange. Celera President Kathy Ordoñez is listed as president, CEO, and director of the firm, which will continue to be based in Alameda, Calif.
Among the risk factors cited in the prospectus is that the allocation of intellectual property rights between the firms could potentially harm Celera’s business.
“Under the separation agreement with Applera, intellectual property that has been developed by the Celera Group or used primarily in our business will be transferred to us on or prior to the split-off date,” Celera said in the filing.
“However, some intellectual property currently used in substantially all of our diagnostic products is also used by the Applied Biosystems Group and will be retained by Applera," it added. "All intellectual property that will be retained by Applera and that is used in our diagnostic products will be made available to us through a supply agreement we will enter into with Applera on the split-off date, except that intellectual property used in our hepatitis C virus, or HCV, analyte specific reagents will be made available to us under a license agreement that we will enter into with Applera on the split-off date.”
Celera also said it would no longer have early access to ABI’s instrumentation, reagents, and other technologies for use in its diagnostic products and services.
In addition, Celera said that after the split, “Applera may directly compete with us or enable others to compete with us in human diagnostics, except that for a period of three years following the split-off date, Applera, subject to specified exceptions, will be restricted in its ability to supply any reseller with capillary electrophoresis sequencers for commercialization of human diagnostic tests outside of Asia, Africa and South America, nor will it be able to itself commercialize these tests anywhere in the world for the same three year period.”
ABI’s common stock will continue to trade on the New York Stock Exchange.
The split-off date has not been finalized, but officials from both Celera and ABI have previously said that they expect it to happen by the end of the firms’ fiscal year on June 30.

Barley Genome to be Sequenced by 2012
An international group of scientists expects that by 2012 it will complete the genome sequence of the barley genome, a program that could potentially increase survival and yield of the crop.
The effort to sequence the barley genome includes eight institutions in the US, Australia, Japan, Finland, Germany, and the UK, which together make up the International Barley Sequencing Consortium.
Andreas Graner, of the Leibniz Institute of Plant Genetics and Crop Plant Research, said in a statement that the partners “are providing active contribution toward sequencing the barley genome, which is aimed to be completed by 2012.’’
The plan was announced at the 10th International Barley Genetics Symposium, which is currently being held in Alexandria, Egypt, by the International Center for Agricultural Research in the Dry Areas and Bibliotheca Alexandrina.
“The better we have deciphered the genome of the plant, the better will be our understanding of its ability to produce more and its resistance to biotic and abiotic stresses,” Graner said in a statement.
Comprised of around 5.3 billion base pairs, the barley genome is almost twice as large as the human genome.
’’Farmers will benefit by having improved varieties that can produce more yield. It would also help reduce input of fertilizers and chemical plant protection to facilitate more sustainable agriculture,’’ Graner said.

CLC Bio to Develop Software for Potato Genome Study
CLC Bio said last week that it is partnering with several Danish research institutions to develop bioinformatics software for potato genomics research.
The project will include next-generation sequencing, digital gene expression, and bioinformatics technologies in order to learn more about how the potato could be engineered to satisfy food, energy, and chemical needs, the company said.
In addition to CLC Bio, the partnership includes the Institute of Food and Resource Economics and the Department of Plant Biology at Copenhagen University; Aarhus University; Aalborg University; Landbrugets Kartoffelfond; Andelskartoffelmelsfabrikken Vendsyssel; and Kartoffelmelscentralen.
The company said the project is centered on the potato because it produces twice the amount of energy per area as maize or wheat, “making it ideal for energy and food production.”
The project will analyze gene expression data for 40 growth conditions for 15 different cultivars.
CLC Bio said a number of new bioinformatics algorithms will be developed for the project and bundled into a comprehensive package that is based on CLC Bio’s workbench.

Czech Biotech Institutes License DNAStar's Software
Two research institutes based in Prague in the Czech Republic will use DNAStar’s software for sequence analysis under a multi-site license agreement, the Madison, Wis.-based company said last week.
Under the agreement, two units of the Academy of Sciences of the Czech Republic will access the company’s Lasergene sequence analysis software for an unlimited number of users for a four-year period.
The agreement gives the Institute of Molecular Genetics and the Institute of Biotechnology access to the software, which offers a range of analysis tools for use in traditional and next-generation sequence analysis projects.

Researchers Test 454 Sequencing for Characterizing Potential Outbreak Bacteria
French and Swedish researchers have used the 454 GS20 sequencing platform to sequence and compare virulence and resistance factors in Francisella tularensis subspecies holarctica — a bacterium that’s considered a potential bioterrorist threat — in a matter of weeks.
“With this technique it’s possible now to obtain the complete sequence of a bacterium in just six weeks time,” Bernard La Scola, a bacteriologist at the University of the Mediterranean in Marseille, told In Sequence’s sister publication GenomeWeb Daily News. He is the lead author of the study, which appeared in Genome Research last week.
Many worry that F. tularensis, which causes tularemia, could be manipulated and used as a biological weapon. “It’s considered one of the three high-risk bacteria in bioterrorism,” La Scola said. “You can introduce a resistance gene or you can cultivate it on an antibiotic and select resistance — and it’s not difficult to do.”
In such an event, La Scola explained, having the ability to sequence an outbreak strain as quickly as possible may be critical. While it’s possible to detect antibiotic resistance without sequencing, the sequence data can reveal the mechanism of resistance. It also can help researchers track a strain’s origin.
While acquiring sequence data is relatively fast, taking only about a day, the analysis is more time consuming, which is why the researchers reported a six-week turnaround. Sequencing the entire F. tularensis genome by Sanger sequencing could take two or three months, he said.
The team also further streamlined the process: instead of sequencing and assembling the entire genome, they decided to forego the finishing process. The researchers assembled 480 URFT1 contigs and compared these with sequence from other known F. tularensis strains.
Most of the remaining sequence gaps fell within repeat regions. Because these repeat sequences don’t contain information about virulence factors or other genes of interest, La Scola explained, sequencing them is unnecessary in the outbreak context.
He and his colleagues detected various polymorphisms, modifications, and deletions that could infer changes in characteristics such as virulence and antibiotic resistance. They also used the information they gleaned to develop a typing system that allowed them to categorize dozens of F. tularensis holarctica strains, including URFT1; a live vaccine strain; 74 Swedish, clinical isolates collected over ten years; and five clinical specimens.
“In the bioterrorism context, it allows the rapid detection of strain manipulation, including intentionally added virulence genes and genes that support antibiotic resistance,” the authors wrote.
— By Andrea Anderson, originally published on GenomeWeb Daily News

Northeastern U., Broad to Sequence Pathogens Using Illumina GA
Researchers at Northeastern University, in collaboration with the Broad Institute, will use a $1.4 million grant from the National Institute of General Medical Sciences to sequencing pathogenic bacteria, using Illumina’s Genome Analyzer, in order to find genes responsible for drug resistance.
Northeastern professor Kim Lewis told In Sequence’s sister publication GenomeWeb Daily News last week that he will collaborate with the Broad Institute on the four-year grant, which will fund his lab’s ongoing program focused on the formation of dormant persister bacterial cells. Lewis’ research teams hopes to identify the genes responsible for the cells’ formation and maintenance and to develop a therapy to destroy them.
The genomes of several bacteria, such as E. coli, Y. pestis, P. aeruginosa, and M. tuberculosis, contain critical information about this “devious mechanism pathogens have come up with” that grants them tolerance to multiple drugs, Lewis explained.
The Antimicrobial Discovery Center at Northeastern, which Lewis directs, is developing 100 mutant strains of these bacteria, beginning with E. coli, to send on to the Broad Institute for sequencing. Lewis and his co-investigator, James Galagan, will then look for common traits that may be used to help decipher the mechanisms responsible for antibiotic tolerance. Galagan is associate director of microbial genome analysis at the Broad.
Lewis said the sequencing, which will be done using an Illumina Genome Analyzer, does not need to be deep, and “we don’t need to assemble anything, but you do need to have pretty good coverage.”
Lewis explained that his team hopes to get around 20 genes for the 100 mutants that could be used in dormancy regulation, and he thinks the project may be completed within around a year.
"We know that pathogens produce dormant persister cells, which then resist antibiotics, but we need to know how it happens in order to develop effective treatments against these dormant cells," Lewis said in a statement.
— By Matt Jones, originally published on GenomeWeb Daily News

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.