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Beijing Genomics Institute, USPTO, Affymetrix, Illumina, NIH, 454, Myriad Genetics, University of Maryland, CLC Bio

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Beijing Genomics Institute to Offer Sequencing Services on Sanger, Solexa, SOLiD Instruments
           
The Beijing Genomics Institute said last week that it plans to use its fleet of 120 Sanger and next-generation sequencing instruments to offer sequencing services to the global market.
 
In a statement, BGI said that it currently has more than 100 Applied Biosystems 3730xl sequencers, seven Illumina Genome Analyzers, and two ABI SOLiDs. The institute said these instruments enable a sequencing throughput of 250 million base pairs per day using Sanger, and 4 billion base pairs per day using the next-generation instruments.
 
BGI said that it plans to provide these services at “dramatically reduced cost and improved speed,” but did not provide further details.
 
The institute said it considers its bioinformatics capabilities to be an advantage in the sequencing services market. BGI said it has more than 100 bioinformatics specialists, 10 supercomputers, access to 2,000 CPUs, and more than 500 terabytes of storage.
 
In addition to sequencing, BGI said it will offer bioinformatics services, including sequence data processing, sequence assembly, gene annotation, expression level research, EST and microarray analysis, SNP discovery, genotype and haplotype analysis, primer design, software development, system integration, structure modeling, and database and website construction.
 
Last fall, BGI researchers and their collaborators said they finished sequencing the first Chinese individual using Illumina’s technology (see In Sequence 9/25/2007).
 

 
USPTO to Re-examine Four Patents in Affymetrix, Illumina Litigation
 
Illumina said last month that the US Patent and Trademark Office will re-examine four patents that are part of an intellectual property infringement suit filed by Affymetrix against Illumina.
 
Illumina said the USPTO will re-examine patents No. 5,545,531, entitled “Methods for making a device for concurrently processing multiple biological chip assay;” No. 6,355,432, entitled “Products for detecting nucleic acids;” No. 6,646,243, entitled “Nucleic acid reading and analysis system;” and No. 5,795,716, entitled “Computer-aided visualization and analysis system for sequence evaluation.” The first patent was initially assigned to Affymax, which spun out Affymetrix; the second and third patents are assigned to Affymetrix; and the fourth patent is assigned to Mark Chee, a former Affymetrix employee and co-founder of Illumina.
 
All four patents are part of Affy’s patent infringement suit filed against Illumina in July 2004 in the US District Court for the District of Delaware.
 
In March of 2007, a jury sided with Affy in the first phase of the litigation. It found that Illumina's arrays, assays, scanners, software, and related products infringe “one or more claims” of all five of the patents Affy mentioned in the suit.
 
The jury awarded total damages of more than $16.7 million for the period of 2002-2005 and imposed a royalty of 15 percent.
 
The next phase of that case will focus on the validity of Affymetrix's patents and is scheduled to begin on Feb. 11. The following phase is expected to occur in May or June and will determine whether Illumina's infringement was willful.
 
Last October, Affy filed additional suits against Illumina, claiming among other things that Illumina’s Genome Analyzer infringes two of its patents (see In Sequence 10/30/2007).
 

 
NIH Launches Human Microbiome Project
 
The National Institutes of Health has officially launched its Human Microbiome Project, saying it will use $115 million over five years under the NIH RoadMap for Medical Research program to fund research into microbes that inhabit the human body and discover how they affect human health and disease.
 
The NIH already has issued several requests for grant applications, asking investigators to develop informatics and hardware tools that will advance microbial genomics.
 
Under the program, researchers will initially sequence the genomes of 600 microbes, completing a collection of some 1,000 microbial genomes that will serve as a reference for investigators interested in understanding the trillions of microorganisms dwelling in humans.
 
Other microbial genomes are being contributed to the collection by individual NIH institutes and internationally funded projects. A meeting between international partners was recently held to discuss forming an international consortium, according to NIH.
 
Researchers will then study microbial communities in samples taken from five body regions of healthy volunteers: the digestive tract, mouth, skin, nose, and female urogenital tract.
 
In demonstration projects, scientists will also sample the microbiomes from volunteers with specific diseases.
 
“Our goal is to discover what microbial communities exist in different parts of the human body and to explore how these communities change in the presence of health or disease,” said National Human Genome Research Institute Director Francis Collins, who also is serving as a co-chair of the Human Microbiome Project Implementation Group, in a statement.
 
NIH recently awarded $8.2 million to four sequencing centers to start building a framework and data resources for the Human Microbiome Project. One-year awards were given to the sequencing centers at the Baylor College of Medicine, Washington University School of Medicine, the Broad Institute of MIT/ Harvard, and the J. Craig Venter Institute.
 
These centers will sequence the genomes of 200 microbes that have been isolated from the human body as part of the 1,000 microbial genomes collection. Researchers will also begin recruiting healthy volunteers who will donate samples from the five body regions.
 
“The recent emergence of faster and cost-effective sequencing technologies promises to provide an unprecedented amount of information about these microbial communities, which in turn will bolster the development and refinement of analytical tools and strategies,” said NIAID Director Anthony Fauci, co-chair of the Human Microbiome Project’s Implementation Group, in a statement.
 

 
Scientists Use Sanger, 454 to Read Pinot Noir Genome  
 
A recently published genome sequence of a pinot noir grape could help with wine production, according to the research team that conducted the study.
 
The study, conducted by researchers at Italy’s Istituto Agrario di San Michele all'Adige and Myriad Genetics, was published in the open-access journal PLoS One last month. The research team used a combination of Sanger and 454 sequencing, using 454’s GS 20, to analyze the pinot noir plant’s 500 million base pairs (see In Sequence 1/23/2007).
 
The researchers used Sanger sequencing to generate 6.5X coverage and 454 sequencing to produce 4.2X coverage of Vitis vinifera pinot noir ENTAV 115, a variety grown in a range of soils for red and sparkling wines.
 
The researchers expect that the pinot noir genome will provide insight into creating disease-resistant grape varieties, without altering the quality of the resulting wine. As part of the sequencing study Velasco and colleagues identified a number of genes that are related to disease resistance, of which 289 contain one or more SNPs.
 
The study found that the grape plant has a relatively small genome for a crop plant, with more than two million SNPs and 28,585 genes.
 
The genome also could provide information about pinot noir evolution, which has been complicated by its history of cultivation.
 
This is not the first grapevine genome sequence to be published. Last August, the Public Consortium for Grapvine Genome Characterization, consisting of French and Italian researchers, reported a draft sequence of a pinot noir variety, generated by Sanger technology, in Nature.
 

 
UMD Team Uses 3D Graphics Card Technology to Improve Next-Gen Sequence Analysis
 
A team of bioinformaticists at the University of Maryland is using technology originally developed for the gaming community to help analyze vast amounts of short-read data from next-generation sequencers.
 
The approach relies on 3D graphics hardware called graphics processing units, or GPUs, to accelerate a range of applications. The UMD team believes that the technology can find a home in the next-generation sequencing and bioinformatics communities.
 
“As sequencing technology is getting very cheap with the new methods, we were concerned that the computing resources required to process the data wouldn’t be getting cheaper,” UMD’s Cole Trapnell told In Sequence’s sister publication BioInform.
 
“You may be generating all this sequence, but you might need a supercomputer to deal with it, so we liked the idea that graphics cards offered a researcher without a $100,000 IT budget the ability to process the data,” he added.
 
In a paper published last month in BMC Bioinformatics, Trapnell and UMD colleague Michael Schatz discussed a version of the MUMmer sequence-alignment program that they developed to run on a graphics card from nVidia.
 
The authors report that the program, called MUMmerGPU, gained speed as read lengths became shorter. For instance, MUMmerGPU was twice as fast as the CPU version for a query length of around 800 base pairs, while a query length of 25 base pairs caused a more-than 10-fold improvement.
 
Although the acceleration was seen only for very short queries, “these read characteristics are beginning to dominate the marketplace for genome sequencing,” the authors note in the paper. They cite as an example Illumina’s sequencer, which creates around 20 million short reads in a single run. “Thus our application should perform extremely well on workloads commonly found in the near future,” the authors report.
 
MUMmerGPU, which is available for download here, is well-suited for aligning many reads to a reference genome, which would have great utility for genotyping, for example. Schatz told BioInform that the team next plans to apply the approach to de novo assembly of short-read data.
 
De novo assembly is the big target. That’s what’s on everybody’s minds,” he said. “You’re talking about millions and millions and millions of reads being produced by centers that don’t have supercomputers, so GPUs seem like an ideal fit for that.”
 
The complete version of this article appears in the current issue of BioInform.
 

 
Over 25 Indian Universities to Use CLC Bio's Sequence Analysis Software
 
Researchers at post-graduate colleges in India will use CLC Bio’s software in genomics research programs, the company said last month.
 
Under the memorandum of understanding, Andhra University, in Visakhapatnam, Andhra Pradesh, and 25 affiliated post-graduate colleges will use the CLC Combined Workbench sequence analysis software and will receive training and customized education materials, the company said.
 
The software implementation and related educational solutions will be provided by CLC Bio’s branch in Hyderabad, Andhra Pradesh.

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.