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Short Reads: Jan 20, 2009

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Life Tech to Launch SOLiD 3.0 Next Month; Sees Dx Opportunities for CE

Life Technologies plans to launch a new version of the Applied Biosystems SOLiD sequencer next month, and is considering new diagnostic opportunities for its capillary electrophoresis technology, according to company officials.

Life Tech Chairman and CEO Greg Lucier said last week that SOLiD 3.0 will have a throughput of up to 20 gigabases per run and will have "very high accuracy."

Lucier, who made the comments during the 2009 JPMorgan Healthcare conference in San Francisco last week, said that "with all of the sample preparation work we are doing, as well as the services we have around the world for this platform, we think it's a very compelling offering."

ABI revealed last September that it was working on an update of its SOLiD platform that would increase throughput and read length and decrease cost per base, DNA input requirements, and run time, and simplify workflows (see In Sequence 9/30/2008)

During his conference presentation last week, which was webcast, Lucier said Life Tech estimated that at the end of 2008 it held a market share of 40 percent in second-generation sequencing.

This year, the company plans to spend "well in excess of" $100 million for sequencing-related research and development, he said. "That's probably two times our nearest competitor."

Life Tech President and COO Mark Stevenson said during a Q&A session at the conference that the research market for capillary sequencing technology continues to decline, but that it continues to grow in the areas of applied sciences, forensics, and clinical diagnostics.

The company sees opportunities for CE technology especially in the diagnostic market, he said. "There are some interesting content providers for us, as we now have the freedom to do some of the things that we could not do before with Celera that had diagnostic assays on the CE platform." He did not elaborate.


Jury Confirms Illumina's Ownership of IP Relating to ABI's SOLiD

Illumina won the first phase of a trial last week that involves plaintiff Applied Biosystems and defendants Illumina, Solexa, and ABI's former IP counsel Stephen Macevicz and covers ownership of intellectual property relating to ABI's SOLiD sequencing system, In Sequence has learned.

An Illumina spokeswoman confirmed by e-mail last week that "a federal jury has determined that Illumina owns the patents that are the subject of the suit with Applied Biosystems, and that the case has now moved on to the infringement phase."

A spokeswoman for Life Technologies, the firm formed by the recent merger of ABI and Invitrogen, told In Sequence by e-mail that while the firm is "disappointed with this outcome, we're looking forward to making our case in phase II" of the trial. The spokeswoman said that the company has no further comment until the trial is concluded.

The dispute started in late 2006, when ABI sued Macevicz in a California state court for allegedly stealing intellectual property belonging to the company, his employer at the time, by failing to disclose a patent application he filed in his name in 1995.
Macevicz assigned the patent application to his new employer, ABI spinoff Lynx Therapeutics, later that year, which merged with Solexa in early 2005. Illumina acquired Solexa in early 2007.

The patent application resulted in three patents that cover aspects of ABI's SOLiD technology, US Patent Nos. 5,750,341; 5,969,119; and 6,306,597, all entitled "DNA sequencing by parallel oligonucleotide extensions."

In 2007, ABI moved the lawsuit to a federal court, and Solexa filed three counterclaims, accusing ABI of willfully infringing all three patents with its SOLiD technology.

Last summer, the judge ordered a jury trial with two phases. The first phase was going to deal with the issue of ownership, the second with Illumina's infringement claims.

In August, the judge, in a summary judgment, ruled that ABI does not infringe the asserted claims of the '341 and '597 patents. However, he denied to rule that ABI does not infringe the first claim of the '119 patent. In a later statement, the judge clarified that his order applied only to ABI's two-base encoding technology, not its prototype one-base version.

At a final pretrial conference held in September, the judge ruled that the defendants will not be permitted to seek damages for alleged infringement of the '341 or '597 patents by the one-base encoding process. ABI withdrew its request regarding evidence of willful infringement after the defendants said their allegation of willful infringement is only directed at Agencourt Personal Genomics before ABI acquired it in 2006 (see In Sequence 12/23/2008).

By Julia Karow; originally published on GenomeWeb Daily News. Edward Winnick contributed reporting to this article from the JPMorgan Healthcare Conference in San Francisco.


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Caliper Eyeing Sequencing Sample Prep, MDx Opportunities

Caliper Life Sciences said last week that it is developing its technologies for future uses in front-end sample preparation for next-generation sequencing systems and molecular diagnostics.

Those opportunities are two of three major initiatives in the firm's pipeline, President and CEO Kevin Hrusovsky said last week at the JPMorgan Healthcare Conference in San Francisco. The company also is working on a new, integrated molecular biology workstation, but key future revenue drivers could come in the form of the sequencing sample prep and MDx instruments.

Hrusovsky said that the next-gen sequencing sample prep instrument, called LabChip NextGen, will take a couple of years to develop at an estimated cost of around $3 million. He said that it would eliminate the labor-intensive bottleneck at the front end of next-generation sequencing systems and could potentially bring in annual revenue of $10 million to $20 million.

Even though such a sample prep instrument would not be necessary for single-molecule sequencing or other third-generation sequencing technologies, Hrusovsky is confident that the growing number of instruments placed by firms such as Illumina and Life Technologies will create a "very robust" market for the next 20 years for the instrument he envisions for Caliper. He added that this prediction is based on discussions he has had with genome centers, including the Broad Institute.

Hrusovsky said it is possible the firm would sell such a sample prep instrument system to genome centers on its own, though a partnership with vendors that already serve such customers would be beneficial.

He also said that Caliper sees a major revenue opportunity in creating its own instrument for the point-of-care molecular diagnostics market. He did not provide many details as that project is in the earlier planning stages compared to the sample prep instrument.

By Edward Winnick; originally published on GenomeWeb Daily News


Sheep Genomics Consortium Plans to Sequence Up to Six Sheep; Develops SNP Chip with Illumina

The International Sheep Genomics Consortium said last week that it plans to sequence as many as six sheep this year. In collaboration with Illumina, it has developed a SNP microarray for characterizing variations in sheep genomes that Illumina launched last week.

IGSC is an international group of institutes and companies funded by AgResearch of New Zealand, Australia, the UK, and the US Department of Agriculture, and is aimed at developing tools to explore the sheep genome.

Initial sequencing for the project was conducted in parallel at Otago University in Dunedin, New Zealand, and the Human Genome Sequencing Center at Baylor College of Medicine, while Illumina provided additional sequencing.

The genome assembly, SNP detection, and selection were conducted by AgResearch and Australia's Commonwealth Scientific and Industrial Research Organization. Illumina used this data to create the OvineSNP50 BeadChip for use in selecting traits for breeding.
The goal of this part of the project was to develop a chip that could collect data from over 60 breeds of sheep that could be used in pinpointing traits that may be important economically, ISGC said.

"We took the opportunity to use new DNA sequencing technologies which allowed us to identify over 300,000 SNPs," AgResearch's John McEwan said.

The ISGC, which began in 2002, still plans to produce a reference sequence of the sheep genome and a preliminary study of copy number variation in sheep.

"We began this work by creating what we called a virtual sheep genome, which contained the best bet about where the sheep's vast amount of hereditary information could be found on its 26 chromosomes," ISGC researcher Brian Dalrymple said in a statement.

"We drew on the work that had already been done to sequence the human, cow, horse and dog genomes to create our virtual sheep genome assembly," Dalrymple added.

As sequencing costs decrease over the coming year, Dalrymple continued, "We plan to complete the sequencing of six individual sheep genomes."

"During 2009, as sequencing costs continue to decline, we plan to complete the sequencing of six individual sheep genomes. This will be really important as the availability of reference genome sequences will open up a range of possibilities."


Wellcome Trust Center Using GenoLogics' Tools to Manage Sequencing, Study Data

The UK's Wellcome Trust Center for Human Genetics will use GenoLogics' lab and data management solution in its next-generation sequencing and disease research programs, the company said this week.

The center will use the company's Geneus platform in its studies seeking the genetic basis of multi-factorial diseases such as diabetes, heart disease, multiple sclerosis, hypertension, and psychiatric disorders.

WTCHG chose the software "because of its flexibility to automate data capture from a wide range of genomics instruments and applications, while allowing us to more efficiently track samples and QC results across numerous projects," WTCHG Head of Genomics Ioannis Ragoussis said in a statement.

Ragoussis also said that the "primary consideration" in using the Geneus platform was its capability to "fully integrate our next-generation sequencing instruments from Illumina and Roche, and automatically pipeline data for downstream analysis."

The genomics group also provides services for other groups at the center and at the University of Oxford for microarray experiments, high-throughput quantitative gene expression, high-throughput genotyping, and other applications.


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Consortium Using Genomics to Help Manage Fisheries

An international consortium called FishPop Trace is embarking on a multi-million dollar effort to develop genetic and other markers to help fisheries manage, conserve, and enforce their populations, according to a researcher who spoke at the Plant and Animal Genome conference in San Diego last week.

Rob Ogden, a researcher with the UK-based life-sciences product and services company Tepnel Life Sciences, outlined the FishPop Trace consortium's goals and strategy at a Population and Conservation Genomics workshop at PAG.

The team plans to use molecular, chemical, morphological, genetic, and other markers to understand the population structures for four fish species: cod, herring, hake, and sole.

From a genetic perspective, Ogden said, the project will involve SNP discovery and validation followed by genotyping and population screening, analysis, and selection. With these markers in hand, he explained, the team plans to select a platform and develop a standard operating procedure for applying these genetic tools.

The team plans to use Roche/454 sequencing to discover SNPs in cod, herring, and sole genomes, and a combination of 454 and Illumina sequencing for hake, Ogden said.

The consortium includes researchers from 15 institutions in a dozen countries. It is funded from 2008 to 2011 under the European Union's Seventh Framework Program and has a €4 million ($5.3 million) budget.

The FishPop Trace effort is intended to yield knowledge and tools for facilitating fisheries enforcement — from certification and random testing to DNA forensics. A secondary goal of the project is to inform new, ecosystem-based, fisheries management policies that take into account natural fish population structures, local adaptation, and species biology.

Data generated from the project will be made freely available to the research community. The FishPop Trace is seeking additional participants from academia, industry, non-governmental organizations, and government partners, Ogden noted.


NCI to Give Post-GWAS Cancer Studies $24M per Year

The National Cancer Institute will give up to $96 million over four years to support multicenter collaborations that will use data from genome-wide association studies to identify regions in the human genome that are associated with cancer susceptibility.

The program, "Transdisciplinary Cancer Genomics Research: Post-Genome Wide Association Initiative," will spend up to $24 million per year to support between five and eight awards.

NCI said in a funding announcement that it wants the project to "provide a rigorous knowledge base that would enable clinical translation and public health dissemination of the GWAS findings."

All of the projects funded "must be focused on the post-GWAS research on the significance of genomic variants in specific cancer types."

Of primary interest are projects that study variations in cancers of the breast, colon, prostate, pancreas, lung, melanoma, and bladder, said NIH. Some research components are required, NCI said, and each applicant is "strongly encouraged" to propose sub-projects that address three main areas.

They should involve "discovery expansion and replication," which would include finding new associations through pooled or meta-analyses, independent replication studies, and fine mapping of association signals. The research should involve biological studies that will identify risk-enhancing genetic variants, examine the functional consequence of a genetic variant, and determine biological mechanisms of risk enhancement. These studies also should include epidemiologic studies, such as those that evaluate gene-gene and gene-environment interactions, assess penetrance and populations of attributable risk, develop complex risk models, and evaluate clinical and analytic validity of risk models in observational studies.

Researchers receiving funding under these programs also must agree to data-sharing requirements.

More information about the NCI program is available here.


NIH Starts Recruiting Children for Genes and Environment Study

The National Institutes of Health's study of the interplay between genetics and the environment in 100,000 children over two decades has begun recruiting volunteers, NIH said last week.

The National Children's Study's first phase of recruitment will start seeking volunteers in Duplin County, NC, and in Queens, NY. These drives for volunteers will be conducted by two of the NCS's Vanguard Centers at the University of North Carolina at Chapel Hill and at the Mount Sinai School of Medicine in New York City.

The NCS includes the National Institute of Child Health and Human Development, the National Institute of Environmental Health Sciences, the Centers for Disease Control and Prevention, and the US Environmental Protection Agency.

In August of this year, NIH said, the remaining five Vanguard centers will begin recruiting and enrolling women to participate in the study. By the end of an 18-month period, each center is expected to have a total of roughly 375 volunteers.

When the study is fully operational, NIH expects the NCS to have around 40 study centers recruiting volunteers from 105 study locations throughout the US.


UCSD Gets $16.6M for NIH Roadmap's Epigenome Mapping Center

The University of California, San Diego has received a $16.6 million grant from the National Institutes of Health to help support a center that will study modifications that affect and alter genetic behavior across the human genome.

The five-year grant, awarded under the NIH's $190-million Reference Epigenome Mapping Center program, will fund interdisciplinary studies to comprehensively map elements of the human genome, UCSD said last week.

Researchers at UCSD will generate genome-wide profiles of histone modifications and create a map of DNA methylation.

NIH announced its first awards for the five-year Roadmap Epigenomics Program last September.

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.