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Solexa, NCGR, NMT, Illumina, SeqWright, Third Wave, Genome Canada and Génome Québec, NIMH, USDA, Quiatech, World Economic Forum, Bayer, BASF, Degussa

Solexa Ships 13 Sequencers in ’06, Expects to Post First Instrument Revenues in Q1
Solexa said this week that it shipped 13 Genome Analysis Systems to 10 early-access customers in five countries last year and began invoicing these customers in the fourth quarter.
The company said it will make the system “broadly available” to customers this quarter. The firm added that it expects to begin recording revenue from placements in the current quarter.
Solexa said its instrument has hit the one-gigabase-per-run milestone, noting in a statement that it had completed “multiple runs on multiple instruments” that produced more than one gigabase of DNA sequence data per flow cell after filtering.
Solexa said that it made several improvements to the system in order to reach the one-gigabase milestone, including “various hardware refinements that were largely implemented at customer sites; more powerful computational algorithms yielding more high-quality reads; faster instrument software; and improved protocols yielding denser clusters.”
So far, Solexa said, early-access customers have used its system for a range of applications, including resequencing, gene expression analysis, and small RNA and specialty tag sequencing assays such as DNase hypersensitivity detection and chromatin immunoprecipitation analysis.

NCGR, NMT to Create New Mexico Genome Sequencing Center; Focus Will be on Medical Resequencing
The National Center for Genome Resources and the New Mexico Institute of Mining and Technology said this week that they have established a partnership to create the New Mexico Genome Sequencing Center.
New Mexico has provided $600,000 in funding to establish the center, which will be located at NCGR in Santa Fe. 
The center will focus on medical resequencing using "next-generation DNA sequencing instruments and software that are dramatically increasing the speed and throughput of DNA sequencing," NCGR said in a statement.
Stephen Kingsmore, president of NCGR, told In Sequence sister publication GenomeWeb News that the center is considering acquiring sequencers from Applied Biosystems, Solexa, and 454 Life Sciences.

Illumina Passes Antitrust Hurdle in Bid to Acquire Solexa; Shareholders to Meet Jan. 26
Illumina said it in late December that it had received clearance under Hart-Scott-Rodino Antitrust regulations to continue with its proposed acquisition of Solexa.
The companies separately said that Solexa and Illumina shareholders will vote on aspects of the acquisition on Jan. 26.

SeqWright to Conduct Sequencing for Third Wave’s HPV Clinical Trials
Sequencing services shop SeqWright said last week that it will perform all of the sequencing and analysis for a set of clinical trials being conducted by Third Wave Technologies.
Third Wave is developing two in vitro molecular assays and a genotyping test to screen for human papillomavirus, which has been identified as the cause of approximately 70 percent of cervical cancer cases. Third Wave’s tests will detect and identify 14 HPV high-risk types and HPV types 16 and 18.  
SeqWright uses gene sequencing and bioinformatics technologies to help companies run clinical trials for FDA submission. The company is certified under Clinical Laboratory Improvement Amendment guidelines and also maintains compliance with Good Laboratory Practices as specified in the Code of Federal Regulations.

Canada Grants $330K for C. Difficile Sequencing Project; 454’s GS FLX to be Used
Genome Canada and Génome Québec have provided CA$388,625 ($330,218) to support a project to sequence multiple strains of the bacterium Clostridium difficile, which causes severe colon infections.
Ken Dewar, an assistant professor of human genetics at McGill University who is leading the effort, told In Sequence via e-mail that the project will sequence the genomes of eight “clinically and historically important” phenotypes using massively parallel sequencing. 
Goals of the project include measuring the genetic diversity between strains, constructing catalogs for genes and proteins, searching for other genes that might contribute to increased virulence and/or antimicrobial resistance, and determining how different toxins and genes correlate with disease-causing ability.
Dewar said that his team is collaborating with Elaine Mardis’s lab at Washington University, which will conduct most of the sequencing on a 454 GS FLX. “The subsequent finishing work will be done in Montreal by conventional means,” he said.

NIMH Announces Program on Deep Sequencing, Haplotype Profiling in Mental Disorders
The US National Institute of Mental Health has announced a program that seeks to identify genomic and functional variants that influence susceptibility to mental disorders.
The program, called “Deep Sequencing and Haplotype Profiling of Mental Disorders,” is “related to large-scale genomic or genetic studies in sufficiently powered studies using clinically well-characterized populations from the [Center for Collaborative Genetics Studies] and employing innovative analytical study designs.”
According to the NIMH, possible areas of investigation include high-density whole-genome association analyses for SNP typing and haplotyping, as well as sequencing studies of candidate regions or genes across the genome and “experimental technologies” for large-scale sequencing that would dramatically decrease sequencing costs.
The announcement is a reissue of a program that was previously released in May of 2005. Additional information can be found here.

USDA Awards $10M to Swine Genome Sequencing Consortium
The US Department of Agriculture has awarded the Swine Genome Sequencing Consortium $10 million to support the development of a bacterial artificial chromosome map as part of a longer-term project to sequence the swine genome.
Gary Rohrer, an animal geneticist at the Agricultural Research Service’s US Meat Animal Research Center in Clay Center, Neb., is leading the ARS swine genome research efforts.
The consortium has already identified more than 267,000 markers on the BAC map, ARS said.
Other consortium members include the University of Illinois; the Alliance for Animal Genomics in Bethesda, Md.; the Wellcome Trust Sanger Institute; the Roslin Institute; the Korean Livestock Institute; the Beijing Genome Institute; and France's National Institute for Agricultural Research.

RNA and Sequencing Chemistry Shop Quiatech Changes Name to Oligovation
Quiatech, a developer of DNA and RNA technologies, has changed its name to Oligovation, the company said in December.
The firm, based in Uppsala, Sweden, said it made the change as it prepares to market “a range of DNA and RNA technologies” it developed under the name Quiatech.
Oligovation said it has a modified RNA chemistry that improves synthesis conditions for RNA production, a specific reversible terminator for improving sequencing technology, and an in situ amplification technology for in vitro diagnostics.

World Economic Forum Names 454 as Technology Pioneer
The World Economic Forum has named 454 Life Sciences among 47 Technology Pioneers for 2007.
Technology Pioneers are nominated by venture capital and technology companies. The final selection from 225 nominees was made by a panel of technology experts appointed by the World Economic Forum.
The 2007 Technology Pioneers are invited to attend the Annual Meeting of the World Economic Forum to be held in Davos, Switzerland, Jan. 24-28.

Bayer, BASF, Degussa, Other German Firms Form Microbial Genome Research Consortium
Several German pharmaceutical, biotech, and industrial firms announced in late December that they have launched a consortium to advance industrial applications of microbial genomics research.
The consortium, called the Industrieverbund Mikrobielle Genomforschung (Industry Association for Microbial Genome Research), is partially supported by Germany’s Federal Ministry of Education and Research, which has contributed half of the group’s €42 million ($54.6 million) budget over the next five years.
The consortium intends to improve the efficiency using microorganisms in industrial processes and to develop new products from microorganisms with new properties.
Participating companies include BASF, Bayer Crop Science, Biopract, BRAIN, Degussa, Direvo, Henkel, Milupa, Schering, Südzucker, and Wacker.
Karl-Heinz Maurer, director of enzyme technology at Henkel, will serve as chairman of the association.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.