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Illumina, Solexa, Integrated Genomics, Mayo Clinic, U of Minnesota, Stratagene, Third Wave, Roche, Caliper, ABI, Tessarae, Affymetrix

Illumina Closes Solexa Acquisition
Illumina last week said it had closed its $600 million acquisition of Solexa.
"We are excited to join the two companies, creating the only company with genome-scale technology for genotyping, gene expression, and sequencing, the three cornerstones of modern genetic analysis," Illumina CEO Jay Flatley said in a statement.
"With Solexa's recent technical achievements we look forward to the rapid commercialization of our next-generation sequencing platform," he added.
In connection with the merger, Illumina has increased the size of its board from eight to 10 members, adding Blaine Bowman and Roy Whitfield, both of whom were Solexa directors.
In an e-mail to Solexa employees dated Jan. 24, 2007, and filed with the US Securities and Exchange Commission on Jan. 26, Solexa CEO John West said that the company’s “field-based personnel will become part of the Illumina field organization immediately, and trainings are being planned for the Illumina team on our technology in the first weeks after the merger.”
West added that a “detailed strategy” to fully integrate the Solexa and Illumina platforms “will take some time and thought to develop properly,” but noted that the firm is “already seeing cases where customers want to use Solexa re-sequencing systems to discover SNPs and implement them on custom Illumina genotyping BeadArrays.”

Dairy Company Taps Integrated Genomics to Sequence and Analyze Lactic Acid Bacterium
Integrated Genomics said this week that it will sequence and annotate the genome of a dairy lactic acid bacterium for the European dairy cooperative Arla Foods.
Scientists at Arla, which operates in Sweden and Denmark, will use the sequence data with Integrated Genomics’ ERGO bioinformatics platform to help develop lactic acid bacteria for use in dairy products such as cheese, milk, and butter.
The ERGO software integrates genomic and gene expression data and genetic literature to visualize genes in biological context, and it contains 1,145 genomes in “various stages of completion,” the company said.
Integrated Genomics said it expects the project to last through 2007.

Mayo Clinic, U of Minnesota Open $22M Genomics Facility
A Minnesota research collaboration headed by the Mayo Clinic has established a new genomics and bioinformatics facility in Rochester, Minn., the Minnesota Partnership for Biotechnology and Medical Genomics said last week.
The facility, a three-story addition to a space in downtown Rochester, will house genomics research equipment, a bioinformatics lab, and conference rooms to support the partnership’s research initiatives.
The state legislature provided $21.7 million in backing for the facility, which is the product of a partnership involving the Mayo Clinic, the University of Minnesota, and the State of Minnesota.
The Minnesota Partnership said ongoing research includes "anti-cancer drug development, heart disease, pancreatic cancer, neuromuscular diseases, tuberculosis, auto-immune diseases, transplant rejection, drug addiction and tuberculosis."
Describing itself as "a unique collaborative venture," the Minnesota Partnership aims to head the region’s biotech and genomics sector.

Stratagene to Pay $10.75M to Settle Third Wave PCR Patent Suit
Stratagene has agreed to pay $10.75 million to Third Wave Technologies to settle a patent-infringement suit related to PCR technology, the companies said this week.
The suit was originally filed in 2004 in the US District Court in Wisconsin and Stratagene later filed an appeal in the Federal Circuit in Washington, DC, following a judgment in Third Wave’s favor.
The firms have also agreed to a nine-month stay on further litigation. The companies will either seek a dismissal without prejudice or an extension of the trial date for a countersuit that Stratagene’s filed against Third Wave in the US District Court in Delaware. As part of the agreement, the companies have brokered a process that would resolve the Delaware case or any other disputes either through arbitration or a royalty-bearing license, Stratagene said.
Under the settlement, Stratagene will redeem a $21 million cash bond it posted in Wisconsin last year, after a judge tripled the $5.3 million in damages that a jury had awarded in September.
Third Wave’s suit claimed that Stratagene’s quantitative PCR and RT-PCR reagents violated some of the more than 30 patents on Third Wave’s Invader product line.
Joseph Sorge, Stratagene chairman and CEO, said in a statement that the settlement will enable the company to “focus more resources on executing our long-term growth strategy in molecular diagnostics, including the pursuit of additional partnerships and product development opportunities.”
Calling the settlement a “positive outcome” for both companies, Kevin Conroy, Third Wave president and CEO, said the agreement increases the company’s balance sheet by $50 million, cuts out costly litigation bills, and gives the company the freedom to continue to market and expand its molecular diagnostics products.

Roche, Caliper Integrate PCR and Liquid-Handling Tools; Pen Co-Marketing Deal
Roche Diagnostics has integrated its LightCycler 480 PCR system with Caliper Life Sciences’ Twister microplate handler into a single platform.
The firms have also signed a co-marketing agreement for the integrated product.
Financial terms of the agreement were not released.
Roche also recently integrated the LightCycler with a bench-top robotics system made by Protedyne to help enable high-throughput PCR applications.

Researchers Use ABI SNPlex to Identify Genes Linked to Crohn’s Disease
Researchers from the University Hospital of Christian-Albrechts University in Kiel, Germany, and Applied Biosystems have used ABI’s SNPlex genotyping technology to identify a novel genetic variation associated with Crohn’s disease, ABI said last week.
The study results will be published in the February issue of Nature Genetics.
The researchers tested DNA samples from patients with Crohn's disease using the SNPlex system, which runs pre-designed assays on the company’s 3730 and 3730xl sequencers. They conducted a genome-wide association study of around 20,000 genetic variants and identified a protein-coding SNP in the autophagy-related 16-like (ATG16L1) gene, which had never been previously implicated in Crohn's disease.
"With the discovery of APG16L1 as a new gene associated with Crohn's disease, we have demonstrated the power of a targeted, genome-wide investigation of coding SNPs," said Stefan Schreiber, professor of medicine at Christian-Albrechts University and lead author of the study, in a statement.
ABI is providing access to the list of SNPs selected for the study here.

Tessarae Will Use Affy Resequencing Arrays to Develop Pathogen-Detection Kit
Tessarae, a maker of tests to identify infectious diseases, will use Affymetrix resequencing microarrays to develop and market new epidemiological research tests for public health surveillance, Affy said last week. 
Under the terms of the agreement, Tessarae has non-exclusive rights to Affy’s CustomSeq resequencing arrays to develop kits that will recognize viral and bacterial pathogens based on genotypic signatures.
Affy said the arrays have been tailored to detect upper respiratory pathogens from target sequences provided by the US Naval Research Laboratory. The tests will be designed for common pathogens such as those causing respiratory disease and pneumonia, as well as respiratory biothreat agents.
Tessarae’s PCR-based kits will be used by public health officials to identify pathogens during an outbreak. Affy said the TessArray RPM-Flu3.0 kits will allow physicians to simultaneously detect particular strains, substrains, and nucleotide changes.
Financial terms of the agreement were not released.
Tessarae started this program with a $35-million infusion from US Department of Defense. The company patented the platform in November 2006.
Tessarae plans to develop test kits for encephalitis, hemorrhagic fever, and other blood-borne infections.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.