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Thermo Fisher Scientific, PerkinElmer, Affymetrix, Illumina, Bruker BioSciences, Beckman Coulter, Sigma-Aldrich, Sequenom, Agilent Technologies, Roche, Ventana, Celera

Thermo Fisher’s Q3 Revenues Rise 7 Percent
Thermo Fisher Scientific last week said that its third-quarter revenues rose 7 percent to $2.4 billion on a pro forma basis.
The company also hinted in a statement that the “highly fragmented” market in which it plays “presents opportunities” to make additional acquisitions.
Thermo Fisher stressed that last year's results reflect Thermo Electron's operations before its merger with Fisher Scientific last November.
Total receipts for the three months ended Sept. 30 increased to $2.4 billion from $725 million year over year. On a pro-forma basis — reflecting the combined results last year of Thermo Electron and Fisher Scientific — the firm's third-quarter revenues grew 7 percent from $2.24 billion last year.
Thermo said revenue from its Analytical Technologies segment rose 12 percent to just over $1 billion, while receipts from the Laboratory Products and Services segment increased 4 percent to $1.44 billion.
The firm’s R&D spending increased to $58.8 million from $38.6 million in the third quarter of 2006.
Thermo Fisher said profit rose to $218.5 million from $48.8 million in the year-ago period.
Thermo Fisher said it had around $830.8 million in cash and equivalents and $15.4 million in short-term investments as of Sept. 30.
The company said it is increasing its revenue guidance to between $9.6 billion and $9.65 billion for 2007 from its earlier prediction of between $9.5 billion and $9.55 billion.
Thermo Fisher President and CEO Marijn Dekkers also said that the “highly fragmented” life, lab, and health sciences industry “presents opportunities for us to make acquisitions that create tremendous value by expanding our global reach, our commercial capabilities or our technology portfolio.”
During a conference call following the release of the results, Dekkers noted the firm’s recent tuck-in acquisitions. “I am not saying we are going to keep up this pace of acquisitions, but we expect to continue doing these type of bolt-on acquisitions on a regular basis,” he said.

PerkinElmer’s Q3 Revenues Up 13 Percent
PerkinElmer last week reported that third-quarter revenues increased 13 percent as R&D spending jumped 12 percent and profit ticked up about 3 percent.
Total receipts for the three months ended Sept. 30 increased to $435.7 million from $386.9 million year over year, PerkinElmer said.
Revenue for the company’s Life and Analytical Sciences business and its Optoelectronics unit swelled 13 percent year over year apiece, to $319.3 million and $116.3 million, respectively. Feeding the increase was “strong growth in genetic screening, medical imaging, and service,” PerkinElmer said in a statement.
CEO Gregory Summe said in a statement that the company’s “investments in new products, services and geographic expansion continue to yield attractive results.”
Biopharma sales represented roughly 34 percent of PerkinElmer’s LAS revenue for the quarter, company officials said during a conference call last week.
“In the drug discovery research area, we would characterize the overall market as stable and growing mid-single digits,” Rob Friel, president and COO of PerkinElmer, said during the call.
“Some of our customers are going through significant restructurings including closing or consolidating screening centers, which negatively impacts us on the instrument side, but appears to be having a favorable impact on our OneSource service business,” he said.
PerkinElmer said profits in the period rose to $30.7 million, or $.26 per share, from $29.8 million, or $.24 per share, in the prior-year period.
The firm’s R&D spending in the quarter increased to $27.7 million from $24.8 million year over year, while selling, general, and administrative costs climbed to $106.4 million from $94.7 million.
PerkinElmer said it had around $160.9 million in cash and equivalents as of Sept. 30.
The company said it expects fourth-quarter revenue to increase in the mid-teens with acquisitions and changes in foreign exchange rates contributing approximately 7 percent of that growth.

Affymetrix Files Additional IP Suits Against Illumina
Affymetrix last week said that it has filed additional patent-infringement lawsuits against Illumina in the US, UK, and Germany claiming that the genome-analysis and array technologies Illumina acquired when it bought Solexa, as well as all of Illumina’s BeadArray products, infringe certain of its patents. 
Affy’s patents involved in the complaints include: US Patent No. 5,902,723, Analysis of Surface Immobilized Polymers Utilizing Microfluorescence Detection; No. 6,403,320, Support Bound Probes and Methods of Analysis Using the Same; No. 6,420,169, Apparatus for Forming Polynucleotides or Polypeptides; No. 6,576,424, Arrays and Methods for Detecting Nucleic Acids; No. 7,056,666, Analysis of Surface Immobilized Polymers Utilizing Microfluorescence Detection; and European Patent No. 0834575, Identification of Nucleic Acids in Samples; No. 0853679, Expression Monitoring by Hybridization to High Density Oligonucleotide Arrays; and No. 0799897, Kits and Methods for the Detection of Target Nucleic Acids with the Help of Tag Nucleic Acids.
In response, Illumina CEO Jay Flatley said the company is “disappointed to see that Affymetrix continues to choose to compete with Illumina in the courtroom rather than in the marketplace.
“Our policy is to respect the valid and enforceable intellectual property rights of others and to take licenses where appropriate,” Flatley added. “In that regard, we believe that we do not infringe any valid claims of the patents asserted by Affymetrix in its recent complaints.”
Illumina said it has “already taken several steps to curtail Affymetrix' overly broad approach to patent protection,” including seeking a declaration that a number of the patents are invalid, and asking the US Patent and Trademark Office to “reexamine and invalidate" the five US patents included in Affy's suit.
The suits come seven months after a jury sided with Affy in a patent-infringement suit Affy filed against Illumina in 2004. The jury in that case, filed in the US District Court for the District of Delaware, 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 its 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, 2008. The following phase is expected to occur in May or June 2008 and will determine whether Illumina's infringement was willful.
Affymetrix said it has also requested injunctive relief in this case, and will ask that the court take up this request once the patents are found to be valid.

Bruker BioSciences’ Q3 Revenues Jump 25 Percent
Bruker BioSciences this week said third-quarter revenues increased 25 percent as R&D spending rose 24 percent and profit more than doubled.
Total receipts for the three months ended Sept. 30 increased 25 percent to $131.6 million from $104.9 million in the third quarter of 2006. Excluding the effects of foreign currency translation, third-quarter 2007 revenue increased by 20 percent, Bruker said.
Product revenue increased 25 percent to $115.2 million; service revenue increased 28 percent to $16.2 million; and "other" revenue fell 22 percent to $245,000.
The company did not offer revenue projections for the rest of the year.
R&D spending rose to $14.8 million from $11.9 million in the year-ago period.
Net profit rose to $8.7 million from $3 million in the year-ago period. The company said that income in the third quarter included a one-time tax benefit of $2.4 million related to a tax-law change in Germany that required a revaluation of Bruker’s deferred tax assets and liabilities.
Bruker held around $38.9 million in cash and cash equivalents, and short-term investments as of Sept. 30.

Beckman Coulter’s Top-Line Growth Hampered by Life Science Sales in Q3;
Inks Cancer Genomics Deal with Johns Hopkins
Beckman Coulter this week said third-quarter revenues increased 6 percent as strong sales for its clinical diagnostics were offset by lower-than-expected sales for its life science products.
Total receipts for the three months ended Sept. 30 increased to $669 million from $631.2 million year over year.
The company said it saw an increase of 9.4 percent in clinical diagnostics, while life science products declined 8.6 percent.
Product-related revenue increased 6 percent to $560.5 million, while service-related revenue was up 9 percent to $108.5 million. Sales of consumables grew by 8.7 percent, the company said.
"Although we continued to experience strong demand for our industry-leading clinical systems, total revenue in the third quarter was lower than anticipated," Beckman CEO Scott Garrett said in a statement. He said the lower revenues were due to flagging academic funding and a "short-term supply disruption" for the company's cellular products.
That disruption left the company with around $10 million in cellular instrument backorders, Garrett said, adding that the company expects to "work down these backorders sufficiently in the fourth quarter to achieve our goals for the full year."
R&D spending fell to $59.9 million from $80.9 million in the third quarter of 2006. However, excluding $27.5 million attributed to its R&D spending in the third quarter of 2006, R&D spending was up 12.2 percent for the quarter.
The company said the increased R&D investment was caused by its programs to develop a "sample-to-result system for molecular diagnostics," for its UniCel DxN, which is scheduled for commercial launch in 2010.
Beckman’s net income increased to $60 million from $47.4 million in the year-ago period.
The firm finished the quarter with around $84.8 million in cash and cash equivalents.
The company said it expects 2007 revenue to grow between 7 percent and 9 percent year over year.
In a separate announcement this week, Beckman Coulter said that it has inked two deals with Johns Hopkins University for exclusive licenses to intellectual property tied to cancer genomics research.
Terms of the agreements give Beckman Coulter the “exclusive option to license any of the genetic mutations discovered in these studies that have diagnostic potential,” Bruce Wallace, vice president of Beckman Coulter's Molecular Diagnostics Business Center, said in a statement.
The first agreement covers 200 genes that have been linked to breast and colon cancer that were discovered in a study at the Johns Hopkins Kimmel Cancer Center.
The other agreement is for sequencing services and options to license genomic IP related to six additional cancers.
Beckman Coulter’s molecular diagnostics assay group is already evaluating the breast and colon cancer genes. “The success of our strategic plan is dependent in part on our development of a robust molecular diagnostics business.”
He said the company is “already in the process of moving our research genomics technologies into platforms for diagnostic use. Building content, or approved tests for that platform, from research such as the John Hopkins cancer genomics studies, will enhance our success.”
Financial terms of the agreements were not released.

Beckman Coulter Integrates Biomek Workstation with Vi-CELL Analyzer
Beckman Coulter last week said that it has integrated its Biomek Laboratory Automation Workstation with its Vi-CELL XR Cell Viability Analyzer for imaging and culture-analysis tasks.
Beckman said the joined platform will enable researchers to monitor cell growth over time and to provide analysis and data needed to “evaluate clone selection, cell expansion, and protein-expansion results.”
Beckman said the integrated solution includes the Vi-CELL XR, a Biomek NXP workstation configured with a Span-8 Pod and gripper, a Biomek FXP dual-bridge workstation, storage devices, incubator, plate hotel, and two detectors.

Judge Sides with Sigma-Aldrich in Markman Ruling
A federal judge has agreed with Sigma-Aldrich and Oxford Biomedica’s definition of terms for RNAi-related intellectual property at the heart of a pending patent-infringement suit the companies filed against Open Biosystems last year, Sigma-Aldrich said last week.
Sigma-Aldrich alleges that Open Biosystems’ Lentiviral shRNAmir library and certain other products infringe Oxford Biomedica’s IP, to which Sigma-Aldrich holds an exclusive license in the research field.
The patents that are allegedly being infringed are US Patent Nos. 6,924,123 and 7,056,699, both entitled "Lentiviral LTR Deleted Vector."
According to Sigma-Aldrich, the court sided with its description of the technology as being used to “'deliver new genetic material into specific cells, such as cells that do not divide or that divide slowly," giving the delivery of genes that produce dopamine into a Parkinson's disease patient's brain cells, as an example.
Judge Charles Shaw of the US District Court in Missouri said that “the constructions of the disputed terms and phrases proposed by plaintiff are correct," according to Sigma-Aldrich.
The decision “reinforces Sigma's belief that the Oxford Biomedica patents are ‘core patents’ in the RNA-interference field, and validates Sigma's decision to license these patents and make other significant investments,” David Smoller, president of Sigma-Aldrich’s Research Biotechnology business, said in a statement.
Open Biosystems did not return a call seeking comment.

Sequenom Seeks $28M in Private Financing
Sequenom said last week it hopes to net $28 million in a private placement of 3.4 million shares of common stock at $9 apiece.   
The company said it plans to use the money to research, develop, and commercialize “various diagnostic tests,” and for general corporate purposes.
Sequenom also reaffirmed its full-year 2007 revenue guidance of $39 million to $41 million, which would be an increase of between 37 percent and 44 percent over 2006 revenues.
The company said Lehman Brothers and UBS Investment Bank were joint-lead placement agents in the private placement and Oppenheimer & Co., Leerink Swann, and Rodman & Renshaw were co-placement agents.

Agilent Offers $600M in Senior Notes
Agilent Technologies last week said that it is offering $600 million in senior notes and plans to use the net proceeds for general corporate purposes, including repurchases of outstanding shares of common stock, acquisitions, working capital, and capital expenditures.
The offering, which closed Oct. 29, was handled through book-runners Citi Markets & Banking and J.P. Morgan Securities.
Agilent said the notes will mature in November 2017 and will bear interest at 6.5 percent per year.

Roche Extends Bid to Acquire Ventana, Again
Roche has again extended its unsolicited bid to buy Ventana Medical Systems for $75 per share, and Ventana again has said that the number is too low.
Roche said this week that it has extended for a fourth time the offer it made in June to buy the company for around $3 billion, which amounts to a 44-percent premium over Ventana’s closing share price of $51.95 on the eve of the first offer. Ventana's shares closed Tuesday at $86.98.
The new extension runs out Jan. 17, 2008. Roche said other terms of the proposed deal are unchanged, as was Ventana’s response.
Ventana CEO Christopher Gleeson swatted the renewed offer. “More than 99.5 percent of our investors have now essentially turned down Roche’s inadequate offer four times, and yet Roche persists with its futile and costly tactics,” Gleeson said in a statement.
"Virtually all of our investors agree with us that $75 [per share] is a non-starter and they recognize that we are gaining real momentum in our marketplace.”
As of the close of business yesterday, Roche said that around 64,000 Ventana shares had been tendered in the offer, a number that Ventana said amounts to around .2 percent of the company’s roughly 35 million outstanding shares.
Ventana has consistently urged its shareholders to disregard the “potential for distraction” that the Roche offer may stir.

Celera Trims Proteomics Research Staff
Celera is cutting back its proteomics research staff at its facility in Rockville, Md., as the company gradually evolves into a diagnostics developer, BioCommerce Week sister publication GenomeWeb Daily News reported this week.
Company spokesman David Speechly confirmed that Celera is “trimming” its staff in proteomics research but would not provide details. He said the job cuts are part of a strategic shift that includes cutting out proteomics research but continuing to use proteomics resources for clinical development.
“We have been reducing our resources” in Rockville, “and the small team there is more aligned to diagnostics” and the proteomics branch will “continue to be trimmed down,” Speechly told GenomeWeb Daily News this week.
The remaining proteomics staff is still “working on licensing proteomics programs” and “applying proteomic discoveries to diagnostics and development,” Speechly said. 
Celera President Kathy Ordoñez said during the company’s fiscal first quarter conference call last week that Celera is “shifting funding from discovery to development, and we curtailed our proteomics-based target discovery and validation activities while we continue to fund diagnostic proteomics-based work.”
Speechly said he could not estimate how many proteomics researchers may get pink slips because Celera has not yet broken down how the restructured division will eventually shape up.
The disclosure comes soon after Celera bought two San Francisco Bay-area companies, including the $195 million pick-up of diagnostics company Berkeley Heartlab and the $33 million deal for Atria Genetics.
Speechly said that, over the long term, Celera’s increasing focus downstream could cause it to shift its presence from Maryland to the West Coast, though he stressed that this would not mean the company would close its Rockville facility.
In August, Applera hired investment bank Morgan Stanley to look into strategic alternatives for Celera and Applied Biosytems, including the possibility of spinning the two shops into independently traded public companies in place of the two tracking stocks they currently occupy.

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.