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Short Reads: Feb 17, 2009

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This section includes last week's Short Reads that were inadvertently omitted from last week's In Sequence.

Life Technologies Posts $107M Q4 Loss on Merger Charges

Life Technologies posted a fourth-quarter loss of $106.9 million last week due to a variety of charges associated with the merger of Applied Biosystems and Invitrogen last November that created the company.

Though the company's revenues fell short of analysts' expectations, the legacy Invitrogen business recorded organic revenue growth of 7 percent.

The Carlsbad, Calif.-based firm brought in total revenues of $540.6 million for the three-month period ended Dec. 31, compared to revenues of $336.4 million for Invitrogen alone in the 2007 fourth quarter. That tally fell short of analysts' consensus estimate of revenues of $572.6 million for the quarter.

The firm said that ABI contributed $191 million in revenues for the five weeks during the fourth quarter of 2008 that it was part of Life Technologies. Organically, revenues for the legacy Invitrogen business grew 7 percent year over year.

In addition to the ABI revenue, the firm's BioDiscovery segment brought in revenues of $240.1 million for Q4 2008 — up .5 percent year over year, including a negative affect from currency translation of 4.5 percent, while the Cell Systems segment had revenues of $113.7 million — up 17 percent year over year, including a 4-percent benefit from currency translation.

Life Technologies' R&D spending for the quarter was $47.3 million, while its SG&A spending was $151.7 million. The company took charges of $74.4 million related to in-process R&D and charges of $22.6 million related to business consolidation costs.

As a result of the merger-related costs, Life Technologies posted a net loss of $106.9 million, or $.89 per share, compared to a profit of $41.1 million, or $.41 per share, for Invitrogen in the 2007 fourth quarter.

For full-year 2008, Life Technologies had revenues of $1.62 billion, compared to revenues of $1.28 billion for Invitrogen in 2007. The BioDiscovery segment had FY 2008 revenues of $989.9 million, while Cell Systems contributed $443.7 million, and ABI contributed $191 million for the five weeks as part of the parent company.

Life Technologies' R&D costs for the year were $142.5 million, and its SG&A spending for the year was $499.3 million.

The firm posted a profit of $31.3 million, or $.29 per share, versus a profit of $143.2 million, or $1.34 per share, for Invitrogen for FY 2007.

Life Technologies finished the year with cash and investments of $448.3 million. The company also holds $3.5 billion in long-term debt, and company officials said during the call that repayment of debt was the top priority for use of its cash.

Life Technologies said that it expects to post low single-digit organic revenue growth for 2009, with an expected negative impact from currency translation of around 4 percent. It also predicted non-GAAP EPS of between $2.40 and $2.55.


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Neandertal Draft Genome Completed Using 454, Illumina Sequence Data

Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig said last week that they have completed a draft of the Neandertal genome.

At the American Association for the Advancement of Science annual meeting in Chicago last week, Svante Pääbo, director of the MPI's Department of Evolutionary Genetics, said the results suggest that Neandertals were not that different from humans from a genomic perspective. Rather, the Neandertal DNA sequence often falls into the same patterns of genetic variation observed in modern humans.

In the future, researchers hope to get a better handle on human evolution by comparing human, Neandertal, chimpanzee, and other ape genomes and looking at regions where there are differences, Pääbo explained. "The attraction of getting the Neandertal genome is that it's our closest relative."

His team also recently completed an 18-fold draft sequence of the bonobo genome,
an endangered close relative of the common chimpanzee (see In Sequence 5/13/2008).

Pääbo and his team sequenced a total of 3.7 billion base pairs of Neandertal DNA. While part of the data was generated by 454 Life Sciences under a collaboration (see In Sequence 8/12/2008), the scientists generated Illumina sequence data during the last phase of the project to achieve the one-fold coverage. The current sequence data represents about 63 percent of the Neandertal genome.

Compared to previous work, Pääbo said contamination with human DNA was less than 1 percent. Based on mitochondrial sequence data, the estimate of contamination is 0.3 percent, whereas estimates based on Y-chromosome data suggest 0.5 percent contamination.

So far, the results indicate that there is a roughly 10 percent divergence between Neandertals and human reference sequences. Based on estimates calculated from DNA and from population genetic variation, the results suggest Neandertals and humans diverged between 300,000 and 830,000 years ago.

The team has already started comparing specific regions of the Neandertal and human genome. For instance, they found that Neandertals had a version of the lactase gene that would not have allowed them to digest milk after weaning.

When the researchers examined the FOXP2 gene, which is involved in human brain function and contributes to speech and language, they found that Neandertals have the same two FOXP2 changes found in humans but absent in other apes. That suggests changes in FOXP2 occurred in a shared common ancestor to humans and Neandertals.

In addition, Pääbo said, the researchers have identified a region on chromosome 7 where Neandertal sequence resembles ape sequence but not human sequence, indicating the human genome has undergone a selective sweep in that part of the genome.

Over the next two to three years, Pääbo said the team plans to sequence the Neandertal genome to much deeper coverage — probably 15- to 20-fold. They intend to publish results related to the Neandertal draft genome and its analysis later this year.


Baylor, ABI Contribute 460 Gigabases to First 1,000 Genomes Data Release

Life Tech's Applied Biosystems division said this week that together with its collaborator, the Human Genome Sequencing Center at Baylor College of Medicine, it has contributed more than 460 gigabases of "unique mappable" sequence data generated on the SOLiD platform to the first data release of the 1,000 Genomes project.

According to the company, this represents 65 percent more data than the two organizations had originally planned to contribute.

ABI said that the HGSC sequenced 24 individuals at 2.6-fold coverage, and one individual at 26-fold coverage, generating 256 gigabases of total data. For its own contribution, ABI generated more than 206 gigabases of data.

ABI's collaboration with the HGSC started last April, when the company provided the center with six SOLiD systems to expand its contribution to the pilot phase of the 1,000 Genomes project. At the time, the HGSC planned to provide 200 gigabases of sequence data. In June 2008, ABI joined the project as a commercial participant (see In Sequence 6/17/2008) and committed to contribute at least 75 gigabases of sequence data generated on the SOLiD platform.


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UK Centers Land £1.7M Grant to Sequence Wheat Genome

Scientists at the University of Bristol, the University of Liverpool, and the John Innes Centre in the UK will use a £1.7 million ($2.4 million) grant from the UK government to sequence the wheat genome, two of the institutions said last week.

Scientists at the centers will generate sequence from a standard wheat strain and from four varieties. The genome sequencing will take approximately a year to complete.

The project, funded by the Biotechnology and Biological Sciences Research Council, will "pave the way for comprehensive sequencing of the bread wheat genome by exploring the application of new sequencing technologies and analysis methods," according to the University of Bristol.

By giving breeders ways to identify various wheat varieties, the data from the study "will dramatically increase the efficiency of breeding new varieties and identifying regions of the genome that carry key traits such as disease resistance, improved quality, and yield," said Keith Edwards, a professor of cereal functional genomics at Bristol, in a statement.


Helicos Files Shares for Sale by Investors from December Placement

Helicos BioSciences filed a prospectus with the US Securities and Exchange Commission last week for the sale of 68.4 million common shares owned by shareholders who participated in the firm's private placement in December.

Helicos would not receive any proceeds from the sale of shares of common stock sold from time to time under the prospectus by selling shareholders, it said. The roughly 68.4 million shares include nearly 25.7 million shares issuable to the selling stockholders upon exercise of their warrants.

In the December placement, the firm raised gross proceeds of around $18.6 million from the sale of 42.8 million units to investors, which included Atlas Ventures, Flagship Ventures, Highland Capital, Versant Ventures, Stephens, Vision Capital Advisors, and Stephen Quake, a Stanford professor and co-founder of Helicos.

Each unit consisted of one common share and one warrant to purchase .6 of a share of common stock at an exercise price of $.45 per share. The warrants have a five-year term and were exercisable immediately following closing of the transaction in December.
The filing of the shares with the SEC does not mean the shares will be sold by the investors. "The selling stockholders may sell some, all, or none of their shares," Helicos noted in the filing.


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Febit to Participate in Setup of Biomarker Discovery Center Heidelberg

Febit will help establish a Biomarker Discovery Center Heidelberg this month, a project recently awarded funding from the Excellence Cluster Initiative of the German Federal Ministry of Education and Research.

The project is being funded as part of a €40 million ($51.6 million) grant to develop a biotech excellence cluster in the region of Rhine Neckar in Germany for the development of innovative drugs, diagnostics, and technologies in cellular and molecular biology.

As part of its contribution, Febit said last week that it will offer both array- and second-generation sequencing-based analysis to aid in the development and validation of novel biomarkers. The company will also work with the German Cancer Research Center on studies to identify markers for various cancer types and to develop these markers into standardized diagnostic assays.


Genesis Swaps Software Rights for Stake in Real Time Genomics

Genesis Research and Development will trade its rights to royalties on the sale of a genomics data querying software package for a stake in start-up bioinformatics company Real Time Genomics.

Auckland, New Zealand-based Genesis said last week that it is converting the royalty rights to NetValue's SLIM Search software, which is based on Genesis' Cartesian technology, to a 10-percent stake in Real Time Genomics. Genesis' interest will be held by New Zealand holding company Gene Value.

The SLIM Search software can search and analyze short genomic reads, data generated by 454 Life Sciences' instruments, and 10-kilobase and larger reads in real-time, the company said.


Expression Analysis Enters UK Services Partnership with Complement Genomics

Expression Analysis said last week that it is partnering with Complement Genomics of Sunderland, UK, to offer genomic services to the UK market.

EA said that the partnership will enable it to expand its client base beyond its primary market in the US.

Complement Genomics offers a range of services through its Geneblitz unit, including genotyping, DNA sequencing, forensic testing, and toxicology and drug analysis protocols.

The companies plan to focus the partnership on genome-wide association studies, which EA said have become an "increasingly larger part" of its business.


Research Team Sequences Common Cold Virus Collection

In a paper appearing online in Science last week, researchers from the University of Wisconsin at Madison, the J. Craig Venter Institute, and the University of Maryland School of Medicine reported that they have sequenced the genomes of all 99 catalogued human rhinoviruses, the viruses that cause the common cold, along with ten new field samples.

Together, the genome sequences and other biological data are garnering new insights into HRV biology and providing the basis for a new HRV phylogenetic tree that reveals relationships between HRV strains with unprecedented resolution. Researchers say such findings could eventually lead to new treatments and better diagnoses for the common cold.

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Scientists at the University of Maryland School of Medicine and The Institute for Genomic Research, now part of the J. Craig Venter Institute, generated enough data to get about six times coverage each for all 99 HRV strains in the existing repository — along with ten new field isolates. Because other groups had done some of the sequencing already, the team did not have to do this from scratch: they ultimately sequenced about 80 historical strains and 10 field samples.

When the researchers generated a phylogenetic tree using the new sequence data, published HRV-A and HRV-B sequence data, and HRV-C sequence data, they came up with a tree distinct from any seen before — not because previous studies were inaccurate, but because they did not have as much data available.

With the genomes and new phylogenetic analysis in hand, it may now be possible to come up with new drug candidates against specific HRV sub-groups.

In an effort to flesh out the new reference sequence collection and gain new insights into clinical characteristics associated with various strains, the researchers now plan to sequence 1,000 additional HRV field isolates collected from across the US. Sequencing for that project will likely be done at the University of Maryland using one or more types of high-throughput sequencing approaches.

By Andrea Anderson; originally published on Genome Web Daily News


RNA-Seq Provides Clues to Bacterial Niche Specialization

In a paper appearing online in PNAS last week, an international research team used RNA sequencing to uncover gene expression and regulatory changes associated with bacterial adaptation to two distinct niches.

Burkholderia cenocepacia can cause health problems for individuals with cystic fibrosis and other immunocompromised patients. To better understand the niche adaptation of this bug, researchers compared two B. cenocepacia strains isolated from cystic fibrosis patients and soil samples.

The scientists used RNA-Seq to compare the gene expression and regulatory pathways in AU1054, a strain isolated from the sputum of a cystic fibrosis patient, and HI2424, a strain isolated from agricultural soil in New York state. Each strain was tested several times and grown in both cystic fibrosis and soil extract media.

After growing the strains in media and temperatures mimicking cystic fibrosis and soil conditions, the team isolated RNA, enriched for messenger RNA, and generated cDNA libraries. Researchers at the US Department of Energy's Joint Genome Institute then sequenced the cDNA on an Illumina Genome Analyzer.

The team reported that HI2424 had more highly expressed genes than AU1054, though they found that differential gene expression in both strains depended on the growth conditions used.

The researchers also found that growing B. cenocepacia under the cystic fibrosis-like conditions induced virulence factors, whereas the soil-mimicking conditions upped the expression of genes involved in nitrogen scavenging and environmental sensing.

In addition, the researchers identified what appear to be 13 new non-coding RNAs. A dozen of these are preferentially expressed in the soil conditions, fueling speculation that non-coding RNAs may aid B. cenocepacia's soil survival.

Finally, when the team directly compared the two strains under the same conditions, they found that 179 genes were differentially expressed in sputum-like conditions while 120 genes were differentially expressed in soil-like conditions.

The results provide insights into the differences between the strains as well as the adaptive techniques used by B. cenocepacia in general. And, the researchers noted, by honing in on AU1054 genes that are specifically expressed under cystic fibrosis conditions, it may be possible to find key virulence factors.


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Dana-Farber Cancer Institute to Install Helicos Sequencer

Dana-Farber Cancer Institute plans to install a Helicos Genetic Analysis System this month, In Sequence has learned. The instrument is scheduled to be shipped from Helicos BioSciences later this week.

Under an agreement with Helicos, Dana-Farber will have the instrument on site for six months free of charge.

During that time, researchers from 12 institute labs are planning to run a total of 600 samples — 50 samples every two weeks — for applications that include ChIP-Seq and digital gene expression analysis of samples involved in cancer, according to Paul Morrison, director of molecular biology core facilities at DFCI. The labs are paying for reagents required for these projects.

Projects will start "as soon as we get [the instrument] off the elevator," according to Morrison.


Wash U. to Add 21 Illumina Genome Analyzers to Genome Center

Illumina has reached an agreement in principle with Washington University to sell it 21 additional Genome Analyzer sequencers in the coming months for use in its human genomics programs, the firm said last week.

The new machines will bring to 35 the installed base as the Genome Center at Washington University's School of Medicine, Illumina said. With the additional sequencing capacity, and after "continued improvements" are made to the system, the center will be able to sequence one human genome per day at 25x coverage, the company said.

"Our intention to substantially scale-up with this technology reflects our commitment to large-scale sequencing projects that aim to uncover the underlying genetic basis of various human diseases," Richard Wilson, director of the Genome Center, said in a statement. "With the rapid decline in the cost of whole-genome sequencing, we believe now is the time to embark on initiatives which were previously not possible."


ABRF Survey Finds Half of All Second-Gen Sequencer Owners Plan to Buy More

A recent survey by the Association of Biomolecular Resource Facilities' DNA Sequencing Research Group (see In Sequence 1/13/2009) found that around half of all labs that currently own a second-generation sequencing instrument plan to buy another system some time in the next two years.

Peter Schweitzer of Cornell University told attendees of ABRF's annual meeting in Memphis, Tenn., this week that the results are just a "snapshot" of the current state of second-generation sequencing instrumentation, and noted that the DSRG plans to conduct further analysis on the survey data and submit its findings to the Journal of Biomolecular Technology in the near future.

Of the survey's 69 participants, which primarily included core labs and academic institutes in the US, 37 currently have one or more sequencer from Roche/454, Illumina, or Life Technologies division Applied Biosystems. Of those, 47 percent indicated that they plan to buy at least one more instrument in the next two years.

Of those participants who do not currently have second-gen sequencers, 15 said they have no plans to purchase one in the future, while 15 said they are considering a purchase in the next two years.

Fifty-seven percent of all respondents said that they eventually plan to purchase a second- or third-generation sequencer. Of those, 10 institutes said they plan to purchase a system "immediately," 20 said they plan to make their purchase in the next six months, 17 said they plan to buy one in six to 12 months, and 12 said they plan to buy in the next one to two years.

The mix of platforms that these respondents intend to buy was split relatively evenly between Roche/454, Illumina, and Applied Biosystems, Schweitzer said.

The most common application for second-gen sequencing among responding labs was whole-genome sequencing, followed by ChIP-Seq and transcriptome profiling. The least common applications were digital gene expression and methylation analysis.

Three responding labs said they perform only whole-genome sequencing with their systems, while one lab exclusively performs small-RNA sequencing with its instrument.

The survey results indicate that second-gen sequencing is having some impact on Sanger sequencing, but perhaps not as much as some may have expected: Three responding labs said that their use of Sanger sequencing has "dramatically" decreased due to second-gen technology, while 10 labs said their use of Sanger sequencing has decreased "somewhat."

The majority of respondents, however, indicated that they have seen little or no change in their use of Sanger sequencing: 15 labs reported that there has been no change in their Sanger use, while 12 labs reported that their use of Sanger sequencing has actually increased.

By Bernadette Toner, originally published on GenomeWeb Daily News


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St. Jude's Leukemia Researcher Receives ABI Sequencing Prize

Applied Biosystems said last week that St. Jude Children's Research Hospital pathology researcher Charles Mullighan has won the company's "What Would You Do with a $10K Genome" grant, which will support his research into acute lymphoblastic leukemia.

Under the program, Mullighan will collaborate with ABI researchers to sequence normal tissue, leukemia cells at diagnosis, and relapse samples from five pediatric patients at St. Jude.

The researchers plan to generate 60 gigabases, or 750 million tags, of sequencing data in an effort to identify SNPs, large and small insertion/deletions, translocations, and copy number variants associated with ALL, a white blood cell cancer.

ABI, a subsidiary of Life Technologies, will perform sample processing, data generation, and primary data analysis on the SOLiD 3. The project is aimed at uncovering structural variations and other genomic changes associated with ALL in order to understand genomic changes associated with relapse and identify new therapies for the disease.

Mullighan, who received the first prize award at the annual Advances in Genome Biology and Technology meeting in Marco Island, Fla., was selected from more than 200 applicants.


Roche Says GS FLX Sales Nearly Doubled in '08 as Applied Sciences Revenues Rise 11 Percent

Roche said last week that sales of its 454 GS FLX sequencer nearly doubled in 2008. Full-year 2008 revenue for its diagnostics division declined 3 percent to 9.7 billion Swiss francs ($8.4 billion) from 9.4 billion Swiss francs in 2007.

The division includes several business areas, including molecular diagnostics, whose revenues declined 2 percent to 1.1 billion Swiss francs, and applied science, whose receipts increased 11 percent to 765 million Swiss francs. Applied science includes 454 Life Sciences.

Within the applied science group, Roche said that sales of its Genome Sequencer FLX system "nearly doubled, despite increased pressure from competitors." Applied science also saw double-digit growth in sales of LightCycler 480 real-time PCR instruments and reagents, with particularly strong sales increases in North America and China.

In addition, microarray systems "made a significant contribution to full-year sales" in the applied science group, Roche said. "Sequential quarterly sales growth for these products has been steady and strong since Roche acquired NimbleGen in August 2007."
Roche's total revenues, including sales for its diagnostics and pharmaceuticals divisions, dipped 1 percent to 45.6 billion Swiss francs from 46.1 billion Swiss francs.

The diagnostics division comprised 21 percent of the company's total sales while the pharmaceuticals division contributed to 79 percent.

For 2009, Roche said that it expects full-year sales for both divisions to grow "ahead of the market, with increases in the mid-single-digit range in local currencies."

Priorities for the applied science group this year include "developing new and more powerful NimbleGen microarrays and enhancing the flexibility and efficiency of Genome Sequencer technology for the research market," Roche said. The company also plans updates of the LightCycler 480 instrument and the MagNa Pure sample-prep system.

Planned product launches for the applied science group include a high-resolution microarray scanner and the MagNa Pure 96 high-throughput system.


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Illumina's Q4 Revenues Rise 43 Percent, Loss Swings to Profit

Illumina reported last week that its fourth-quarter revenues increased 43 percent year over year and a prior-year loss swung to a profit.

The company reported total revenues of $160.9 million for the three-month period ended Dec. 28, 2008, compared to $112.6 million for the fourth quarter of 2007. Its product revenues increased to $152.8 million from $101.1 million, while service and other revenue decreased to $8.1 million from $11.5 million.

Illumina CFO Christian Henry said during the firm's conference call last week that consumables revenue grew 76 percent year over year to $98.6 million for the quarter, driven by demand for the company's Infinium HD BeadChips and sequencing kits.

He also said that the firm's instrument revenue rose 23 percent to $51.2 million from $41.8 million for Q4 2007.

"Our revenue growth reflects our strong market position in both arrays and sequencing," Illumina President and CEO Jay Flatley said during the call. "By our estimates, we believe that we have more than 70 percent market share in the high-multiplex genotyping market, and more than 60 percent market share in the next-generation sequencing market."

Flatley said that Illumina shipped "a record" 38 BeadExpress systems during the quarter, each with a "consumable pull-through at the high end of our forecasted range of $50,000 to $100,000 per year." He did not mention the number of Genome Analyzer sequencers shipped during the quarter or in 2008.

Illumina posted a profit of $28.9 million, or $.22 per share, compared to a net loss of $4.1 million, or $.04 per share, for the fourth quarter of 2007. The 2007 fourth quarter included charges of $54.5 million related to the settlement of litigation.

R&D spending rose 41 percent to $28.3 million from $20.1 million, while SG&A spending increased 31 percent to $39.2 million from $30 million.

For full-year 2008, Illumina's revenues jumped 56 percent to $573.2 million from $366.8 million. Its product revenue for the year was $532.4 million versus $326.7 million in 2007, while its service and other revenue remained flat at $40.8 million.

Illumina's net income for 2008 was $50.5 million, or $.38 per share, compared to a net loss of $278.4 million, or $2.57 per share, for 2007. The 2007 results include charges of $303.4 million for acquired in-process R&D, versus $24.7 million for similar charges in 2008.

R&D costs for the year increased 35 percent to $100 million from $73.9 million for 2007 and SG&A spending rose 46 percent to $148 million from $101.3 million.

Illumina finished 2008 with $327 million in cash and cash equivalents.

The company expects to bring in revenues of between $158 million and $164 million in the first quarter of 2009, along with earnings per share of between $.23 and $.26. For full-year 2009, it is guiding for revenue between $690 million and $720 million, with EPS of between $1.10 and $1.20.


EMBL Purchases Genomatix's Software

The European Molecular Biology Laboratory has installed second-generation sequencing data analysis software from Genomatix Software for use in its Genomics Core Facility in Heidelberg, Germany, Genomatix said last week.

The Munich-based company said that EMBL has purchased the company's Mining Station, which provides SNP detection and genotyping, copy number analysis, and small RNA analysis, and its Genome Analyzer software, which conducts deep biological analysis of data from the GMS. Together, the systems offer an integrated solution for analyzing raw second-generation sequencing data, according to Genomatix.

EMBL's GeneCore is focused on studying the benefits and use of new technologies developed at EMBL, and on improving the quality, efficiency, and relevance of lab data.


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ABRF Study Explores microRNA Analysis Platforms

Several research groups under the auspices of the Association of Biomolecular Resource Facilities are comparing how different microarray platforms, and second-generation sequencing, stack up when it comes to microRNA analysis.

According to preliminary results of the ongoing study, which were presented at ABRF's annual meeting in Memphis, Tenn., this week, miRNA arrays from Affymetrix, Illumina, Agilent, and Exiqon all show different strengths and shortcomings regarding sensitivity and reproducibility.

The study, conducted jointly by ABRF's Microarrays Research Group and DNA Sequencing Research Group, compared the four array platforms to Applied Biosystems' TaqMan miRNA assay. The participants are also comparing the results to miRNA data from the Illumina Genome Analyzer, but that part of the project has not yet been completed.

In a talk outlining the preliminary results, Susan Hester of the US Environmental Protection Agency noted that the research groups aimed to assess the effectiveness of second-generation sequencing and microarrays for miRNA expression profiling.

Participating sites analyzed brain and liver RNA and ran three replicates on each array platform. The study used Applied Biosystems' RT-PCR platform as a baseline for comparing the accuracy of the different array technologies.

The study evaluated a number of parameters, including the number of miRNAs reproducibly detected with each platform, the number of miRNAs that were differentially expressed in brain and liver tissue by an arbitrary cutoff of more than two-fold, and the reproducibility within and across platforms.

The Illumina array platform was the most sensitive, detecting 1,146 miRNAs, while the TaqMan assay detected 673. The Affy, Agilent, and Exiqon platforms detected 847, 723, and 732 miRNAs, respectively.

The Illumina platform was also the most sensitive when it came to differential expression, picking up 394 miRNAs with a fold change of more than two. The lowest in that category was the Affy platform, which measured 292 differentially expressed miRNAs with the cutoff fold change of two.

The Agilent platform had the best correlation with the TaqMan platform and demonstrated the highest sensitivity for miRNAs that were measured on all platforms, as well as the highest reproducibility of results generated by other platforms.
In terms of overall technical reproducibility, Affy came out ahead, according to the preliminary results, while the Exiqon and Agilent platforms showed the best cross-platform correlation of results.

While the analysis of the data is still ongoing, Hester said that the early results indicate that all platforms show both "strengths and underperformance on some sensitivity parameters."

One possibility for the variation in results, she said, could be differences in miRNA probes across the platforms, though she stressed that is just conjecture.

Peter Schweitzer of Cornell University discussed his group's work to generate miRNA data from the Illumina Genome Analyzer for the study, but noted that so far the group has only sequenced the brain sample.

Schweizer said that the sequencer detected 359 miRNAs in that sample, and that an initial comparison to the Agilent array results indicates "good correlation," but stressed that the results are preliminary. He did not provide a timeline for the expected completion date of the sequencing component of the study.

By Bernadette Toner, originally published on GenomeWeb Daily News


New FDA Effort to Take Aim at Genomics

The US Food and Drug Administration is creating a new position at the Office of FDA's Chief Scientist that will focus on the agency's genomics-related programs, FDA said last week.

Frank Torti, acting commissioner of food and drugs, mentioned the new position in a weekly address on the FDA's website. He said the new hire will be dedicated to "coordinating and upgrading our agency's activities in genomics and the related fields of science that are involved in the analysis of complex DNA, protein, and smaller expression platforms."

The first person to hold this post will be Liz Mansfield, who has been involved in policy and scientific positions at FDA and in the private sector. Mansfield will work on FDA's goal of providing agency scientists with tools and personnel capable of high-level analysis of complex genetic data.

In his address, Torti said that the "emphasis on a coordinated genomics effort" resulted from an FDA retreat last summer that focused on genomics, recommendations from the FDA Science Board, and "our own internal planning."

In order for personalized medicine to advance, "FDA must use the most advanced tools for evaluating the new and frequently highly complex products regulated by our agency," Torti explained. "Further integration and coordination of the latest genomic technology into the FDA's processes and decision-making will better protect and promote the public health."


Linkage Biosciences Raises $2M in Series A Round

Linkage Biosciences has raised $2 million in a Series A round of financing, the molecular diagnostics firm said last week.

Linkage Bio said the funding round was led by Greenhouse Capital Partners and James R. Fisher, managing member of Fisher Capital Corp. II, a firm that works exclusively with Kohlberg Kravis Roberts, a New York-based private-equity firm.

The firm expects to use the cash to continue developing and marketing its molecular diagnostic products, which are focused on human leukocyte antigen typing for organ transplantation. The firm also is developing products for other transplant diagnostics and complex genetic disorders.

The Scan

Renewed Gain-of-Function Worries

The New York Times writes that the pandemic is renewing concerns about gain-of-function research.

Who's Getting the Patents?

A trio of researchers has analyzed gender trends in biomedical patents issued between 1976 and 2010 in the US, New Scientist reports.

Other Uses

CBS Sunday Morning looks at how mRNA vaccine technology could be applied beyond SARS-CoV-2.

PLOS Papers Present Analysis of Cervicovaginal Microbiome, Glycosylation in Model Archaea, More

In PLOS this week: functional potential of the cervicovaginal microbiome, glycosylation patterns in model archaea, and more.