Digital Pathology Blog

Bruker and Carl Zeiss Announce Collaboration to Advance Molecular Histology

Integration of MIRAX Virtual Slide Scanner from Carl Zeiss into Bruker’s MALDI Molecular Imager™ Enables Non-Targeted Molecular Histology -- Combined Solution to be Introduced at German Pathology Society (DGP) Meeting in June 2009

BREMEN, Germany & JENA, Germany--(BUSINESS WIRE)--Bruker Daltonik GmbH and Carl Zeiss MicroImaging GmbH today announced the integration of the MIRAX Virtual Slide Scanner from Carl Zeiss into Bruker’s MALDI Molecular Imager™. The goal of the Bruker–Carl Zeiss collaboration is to advance molecular histology research by providing an integrated solution (for research use only) for biological tissue research and pathology that adds non-targeted molecular information and ‘molecular contrast’ to histology.

The MALDI Molecular Imager is a molecular imaging system based on matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry directly from tissue sections. It allows histology researchers to measure spatially resolved peptide, protein and lipid profiles in tissue sections. MALDI imaging is a non-targeted, broadly applicable molecular imaging approach without the need for any antibody or nucleotide probe. Tissue-type specific molecular signatures (e.g. from tumors) can be generated and used for biomarker discovery and molecular histology.

A major bottleneck in the interpretation of MALDI imaging data in pathology research has been the interpretation of results in a histological context. Until now, this has required repeated switching between evaluated MALDI molecular images and microscope views. The integration of Carl Zeiss’ MIRAX Slide Scanner results into the MALDI Molecular Imager solution allows the direct overlay of the full microscopic image with the full molecular and spectral information in one convenient visualization software tool, enabling true untargeted molecular histology.

Dr. Sören-Oliver Deininger, MALDI Imaging Product Specialist at Bruker Daltonics, explained: “Bruker has been the market and commercial technology leader in MALDI imaging for several years. Proprietary technologies such as the smartbeam™ laser for best spectra quality at highest speed and best spatial resolution, as well as the Bruker ImagePrep™ for easy and reproducible sample preparation, have turned MALDI imaging into a mainstream research application. Now, the full integration of the MIRAX virtual slides allows tissue and pathology researchers for the first time to evaluate their results directly in the histological context with the full spatial resolution of optical microscopy and the molecular information from MALDI imaging.

“This integrated molecular histology solution will significantly accelerate clinical pathology research, particularly in oncology, where the untargeted molecular information is expected to reveal additional subtle changes in tissue that cannot be distinguished by traditional histology methods today.”

“The integration of the MIRAX Virtual Slide Scanner into the MALDI Molecular Imager solution is a very good example of how the combination of two innovative technologies can create new benefits for biomedical research. With two technology leaders working together, we believe that we have a strong foundation for a novel, breakthrough histology solution. We look forward to working closely together with Bruker,” said Dr. Richard Ankerhold, business unit manager from Carl Zeiss.

Dr. Axel Walch, a pathologist at the Helmholtz Centre in Munich, and a user of both the MALDI Molecular Imager and the MIRAX slide scanner, commented: “The protein expression observed in MALDI Imaging data cannot be fully understood without the underlying histological information: the correlation of the MALDI image with a micrometer-resolution microscopic image is therefore mandatory for MALDI Imaging in clinical research. The Zeiss Mirax Scanner has the true advantage of online scalable high lateral resolution that can zoom in quickly to any tissue sections investigated by MALDI. Merging both techniques, Bruker MALDI Imaging and MIRAX virtual microscopy, leads to synergistic effects with outstanding benefits for clinical research. It truly completes the superior Bruker product line for imaging comprising of sample preparation, high performance MALDI mass spectrometry and highly sophisticated software for data interpretation.”

For further product information, please visit www.bdal.com/molecular-histology.

ABOUT BRUKER DALTONICS: For more information about Bruker Daltonics and Bruker Corporation (NASDAQ: BRKR), please visit www.bdal.com or www.bruker.com.

Photos/Multimedia Gallery Available: http://tinyurl.com/n82766

Source: Bruker Daltonik (press release)

Mayo Clinic plans human DNA 'biobank'

Perhaps my DNA could be included in the biggest "biobank" in the country...

ROCHESTER, Minn. - Mayo Clinic researchers are planning to create a human DNA bank using samples from 20,000 area residents, and they say it could become the largest population-based "biobank" in the United States.

The goal is to help researchers find ways to personalize the way illnesses are treated and prevented, based on patients' genetic characteristics.

Only Mayo Clinic patients who volunteer and give expressed informed permission will be included.

"For it to be successful, we have to be able to have the cooperation of people willing to give DNA samples, coordinated with medical records," said Barbara Koenig, co-director of the Program in Professionalism and Bioethics at Mayo.

The biobank will not take volunteers until next year, and the Mayo Institutional Review Board must give final approval to the project.

Donating to the biobank won't be a one-time thing. An ongoing relationship will develop between the local participants and the biobank. For example, researchers might need to learn if a participant lives near a power pole.

The biobank also will ask participants for permission to make their samples and questionnaires "linkable" to their medical records.

"This is vital to study the effectiveness of treatments or prevention strategies over time. There is no other way to do this," Koenig said.

In addition to the population-based biobank, Mayo is planing three disease-specific biobanks focusing on mitochondrial DNA disorders, rare heart conditions and bipolar disorder.

"This is another form of philanthropy in my mind," said Mayo spokesman Bob Nellis, who's involved in planning how to ask for volunteers.

Researchers aim to learn how patients react to information culled from genome scans

In the Los Angeles Times (11/12) Booster Shots Blog, Rosie Mestel asked what individuals should do with the info they receive after spending "a thou' or two" to learn about their "genetic predisposition to Alzheimer's disease, colon cancer, heart disease, [and] more." Zeroing in on that question, researchers at the Scripps Translational Science Institute are planning to find an answer "with the help of 10,000 employees, family members, and friends of Scripps Health, a nonprofit healthcare delivery network in the San Diego area." Participants will "get a discounted scan of their genome from Navigenics," and "as new data roll in on other genetic links to diseases, those will be added to the database." Then, patients "will in a sense serve as their own controls: They'll be assessed for their mood, habits, and the medical care they seek both before and after they get the scan information." Meanwhile, Mestel pointed out an "interesting fact: Adopted people have been especially keen to enroll in the study."

Google co-founder finds he has Parkinson's disease gene through 23andMe test

The New York Times (9/19, C2, Helft) reports that on Thursday, Sergey Brin, a Google co-founder, announced, via his blog, "that he has a gene mutation that increases his likelihood of contracting Parkinson's disease, a degenerative disorder of the central nervous system that can impair speech, movement, and other functions." Specifically, "he carries a mutation of the LRRK2 gene, known as G2019S." While most "medical experts said that those who carry that gene mutation are more likely than not to live disease-free," about "30 percent of people with the gene mutation develop the disease," according to Susan B. Bressman, M.D., of New York's Beth Israel Medical Center.

Notably, "Brin's revelation came after using the genetic testing service 23andMe, which was co-founded by his wife, Anne Wojcicki, and in which Internet giant Google is an investor," according to the San Francisco Chronicle's (9/18, Kopytoff) The Tech Chronicles blog.

In the BBC's (9/18) dot.life blog, Darren Waters quoted Brin as saying, "This leaves me in a rather unique position" because "I now have the opportunity to adjust my life to reduce those odds (e.g. there is evidence that exercise may be protective against Parkinson's)." He added, "I also have the opportunity to perform and support research into this disease long before it may affect me." The Los Angeles Times (9/18, Guynn) also covered the story in its Technology blog, as does the Wall Street Journal (9/19, Vascellaro) in its Business Technology blog.

Genetic company cuts price of its genome scan

The New York Times (9/9, C3, Pollack) reports that a "company called 23andMe, one of the leaders in the new field of consumer genetic information, is expected to announce on Tuesday that it is cutting the price of its service deeply, to $399, down from $999." Company co- founder Linda Avey said that "the move reflected improvements and lower costs for devices, made by Illumina of San Diego, that are used to scan a person's genome."

The "price cut will ideally mean an influx of new information that will speed discoveries in the lab," the AP (9/9, Wohlsen) adds. Furthermore, "the company hopes to increase demand and hasten the day when a full genetic screening becomes routine medical practice." Notably, 23andMe's "main competitors charge anywhere from just under $1,000 to $2,500 for similar services."

But "while the genome companies say they are empowering individuals who want more control over their own healthcare, critics have cautioned that most of the genetic information provided would make little real difference in decisions made by patients and their doctors," the San Francisco Chronicle (9/9, D1, Tansey) notes. Still, Avey maintains that while "such a database of information on the genetics and health histories of many individuals would have huge commercial value," it "will also support 23andMe's long-term plan to act as a liaison between drug researchers and groups of people with specific medical and genetic profiles." The Los Angeles Times (9/8) also covered the story in its Technology blog.

Government Gene Guru Resigns

May 28 (Bloomberg) -- Francis Collins, who led the U.S. government effort to decode the body's DNA blueprint, will step down as head of the National Human Genome Research Institute effective Aug. 1, the agency said.

Collins, 58, helped identify the gene linked to cystic fibrosis in 1989, and in 1993 helped identify DNA tied to Huntington's disease. That same year, Collins was named head of the Human Genome Project and, in 2001, the project published a first draft that identified all 2 billion or so letters that make up the human genetic code.

By providing access to the full catalogue of human genes, scientists have been able to identify variations linked with common and inherited diseases. Researchers have used those results to create medicines such as Tarceva, the Genentech Inc. lung cancer drug developed after a DNA mutation was found to be linked to the tumors. Variations in more than 100 genes have been linked to about 20 diseases, researchers have said.

"The study of the human genome has completely transformed medical research, and is on the way to transforming clinical practice,'' Collins said in a telephone interview today, when asked what he is proudest of from his tenure at the National Institutes of Health.

Alan Guttmacher, the institute's current deputy director, will become acting director on Aug. 1, said NIH director Elias Zerhouni in am e-mailed statement announcing Collins' decision to leave the agency.

`No Heir Apparent'

Bert Vogelstein, professor of oncology and pathology at the Johns Hopkins School of Medicine in Baltimore, said there is "no heir apparent, no one who can easily swoop into the void'' left by Collins' departure. " Francis has both the scientific credentials and an amazing ability to bring people together,'' Vogelstein said. ``He could really explain what was important in understandable terms.''

In the late 1990s and early 2000s, Collins' institute raced against a private company, Celera Genetics, led by Craig Venter, to be the first to publish the genome. A full analysis was completed by Collins' group in April 2003.

Collins, who grew up on a small farm in Virginia and was home-schooled until the sixth grade, got an undergraduate degree in chemistry from the University of Virginia, a doctorate in physical chemistry for Yale University and medical degree from the University of North Carolina. He served on the faculty at the University of Michigan until joining the NIH in 1993.

While at Michigan, he collaborated with researchers at the Hospital for Sick Children in Toronto, Canada, on the gene for cystic fibrosis and Huntington's.

`Insights'

Collins' work at the institute made him "an extraordinary leader in developing tools and applications and insights into what makes us who we are,'' said W. Ian Lipkin, a professor of epidemiology at Columbia University's Mailman School of Public Health in New York, in a telephone interview.

Lipkin was the first to identify the West Nile Virus in the U.S. using genetic technology, and recently isolated one of the causes of a malady killing honeybees using gene sequencing technology created by Roche Holding AG.

"What's not as well-known is that he set the stage for a whole series of projects which followed on the heels of the human genome sequence, and now are probably some of the most valuable studies ongoing in biomedical research,'' Vogelstein said. "The whole idea of having several labs undertake these projects is a different way of doing biomedical science, and you can largely attribute that to Francis as the leader.''

Discovering Biology in a Digital World : The Personal Genome discussion

Bill Gates, Eric Lander, Maynard Olson, Leena Peltonen, and George Church fielded questions recently at a fascinating panel discussion on personal genomics at the University of Washington.

Beware the flood!!
Eric Lander started the night by bringing everyone up to speed on the state of genomics. I’m going to paraphrase his introduction here:

Eric pointed out that even after the region containing the cystic fibrosis gene had been found, it still took 5 years to clone and sequence it and figure out the most frequent mutation. Many biologists agreed that was too long a time and too much money.

The Human Genome Project changed all that. Biology has been industrialized.

Before the Human Genome project, only 70 simple Mendelian disease genes had been found, we know of 2600 genes that code for rare, unusual diseases.

But what about things that lots of people get? Multigenic disorders? How do we find those?

To find those, we need to look at genetic variation. We know now that there are about 12 million common variants in the entire population. We also know that many of these are found in blocks and we’ve mapped many of them through the HapMap project.
By looking at genetic variation we’ve been able to find more genetic information about common diseases. We can use microarrays and new sequencing technologies to look at lots of information and do genome wide studies where we see how often certain genetic changes appear and whether or not their presence is tied to disease, and the rate of the discovery is increasing rapidly.

In 2001, we found 1. This was the same for 2002 and 2004. In 2007 found 5 associations. In 2007 we found 8 (I think). And, in 2007, we found 160 associations between genetic variants and common diseases. The rate of discovery is phenomenal.

He said the key lessons from these studies were:

• Need large samples, 1000’s of samples and stringent thresholds for reproducible results
• Only looked at some types of variants for certain diseases
• Many variants only increase risk by small effects 10-30% higher
• These genes are important for understanding the biology of the disease
• The genes have small implications for risk prediction -
• Beware the flood!!
• Watch out for small dubious studies

And he pointed out that it seems easier to sequence a human genome than it is to get legislation to protect people from having their genetic information against them. [Congress votes on GINA today, it will be interesting to see what happens.]

Questions from the audience

Naturally, the panelists were asked if they had had their genomes sequenced. Only George Church answered yes. It was interesting though, even though Leena Peltonen and Eric Lander said that they weren’t interested in having this done, both of them said they had been tested for certain genetic diseases, Eric, for Tay Sachs, and Leena for 40 diseases common in Finns. Bill Gates said that if the top 20 infectious diseases were to be cured, he would be happy to have his genome sequenced and make it public.

If you could test 1000 genetic traits, what boxes would you check?
Bill Gates said the most important box would be to avoid being born in a poor country.

Should people be given information about genes that are related to diseases if there’s nothing that can be done?
Eric Lander: People should have the information if they want it. Our greatest challenge is to provide them the education to make an informed choice.

George Church: You can always do something. Lorenzo’s oil is a movie about taking action. It shows what people can do.

The idea of education returned later in the talk. George Church suggested that the personal genomics companies may be the most effective at education, since they get people directly involved with their genomes.

What are options for the personal genome to benefit third world populations?
Bill - whenever you divert $1000 away from spending on poor, you lose lives, but if you define the genome as making information free for scientists to gather and use, then the benefit could be much greater.

How will personal genomics affect privacy?
George: We can’t be complacent, but we can’t be overconfident. There may be people who voluntarily decide to give up some of their privacy.
Maynard - if we set the bar for informed consent too high, we will only sequence the genomes of geneticists.
George - Two genomes have been sequenced from Africans and one Chinese person.
Bill: Are relatives asked to sign informed consent forms?
George - they did exclude some people because of relatives.

Then, Eric Lander playfully asked the other panelists if they thought presidential candidates disclose their genomes. He reminded us that we had a president with Alzheimer’s disease and we would have found that potential if we had tested him. In the future, will we ask the older candidates to get tested for Alzheimer’s?

Are we going to make designer babies?
All the panelists agreed this would be too risky, even though they could imagine people wanting better options for their children.

George Church pointed out that people can be proactive now and use preimplantation diagnosis and in vitro fertilization to prevent having children with some kinds of serious genetic diseases. Eric and Maynard countered that they felt it likely that sex would remain the most popular method for creating babies.

Google invests in DNA-screening start-up aimed at boosting disease prevention

BusinessWeek (4/18, Backman) reported that after investing "in a genetic screening company, 23andMe," Google is now "also putting money into a second Silicon Valley DNA-screening startup, Navigenics." The company "aims to boost disease prevention by providing customers reports on their DNA that they can share with their doctors," and "[m]uch in the way it invested in 23andMe, Google wants to plant an early stake in a potentially large new market around genetic data." Notably, "[i]f genetic screening proves popular, the nascent technology also stands to benefit Affymetrix, which not only invested in Navigenics but also makes the GeneChip system used...to analyze customers' DNA." Speaking before a group hosted by Navigenics "about the product's potential," former Vice-President Al Gore, said, "On all these new genetic breakthroughs there is always some resistance culturally." But "then when there's an evaluation of the inherent value, if the ethics are right, if the surrounding culture is right, then it just breaks through. I think this company has it right," he added.

DNA pioneer Watson undergoes mass genome sequencing

The U.K.'s Guardian (4/17, Randerson) reports that the "era of mass genome sequencing to assess risks of genetic disease comes a step closer today with the publication of" a second "human genome sequence," according to an article published in today's issue of Nature. Professor James Watson, who along with "Francis Crick discovered the double-helix structure of DNA in 1953," was "[t]he subject of the latest genome sequencing," which "will tell the scientist much about his own genetic makeup." Jonathan Rothberg, of 454 Life Sciences, said, "Jim Watson is one person. We have to do this many times to correlate those changes in his genome to how his children will be predisposed to disease." But "[o]ver the next 10 years and the next 10,000 genomes we will be able to have those correlations and we will be able to do amazing things," he added.

University of Alberta Transplant Applied Genomics Centre Chooses Scientific Data Management Solution from GenoLogics

Chooses Scientific Data Management Solution from GenoLogics

GenoLogics, a leading developer of lab and data management software solutions for life sciences research, based in Victoria, British Columbia, today announced that the University of Alberta has selected Geneus™ for their informatics infrastructure and scientific data management system. GenoLogics installed Geneus™ at the Alberta Transplant Applied Genomics Centre (ATAGC) at the University of Alberta in September of this year.

Today, ATAGC is conducting diagnostic gene expression and transcriptomics research with the aim to develop new molecular diagnostics for organ transplant recipients. The research involves using gene expression microarrays to understand transplant rejection events, and has led to the identification of a series of gene expression (transcript) sets that provide new robust quantitative measurements for assessing rejection. These sets form the basis of a potentially new diagnostic system to use in conjunction with the current pathology system. In the future, they expect to use proteomics and metabolomics research to augment the research they are conducting, and they also plan to partner with pharmaceutical organizations to develop commercial therapeutic drugs to counter organ rejection.

Dr. Philip Halloran, Director of the Alberta Transplant Applied Genomics Centre, stated, “The challenge of applying the new sciences is that they are so rich in data – in information. To be successful in bringing the new genetic sciences to the bedside requires new approaches to managing information. We are doing this in organ transplants now, but every area of medicine will eventually be changed by these new technologies.”

The Geneus solution will be used primarily as a scientific data management system (SDMS) to handle the data management component of the Centre’s gene expression and transcriptomics research. Geneus will provide the research informatics infrastructure to handle the Centre’s massive amount of scientific data, for example, an Affymetrix GeneChip® microarray with over 50,000 genes in a single experiment. Geneus also provides a powerful LIMS which the Centre will use to handle lab operations and sample tracking and management.

The Alberta Transplant Applied Genomics Centre is devoted to using microarrays and other methods for gene expression both for new diagnostic insights and for exploring disease mechanisms. The Centre is in the process of establishing a service where research conducted on understanding the mechanisms and biological events associated with rejection of transplanted organs may be made available to other labs, institutions and clinicians. ATAGC has a unique database that houses gene expression data that comes from patient biopsies along with the related patient information, in which confidentiality and privacy are completely protected. This comprehensive database provides a view of molecular events and how the relate to clinical events, which can be used by researchers across multiple sciences within the University of Alberta and elsewhere.

Initially, over 50 people consisting of lab technicians, researchers, bioinformaticians, and physicians will access and use this system. The Geneus solution will scale as the Centre expands and to enable collaboration between many remote users (through GenoLogics’ LabLink™ web collaboration system) and access to data across multiple labs. As the Genomics Centre grows, this configurable informatics platform can be adapted on the fly to include processes and workflows for other sciences.

The ATAGC needed a robust, flexible system, purposed for their science, with an open database schema. They also wanted to work with a collaborative and experienced team that could implement a production solution quickly, and that provided long-term informatics services and support. GenoLogics met these requirements.

About GenoLogics

GenoLogics provides enterprise software solutions to the discovery life sciences market. Our core competency is developing solutions for lab informatics and scientific data management. Our application specific modules are complemented by our configurable, integrating lab informatics platform, and a broad range of professional services. Our LIMS platform is scalable to service many different labs across one organization. GenoLogics services core and research labs involved in genomics, proteomics and other discovery research areas. As well, our platform can provide significant value to organizations with a systems biology or translational medicine initiative. For more information, please visit [http://www.genologics.com] www.genologics.com.

About Alberta Transplant Applied Genomics Centre

Located at the University of Alberta, the Alberta Transplant Applied Genomics Centre is applying the new omic technologies, particularly transcriptomics, to understand the relationships between molecules, pathology and clinical presentation. This information will guide in the development of new drugs and diagnostics to manage disease. For more information, please visit [http://www.atagc.med.ualberta.ca/] www.atagc.med.ualberta.ca.

###

Contact info:

Tanis MacSween, Manager, Marketing Communications

GenoLogics Life Sciences Software, Inc.

[mailto:tanis.macsween@genologics.com ] tanis.macsween@genologics.com

250.483.7063

This message was sent by: Genologics, 4464 Markham Street, Suite 2302, Victoria, BC V8Z 7X8, Canada