Revolutionize lifehmpdacc.org/doc/GT_20091001_Oct_2009.pdf2009/10/01 · Meredith W. Salisbury, Editor What do you think of Genome Technology? Let me know how we’re doing by e-mailing

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BONUS: TRADITIONAL & DIGITAL GENE EXPRESSION

OCTOBER 2009

Companion Diagnostics I Gene Expression in the Brain

The Human Microbiome

GEORGE WEINSTOCK, WASHINGTON UNIVERSITY IN ST. LOUIS

Contents | Zoom in | Zoom out For navigation instructions please click here Search Issue | Next Page

Contents | Zoom in | Zoom out For navigation instructions please click here Search Issue | Next Page

Catch Copy Number Variants Genome-WideComprehensively detect CNVs with 720,000 probes per sample and enhanced coverage of low-copy repeat regions of the genome (e.g. segmental duplications).

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Analysis of a Complex CNV Region in Chromosome 17 in a BurkittLymphoma Research Sample Referenced against Normal GenomicDNA. An ~382 kb deletion region and an ~35 kb amplification region are easily detected using the NimbleGen Human CGH 3x720K Whole-Genome Tiling v3.0 array and the NimbleGen MS 200 Microarray Scanner at 2 μm resolution. The combination of high-density NimbleGen microarrays and the high-resolution scanning of the MS 200 provides sensitivity to comprehensively detect genome-wide CNVs. Catch what you’ve been missing:

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OCTOBER 2009 Contents“We just don’t know that much about our relationship between our human cells and our microbial cells.”

Julia Segre, Page 42

GeneExpressionNew Tools in NeuroscienceA brain atlas was once on the order of a coffee table book, known for its large, glossy illustrations. Today’s brain atlases — led largely by the Allen Institute for Brain Sci-ence — capitalize on localized gene expression and other data to truly revolutionize the field of neuroscience.BY MEREDITH W. SALISBURY

30

PGxCompanion Diagnostics Take OffPharma is realizing that it needs to collaborate with diagnostic companies to stratify patients and to make safer, more effective drugs. But obstacles remain in the path to full flight.BY JEANENE SWANSON

33

SequencingHumans as HostParticipants are calling the Human Microbiome Project a second Human Genome Project. The massive global effort aims to get to the bottom of the relationship between microorganism and host, and disease and health.BY CIARA CURTIN

38On The Cover38 The Human Microbiome33 Companion Diagnostics30 Gene Expression in the Brain

PHOTOGRAPH BY BOB BOSTON FOR GENOME TECHNOLOGY O C T O B E R 2 0 0 9 G E N O M E T E C H N O L O G Y 3


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OCTOBER 2009 Contents

MarkersNIH .......................................................10Collins steps into new directorship with goals at the ready; funding stability a priority

NANOMEDICINE................................11Jamey Marth to direct new nano center at UC-Santa Barbara, Burnham

SEQUENCING....................................12UW group sequences exomes from 12 people, confirms gene for rare disease

SYNTHETIC GENOMICS. ................13Venter Institute team demonstrates successful cross-species genome

METHYLATION.................................. 14Markowitz, Vogelstein lead development of novel detection technique

STRUCTURAL VARIATION.............. 14New BreakDancer algorithm performs high-res mapping of indels, more

PCR ......................................................15CDC evaluates rapid flu tests versus rRT-PCR for detecting novel strain of H1N1 influenza

In every issuePRIMER.................................................7We all have our bugs

WHERE ARE THEY NOW? .................9Kathy Hudson, next-gen sequencing on the rise, Centers of Excellence in Genomic Sciences, and more

ZEITGEIST...........................................16A blog around the world

CAREERS............................................19The journal perspective

LAB REUNION ..................................20‘A community of scholars’

UNDER ONE ROOF. ......................... 22A grassroots institute

MYTAKE............................................. 25Project annotation

BRUTE FORCE...................................27Personal supercomputers?

UPCOMING EVENTS....................... 56

BLUNT END....................................... 58

UpstreamPROTEOMICS................................... 45Grant supports proteomics synchrotron work

SEQUENCING....................................47Complete Genomics raises $45 million in Series D

RNAI.................................................... 49UMass, Whitehead fire new salvo in Tuschl IP suit

MICROARRAYS.................................50Affy inks deal with Beckman for custom tools

BIOINFORMATICS ............................51Pharma calls for a pre-competitive approach

DownstreamPGX ..................................................... 52Celera hones panel for non-small cell lung cancer

Q&A..................................................... 53Innovation through imaging

CASE STUDY..................................... 55The peptide blockade

10 20 53

O C T O B E R 2 0 0 9 G E N O M E T E C H N O L O G Y 5


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We All Have Our Bugs

It was several years ago that I first heard about a major study of the human microbiome — it was from Washington University’s Jeff Gordon, presenting at a Marco Island conference some of the earliest genomics-based research into the microbial content of our bodies. At the time, many attendees were surprised to

hear that microbial cells outnumber human cells 10 to one in the average human. Rarely have so many scientists been sent scrambling for hand sanitizer — but, it seems, they also scrambled to participate in the nascent microbiome field.

By 2007, NHGRI launched its large-scale Human Microbiome Project, which has so far issued grants to more than 50 PIs for vari-ous components of the effort. For our cover story this month, Ciara Curtin grabbed her antibiotics and dove into the world of infant guts, skin biomes, and more to report on the ongoing science and the findings already emerging from it. It’s a great story — and one that I recom-mend you don’t read over lunch.

Elsewhere in this issue, we’ve got a feature story on companion diagnostics. Jeanene Swanson reports on growing efforts from pharmas and diagnostic companies alike to find better ways of targeting and dosing therapeutics. An-other feature article explores how gene expression is revolutionizing neurosci-ence, with a particular focus on new programs to build human brain atlases with localized expression data.

This month’s Brute Force column checks in on the paradox of “per-sonal supercomputers,” while our Under One Roof article profiles the new Institute for Genomic Medicine at the University of Califor-nia, San Diego. Our Lab Reunion column focuses on Steve Henikoff at the Fred Hutchinson Cancer Research Center. And in news this month, we highlight the priorities Francis Collins laid out for NIH in his all-hands-on-deck introductory meeting in August. (Yes, he worries about funding stability, too.) Last but not least, Sandra Por-ter writes a My Take column this month, with a great dissection of the debate about using students to annotate genome sequence.

Meredith W. Salisbury, Editor

What do you think of Genome Technology? Let me know how we’re doing by e-mailing me at [email protected] or by calling me at +1.212.651.5635

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WHERE ARE THEY NOW? Update

In Review: Kathy Hudson, Next-Gen Sequencing on the Rise, Centers of Excellence in Genomic Sciences, and More

Kathy Hudson, director of the Genetics and Public Policy Center at Johns Hopkins Uni-versity, appeared on the cover of last year’s October issue of Genome Technology. In the cover story on personalized medicine’s move

into the clinic, Hudson was cautiously optimistic. “I think in general the hype has exceeded the reality, but there is reason to be excited and optimistic,” she said then. Hudson is now expected to join the National Insti-tutes of Health as chief of staff to Director Francis Col-lins. Prior to founding Hopkins’ policy center in 2002, Hudson was assistant director of the National Human Genome Research Institute.

Also in last year’s issue, GT took a look at how the next-generation — and third-generation — sequencing platforms were faring. Roche 454 was just launching its new Titanium chemistry, Illumina’s Genome Analyzer had upgraded to the GAII, and ABI was looking forward to the release of its SOLiD HT System. Currently, the next-gen companies are gaining slightly. Roche’s Applied Science section, which includes 454, had an 8 percent gain in sales during the first half of 2009 as compared to 2008; Illumina reported a 15 percent increase in second-quarter revenue for 2009; and Life Technologies says its Genetic Systems division, which includes SOLiD, saw a 5.5 percent increase in second-quarter revenues.

Back in 2004, the GT cover story discussed the Centers of Excellence in Ge-nomic Sciences program. Nine institutes were given $3 million a year for five years to carve out a place for themselves in integrated genomics. Since then, Deirdre Meldrum, who was at the University of Washington’s CEGSTech, was named a dean of engineering at Arizona State University, where she also directs the Center for EcoGenomics. Mike Snyder, another CEGS leader, was then at Yale’s Human Genome Analysis center and recently headed to Stanford University to lead the Center of Genomics and Personalized Medicine.

A news story five years ago asked readers to consider the CNP, now better known as a CNV. Jonathan Sebat — then a postdoc in Michael Wigler’s lab — and his colleagues at Cold Spring Harbor Laboratory developed a method called representational oligonucleotide microarray analysis to measure how common CNVs are. Since then, Sebat has started his own lab at Cold Spring Harbor; this past summer, he published a paper in Genome Researchon a computational approach to detect CNVs. He and his colleagues plan to apply their method to the 1,000 Genomes Project and to a large-scale schizophrenia study.

— Ciara Curtin

OCTOBER 2008

OCTOBER 2004

>GT ONLINEwww.genomeweb.com

COMMENTS FROM THE DAILY SCANIn response to a post on ageism in the peer-review process, readers wrote:

“The NIH grant review process (without the young investigator adjustment) actively discrimi-nates in the reverse direction — giving preference to long track record and ‘inside the paradigm’ research.”

— cashaw

“I agree that the NIH process actively discriminates again younger scientists. I even had a reviewer comment on a sum-mary statement that cited the ‘Relative youth of the PIs’ as a weakness!”

— rogerb

>NEED HELP?CHANGE OF ADDRESS—To change your address or manage your subscription to Genome Technology, the Daily Scan, or any GenomeWeb publication, login to www.genomeweb.com and click on My Account,or email us at [email protected] SUBSCRIPTION–Genome Technology is free to active researchers in the life sciences. To subscribe, log on to www.genomeweb.com/subscriptions and fill out a 30-second form.REPRINTS– For permission to reproduce material from Genome Technology, or to order offset-printed or Web-ready PDF reprints, write to [email protected] or call +1.212.651.5632.



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>SHORT READS

PerkinElmer has acquiredtwo separate companies: SYM-BIO Lifescience in China for $63.7 million in cash; and Surendra Genetic Labs in India for an undisclosed amount. The acquisitions are expected to help PerkinElmer expand its diagnostics and genetic screening busi-nesses.

The EU has granted €11.3million to support an inter-national genomics research project to identify the genetic and environmental causes of asthma. The studies will be co-ordinated by Imperial College of Science, Technology, and Medicine at Imperial College, London in a research program called GABRIEL.

Stephen Minger joined GEHealthcare’s Life Science business as head of R&D for Cell Technologies. He was previously at King’s College London, where he was direc-tor of the Stem Cell Biology Laboratory.

Complete Genomicsannounced that it had sequenced and analyzed 14 human genomes for custom-ers since it began a limited trial launch in March. The company said customers in-clude Pfizer; Duke University; the HudsonAlpha Institute for Biotechnology; the Ontario Institute for Cancer Research; the Institute for Systems Biol-ogy; and the Broad Institute, among others.

NIH: Collins Steps into New Directorship with Goals at the Ready; Funding Stability a Priority

Francis Collins’ confirma-tion as the new director of the National Institutes of Health may have come as a somewhat anticlimactic

Congressional aside in a summer filled with stormy political debates, but his subsequent address at an all-hands NIH meeting was any-thing but.

On August 17, Collins took the floor for the first time as NIH director, al-ternately praising the institutes, re-assuring people who worried about his potential bias toward genomics, and fretting about funding. He be-gan his address by saying, “Well, it’s great to be home again. That’s what this feels like for me.” He spent some time highlighting a range of promis-ing research at NIH, which, as an in-stitution, “represents everything that

is awesome and wonderful about biomedical research.”

One of the concerns raised about Collins as NIH director was his com-fort level with large, collaborative science. To quell those worries, he told his new employees, “The main-stay of NIH, both intramural and extramural, will be the creativity of individual investigators. Those who fear that this guy who used to direct the genome institute may only be interested in supporting big science need look no further for reassurance than the character of the NHGRI

intramural pro-gram which I was asked to found in 1993.”

He also used the meeting as an opportunity to lay out five major themes he has in mind for NIH. To wit: applying high-throughput technologies to find the cause of specific disease states; translation, including de-veloping “diagnostics and preven-tive strategies and therapeutics for diseases we treat poorly”; “putting science to work for the benefit of healthcare reform,” which includes comparative effectiveness research

and more tailored ap-proaches to medicine; an increased focus on global health; and se-curing stable, reliable funding levels.

On that last point, the man who’s known

in the community as an incurable optimist acknowledged that even his sunny attitude is challenged by the current funding situation. “What is going to happen to the resource support of this amazing organization when the stimulus money runs out?” he asked. “The feast or famine scenario is incred-ibly destructive to the enterprise and it places our country at a disadvantage over other countries that are on very strong growth trajectory.”

— Meredith Salisbury

“What is going to happen to the resource support of this amazing organization when the stimulus money runs out?”

Markers NEWS

10 W W W. G E N O M E W E B . C O M O C T O B E R 2 0 0 9

FRANCIS COLLINS


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“We have to use new techno-logical approaches to inte-grate them and that’s where nanotechnologies come in.”

>SHORT READS

Thermo Fisher Scientific hasagreed to buy German diag-nostics firm Brahms for €330 million in a deal that will complement its immuno-assay test portfolio and expand its reagent manufac-turing capabilities in Europe. Brahms’ flagship product is the procalcitonin biomarker for diagnosis and treatment of sepsis.

The UK’s Human GeneticsCommission released a set of principles for direct-to-consumer genetic testing, focused on the information and counseling consumers are provided before and after taking tests and on privacy considerations. They apply to all aspects of the industry, including marketing and ad-vertising, consumer consent, lab analysis, and support for consumers.

Lab901, a Scottish DNAanalysis firm, received £2.4 million in equity funding from a group of UK investors. The company expects to use the money to expand international sales of its ScreenTape analy-sis platform, which replaces manual analysis of proteins, DNA, and RNA, and to con-tinue to develop its products.

Cell Biosciences signed anagreement to acquire Alpha Innotech for approximately $17.9 million in cash. The acquisition will give the company additional protein analysis business.

Nanomedicine: Jamey Marth to Direct New Nano Center at UC-Santa Barbara, Burnham

While there is no doubt that considerable headway has been made in the under-standing of nucleic

acids and proteins, two macromo-lecular components of the cell — lipids and glycans — are not so easily elucidated when it comes to their roles in disease. “They are not made by template-driven biological approaches, so you can’t get at their structure or regulation by looking at the genome. ... I don’t think there’s any other way of doing it because I believe we’re beginning to see the wall in biomedical research with a purely genomics/proteomics per-spective,” says Jamey Marth, director of the Center for Nanomedicine at the University of California, Santa Barbara. “So we have to use new technological approaches to inte-grate them and that’s where nano-technologies come in.”

It was this belief in nanotechnol-ogy that made it a no-brainer for Marth, previously a professor of cel-lular and molecular medicine at the UC San Diego Medical Center, to accept the position of director of the new Center for Nanomedicine. The

center will be launched and operated by both UCSB and the Burnham Institute for Medical Research. “I needed to make a big change in the

orientation of my career in an envi-ronment that was at the envelope of nanotechnologies, and that’s where Santa Barbara came in,” says Marth, who joined the UCSB and Burnham Institute faculty in early July. “Their expertise in those fields synergize completely with the Burnham’s abili-ties in biomedical research.” Nano-medicine aims to utilize nanotechnol-ogy to develop drug delivery nanoparticles, biosensors, and other medi-cal devices that function at the molecular scale for treating dis-ease and repair-ing tissue.

The biggest challenge ahead for Marth and his team is not so much the development of nanoparti-cles, but learning how best to deliver them in the human body safely and effectively. “For the first time we’re engineering devices that go into the body and we don’t know a lot about them in many cases. … There are over 600 nanomaterials that are on

the market right now, but that’s just the tip of the iceberg,” he says. “We need to understand more about them, their distribution, their fate, how to best use them. Different particles have different profiles in

terms of their in vivo lifetimes and expectations of targeting or drug delivery.”

— Matthew Dublin


JAMEY MARTH


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>SHORT READS

Stephen Davis will be chair of the University of Maryland School of Medicine. Davis was recruited to Maryland from Vanderbilt University, where he spent 20 years and was director of the Division of Diabetes, Endocrinology, and Metabolism and also direc-tor of the General Clinical Research Center.

Helicos BioSciences hiredinvestment bank Thomas Weisel to help evaluate stra-tegic alternatives, such as financings, joint ventures, or partnerships. In other news, the company announced that it had sold four of its sequenc-ing systems to RIKEN.

Harvard Bioscience will buyDenville Scientific, a private molecular biology company focused on liquid handling items and based in New Jer-sey, for around $23 million.

Researchers from the MDAnderson Cancer Center published a proof-of-principle study indicating that micro-RNAs in the blood can be used as biomarkers for pancreatic cancer. The team studied four miRNAs in particular, finding that all of them were elevated in blood samples from indi-viduals with pancreatic cancer.

Advanced Cell Diagnosticsraised $5.4 million in a series A financing, which it says will be used to develop diagnostic tests based on its RNAscope technology.

“We had multiple individu-als, so we could set up the equivalent of what we felt was a real-world situation.”

Sequencing: UW Group Sequences Exomes from 12 People, Confirms Gene for Rare Disease

Jay Shendure’s lab at the University of Washington has shown that exome se-quencing can be used to find a gene behind a rare

genetic disorder. Using an array- and next-generation sequencing-based approach, Shendure and his colleagues sequenced the exomes of 12 people: eight individuals from the HapMap Project and four people with Freeman-Sheldon Syndrome, an autosomal dominant disorder marked by craniofacial, hand, and foot abnormalities.

“For us, the study really had two goals. One was to evaluate how one goes about doing targeted resequenc-ing with next-generation technolo-gies and, within that larger problem, there’s the specific problem of the exome,” says Shendure, who led the Nature study. “And the second goal was to try to put this into a disease context, rather than just being a proof-of-concept around technology itself.”

To home in on the exome, Shen-dure and his colleagues used array

capture followed by next-gener-ation sequencing on an Illumina machine. Instead of working to optimize that initial capture, the researchers used a second array to find data missing from the first. They yielded an average of 6.4 gigabases per person.

Then they turned to looking for MYH3, the gene behind Freeman-Sheldon, to show the method’s ap-plicability to iden-tifying Mendelian diseases. Shendure says they chose to study this disease because the answer was already known. “We sat down and talked through what might be a challeng-ing disease — in the sense that it’s autosomal dominant, so it’s going to be more challenging than a reces-sive [disease],” he says. “And we had multiple individuals, so we could set up the equivalent of what we felt was a real-world situation.”

For that search, Shendure and his colleagues catalogued variants from the exomes of the people with Freeman-Sheldon, looking for genes with non-synonymous variants or indels. They then filtered out com-mon variants from those 2,000 can-didate genes by using dbSNP. That

alone, Shendure says, was inadequate, so they also used variations from the HapMap individuals as an extra filter. Together, those narrowed the can-didate gene list down to one, MYH3. “[This] pres-

ages what is going to happen with 1,000 Genomes and projects like that,” Shendure adds.

He and his lab are currently working on applying this method to Mendelian diseases caused by unknown genes, as well as more complex diseases.

— Ciara Curtin

Markers NEWS

JAY SHENDURE



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“We’ve overcome a barrier that we needed to deal with for the genome to be ‘booted up’ — this allows us to get a step closer to the synthetic cell.”

>SHORT READS

The National CancerInstitute’s Center for Biomedi-cal Informatics and Infor-mation Technology named Caterina Lasome as chief of its informatics branch. Lasome is a retired US Army Lieutenant Colonel who has been chief of healthcare informatics and inpatient requirements for the Military Health System and chair of the NATO Chiefs of the Military Medical Services Medical Communications and Information Systems.

Luminex announced thatit has received US Food and Drug Administration clearance for its second-generation cystic fibrosis test, which looks at 39 CF-causing gene mutations and is used to screen potential parents to determine if they are carriers of the mutations.

Mario Caccamo has joinedthe Genome Analysis Centre to lead its bioinformatics divi-sion. Prior to this, he was at the European Bioinformatics Institute, where he worked on the European Genome-Phenome Archive.

Researchers at the Broad Institute and the UK’s Sains-bury Laboratory led an inter-national effort to sequence the 240 million base genome of Phytophthora infestans, the pathogenic water mold behind Ireland’s 19th century potato famine. The study of what was once thought to be a fungus was published in Nature.

Synthetic Genomics: Venter Institute Team Demonstrates Successful Cross-Species Genome

Aresearch team at the J. Craig Venter Insti-tute recently complet-ed work that prom-ises to seriously ramp

up synthetic genomics and bring the concept of a synthetic cell that much closer to reality. So far, the scientists have dem-onstrated a method of transferring genomes between a prokaryote to a eukaryote and back again. Using yeast cells with an added dose of yeast centromeric plasmid sequence, the JCVI team cloned the whole bacterial genome from Mycoplasma mycoides, modified the bacterial chro-mosome using the yeast’s own genetic systems, and fol-lowed that up by transplanting the new genome into the related species Mycoplasma capri-colum. The end re-sult was a new type of mycodies cell never before seen in nature or in a laboratory.

“Mycoplasmas in general do not have very robust genetic tools — or hardly any genetic tools, so you can’t easily add or delete genes. But we can use the nice set of tools that yeast has to manipulate the [mycoides] genome,” says Sanjay Vashee, a JCVI researcher who contributed to the project. “The implications here are several-fold, but one is that we’ve overcome a barrier that we needed to deal with for the genome to be ‘booted up’ — this allows us to get a step

closer to the synthetic cell.”The barrier that had previously

prevented the installation of a modified genome had to do with the restriction enzymes that act as an immune system to help bac-teria defend itself against invading DNA.

The researchers first devised a method of removing that immune system from the recipient cell so that the incoming genome would not be chewed up.

The second method was to use in vitro chemical modification with purified methylases that would install a protective methyl group

on the genome, thereby overcom-ing the restriction enzyme barrier from the recipient cell.

Vashee says that JCVI scientists are currently attempting to boot up their synthetic organism, Myco-plasma genitalium, so that they can eventually whittle away its genome to produce a “minimal cell” — a useful model system that has only the genes absolutely necessary for life.

They also hope that these meth-ods can be utilized to help engi-neer bioenergy sources and indus-trial chemicals.

— Matthew Dublin



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Methylation: Markowitz, Vogelstein Lead Development of Novel Detection Technique

In work appearing in August in Nature Biotechnology, a group of researchers developed a novel, highly sensitive technique to de-tect methylated DNA. Because

methylation signatures change in cancer, they hope it will be useful for early detection of colon and other tumors. A simple, inexpensive, nonin-vasive test that could be used instead of a colonoscopy — this test isn’t fail-proof — is key to saving lives.

“Having an alternative to colonos-copy could make an important contri-bution to public health, so we’ve been interested in whether you could devel-op a molecularly-based, noninvasive screening test for colon cancer for a long time,” says Sanford Markowitz at the Case Western Reserve University School of Medicine, who led the study alongside Johns Hopkins University’s Bert Vogelstein.

The technique combines bisulfite conversion with BEAMing, a tech-nology developed previously in Vo-gelstein’s lab, to come up with methyl-BEAMing. In BEAMing — BEAM stands for beads, emulsion, amplifi-cation, and magnetics — individual

DNA fragments are attached to coated magnetic beads and can be amplified by submerging DNA and the beads in a water-oil mix-ture and then performing PCR. This “supersensitive” technique, says Markowitz, allows researchers to study individual molecules of DNA, which is important when detecting the handful of methy-lated molecules in a sample that might signal early cancer.

“BEAMing is a way to do PCR on a bead starting with a single molecule of DNA,” he says. Building off previ-ous work that showed that a region of the vimentin gene is hypermeth-lyated in a majority of colorectal can-cer patients, the researchers wanted to see whether they could use the technique to detect one molecule in thousands that might be methylated. After performing bisulfite conver-sion, they used BEAMing to amplify the vimentin gene so that there were thousands of copies of the gene at-tached to each magnetic bead. They then hybridized fluorescent probes

for methylated and unmethylated states to the beads, and followed that up with fluorescence-activated cell sorting to count the number of molecules that were methylated.

“It turns out you really do need a method this sensitive,” Markowitz

says. When they applied the method to blood samples from carriers of early stage disease, Markowitz and his team found only one or two molecules of methylated DNA in two milliliters of blood, which is one mol-ecule in about 5,000 un-methylated molecules. “We applied this method as a co-

lon cancer blood test and we were able to pick up about 50 percent of the folks who have these early stage colon can-cers,” he says. That’s four times better than the current standard, a blood se-rum marker used to detect recurrence. Also, the new method could detect 41 percent of colon cancers in the stool, as well as half of pre-cancerous polyps. The researchers say their method im-proves standard methylation-specific PCR by 62-fold.

Next up is looking for genes beyond vimentin, as this was just the first-generation test. “We’re already hard at work looking for additional mark-ers that you could add to the test” to improve it, Markowitz says.

— Jeanene Swanson

Markers NEWS

With the cost of sequenc-ing coming down, looking for structural variation genome-wide is getting easier. Typi-

cally, to find structural variants —

everything that isn’t a SNP, including indels, copy number variants, inver-sions, and translocations — people have been using array CGH, among other array-based tools. Now, how-ever, high-throughput sequencing

analysis is possible and provides a way to predict structural variants more accurately. Challenges to data analysis remain, though, including how to incorporate short inserts into current mapping algorithms and how to take into account varying cover-age, insert size, and read length data from different next-gen platforms. To this end, work out of Elaine Mardis’ lab led by Ken Chen has resulted in a new set of algorithms that improve common variant detection and de-

SANFORD MARKOWITZ

Structural variation: New BreakDancer Algorithm Performs High-Res Mapping of Indels, More



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PCR: CDC Evaluates Rapid Flu Tests Versus rRT-PCR for Detecting Novel Strain of H1N1 Influenza

Researchers from the Cen-ters for Disease Control and Prevention found that while rapid influenza diagnostic test could accurately detect

the virus in high concentrations, re-verse real-time PCR testing should be done if a definitive determination is needed.

“We had gotten an increasing num-ber of inquiries from physicians want-ing to know if the rapid test would work at all on this novel strain, and,

of course, off-shot of that is wonder-ing what the sensitivity and specificity would be,” says Michael Shaw, associ-ate director for laboratory science in the CDC’s influenza division.

The rapid tests, which are enzyme-based, were evaluated on 65 samples, 45 of which contained the novel H1N1 virus, five with seasonal H1N1, and 15 with seasonal H3N2, as determined by the CDC’s rRT-PCR assay. The sensitivity of the tests was determined from their accuracy in calling samples

with different viral titers, as based on the specimens’ cycle threshold value. “They were more likely to yield a valid result if there was more virus there [and] that depends of course on how soon after symptom onset the sample was taken,” he adds.

Shaw points out the study was lim-ited to the common rapid tests and not controlled for how the samples were collected and transported.

Still, the rapid tests, when positive, are accurate. Negative results, howev-er, aren’t necessarily actually negative. In that case, clinicians should base their treatment on what is circulating in the area and, if a more concrete result is needed, rely on the rRT-PCR assay.

—Ciara Curtin

tection of somatic variants in tumor versus normal samples.

Collectively called Break-Dancer, the software pack-age consists of two com-plementary algor ithms. Eva luat ing pa ired-end reads from an Illumina sequencer, the scientists showed that BreakDancerMax detects five types of structural variants, in-cluding deletions, insertions, inver-sions, and intrachromosomal and in-terchromosomal translocations from pooled or individual DNA samples. BreakDancerMini detects small in-dels, typically 10 to 100 base pairs, which BreakDancerMax misses. The software was published in a paper ap-pearing in August in Nature Methods.

In the study, they compared the mapping capabilities of their algo-rithm to similar ones, specifically Evan Eichler’s VariationHunter and Michael Brudno’s MoDIL, on MAQ map files of the Yoruban genome. In general, Chen says, BreakDancerMini showed higher sensitivity and specificity than either of the other algorithms. They

also applied BreakDancer to detecting somatic variations in an AML tumor sample as well as detecting vari-ants in the 1,000 Genomes dataset.

What makes BreakDancer novel, Chen says, is that the other algorithms target indels longer than 100 base

pairs. “What we have intended to do is to cover the entire range, from 10 base pairs to virtually no limit,” he says, significantly increasing the range of indels that can be detected.

Both Max and Mini support pooled samples, or multiple samples and libraries. For looking at variation in the AML samples, for example, they were able to look at a pair of genomes. “We were interested in finding somatic variations, so basi-cally we compared tumor genome versus the normal genome,” Chen says. Because most cancer is caused by somatic alterations in the tumor genome, it’s important to be able to compare tumor to normal. In this, BreakDancer improved the specific-ity of somatic variant prediction by

eliminating germline, or inherited, variants. “This is a novel application,” Chen says, because it can actually perform a “head-to-head” comparison of tumor and normal samples.

After running BreakDancer on the AML genomes to predict approxi-mate size and location of structural variants, the researchers used as-sembly programs Velvet and Phrap to refine their predictions. By mapping all the reads back to their predicted variant loci, they were able to con-firm that the variants do exist. “We found by applying this BreakDancer detection algorithm and assembly af-terwards [to tumor samples], we can very efficiently discover and secure those predictions,” Chen says. “[The] combined approach is [more] effi-cient and accurate than using either approach in isolation.”

Development of the tools began more than a year ago, and the algo-rithm has already been applied to many large-scale sequencing data. Chen says it will continue to evolve alongside big sequencing projects, es-pecially the 1,000 Genomes Project.

— Jeanene Swanson

KEN CHEN



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A Blog Around the WorldSynthetic biology is not ’80s-era computer science, a researcher maps next-generation sequencers, and more. By Ciara Curtin

Not Steve Jobs in a Garage

The efforts of researchers at the J. Craig Venter Institute to move toward creating synthetic life — they recently published a paper in Science on clon-ing a bacterial genome in yeast — have been com-pared to the work of computer scientists during the 1980s. Bloggers Ricardo Vidal and Deepak Singh aren’t convinced by the analogy. “This comparison just brings along a whole truck load of babble that I think is incorrect,” Vidal writes at My Biotech Life.At business|bytes|genes|molecules, Singh adds that “genetic manipulation and sequencing might become available easily and inexpensively some day, but they will never be commodities like a computer.”

my.biotechlife.netmndoci.com

Trials and Tribulations

Georgia Tech professor Rick Trebino’s article on how to publish a scientific comment to a journal has gotten bloggers talking. Trebino’s arduous path went through 123 steps, plus an addendum, and never resulted in a comment. Steinn Sigurðsson at the Dynamic of Cats posts the steps as a PDF and assures his readers it’s a true story. At Adventures in Ethics and Science, Janet Stemwedel wades through the steps and is left wondering about how scientific communication is supposed to occur if there are stumbling blocks throughout the publishing process. “The idea that the journal here seems to be missing is that they have a duty to their readers, not just to the authors whose papers they publish,” she writes.

scienceblogs.com/catdynamicsscienceblogs.com/ethicsandscience

Where in the World Is a 454?

In August, the Cambridge Research Institute’s James Hadfield created a Google Map listing facilities that house next-generation sequencers. He posted a link to the map in the SEQanswers forum and soon opened the map up so anyone could edit it. At Pathogens: Genes and Genomes, Nick Loman did an analysis of the early data to see which next-gen machines were being adopted in the UK. Discounting the Sanger Centre, which Loman says skews the data, the most common next-gen platform is the Illumina Solexa. “Solexa is just in the lead with 12 machines, closely followed by 454 with 9 machines and with ABI SOLiD trailing with just 3,” Loman writes.

seqanswers.com/forumspathogenomics.bham.ac.uk/blog

After the Hood

At her eponymous blog, Female Science Profes-sor wonders what the role of a PhD advisor should be after students graduate. In her experience, she was treated “with the same benign neglect” by her advisors as other students were, but she has problems doing that herself. She blogs that her approach is un-fair as there are some students for whom all she’ll do is write a letter of recommendation, while for others she’ll collaborate or provide other support. Uncertain Principles’ Chad Orzel says that he came away from his old lab with an armload of equipment on a “per-manent loan.” “Obviously, this is not sustainable for any research group graduating more than one student every 4-5 years, but it is food for thought,” he writes.

science-professor.blogspot.comscienceblogs.com/principles

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The Journal PerspectiveSo you’re looking to get published. What’s the best way to interact with journals and editors to help make your case?By Meredith Salisbury

All scientists are well-versed in the “pub-lish or perish” fear — but what about when publishing a

paper is so difficult that you feel like the very process may do you in? Researchers looking to get their results into a highly regarded jour-nal for all the world to see have no easy task ahead of them. One way to get through the process unscathed: get familiar with the journals you’re interested in, and make friends with editors.

Before you do anything with that manuscript you’re sitting on, take a few minutes to peruse the websites of the journals you’re thinking about submitting to. They’ll all have a page with information for authors; this can help you make sure your paper matches the scope of the journal, and it also includes helpful guidelines about formatting and other details of the submission process. Ignore these at your peril: formats are chosen for

a reason, and failing to conform to them can send a couple of bad mes-sages — that you simply don’t care enough to check guidelines, or that your manuscript was formatted for

another journal and that wherever you’re sending it this time wasn’t your first choice. Also, pay attention to data requirements; different jour-nals (especially ones that are open access) can have different rules about where data must be deposited for the paper to be published.

Once you’re familiar with the guidelines, it can be worthwhile to contact an editor at the journal with a simple note to gauge interest level. “It can be good to send a pre-submission inquiry,” says Clare Garvey, editor at Genome Biology, who adds that these inquiries are usually answered very quickly. It’s a simple, fast way to see if the paper fits well with the research scope of the journal.

When you do send your manu-script in, be sure the cover letter is tailored to the publication you’re targeting. Garvey says a common mistake she sees is sending let-ters intended for other journals that have been copied and pasted on a paper that was perhaps sent some-

where else first.If your manuscript is

sent out for review and accepted, you’re in great shape — and interactions with the journal should be straightforward. But what happens if the paper is re-

jected — or, worse, rejected without review? While most scientists will beat themselves up or fume over this, very few feel comfortable fol-lowing up on it. Garvey says it’s quite

acceptable to contact the editor to say you’re not happy with the deci-sion and ask for advice or feedback. “We’re perfectly open to being called or emailed” when this happens, she says. “If we can help authors by being as transparent as we can, then that’s good for everyone.”

Make new friends

The time to think about publishing is not just when you have a manu-script ready to go, though. You’ll be in better shape to submit a paper or to ask an editor about a review deci-sion if you’ve already gotten to know the editor ahead of time. Garvey says that conferences are a great place to take this step — editors routinely attend meetings, and it’s their job to get acquainted with scientists in the field and get a sense of the latest research.

Because editors have a broad per-spective on research across many fields, Garvey says it’s important to remember that they can be “a huge resource” to bounce research ideas off. Editors might “even suggest ad-ditional experiments that might help that paper get into that journal,” she adds.

And if you’re not getting out to conferences as much as you’d like, Garvey says outreach is considered so important that some journals even send editors on lab visits when there’s enough interest in how the editorial process works.

PROFESSIONAL LIFE Careers

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Lab Reunion THE HENIKOFF LAB

‘A Community of Scholars’Steven Henikoff has been a member of the Fred Hutchinson Cancer Research Center for nearly 30 years. When it comes to trainees, his lab is as much a study in independence as it is in nucleosome dynamics. By Meredith W. Salisbury

If Steven Henikoff has thought seriously about leaving the Fred Hutchin-son Cancer Research Cen-ter since he started working

there in 1981, there’s no sign of it today. “I found the Hutch right from the start to be the ideal place to do what I want to do,” he says. “There’s never been an incentive to change.” He’s serious: Henikoff, who has a joint appointment at the University of Washington, has never so much as taken a sabbatical since he joined.

But why should he? Henikoff has made a stellar reputation for his lab — as much for the science performed there as for the credit he gives to the people who join him as grad students or postdocs and the opportunities that open up to them as Henikoff alums.

The lab’s focus includes epigenom-ics — including histone variants and DNA methylation — and centromeric chromatin. His lab has also been the birthplace of tools essential to the community, such as TILLING (or targeting induced local lesions in genomes), a large-scale approach to reverse genetics that relies on muta-genizing whole populations and then screening them for mutations. The approach was invented in Henikoff’s lab years ago, and while it’s no longer part of his research, his team still supports it “as a service for various organisms.”

In a recent project, Henikoff’s team helped tease apart the mystery of

the centromere, such as how it’s maintained “despite the fact that sequence doesn’t seem to matter,” he says. In work just published in Cell, Henikoff and post-doc Takehito Furuyama discovered that, while all nucleosomes wrap DNA in the same direction, the nucleosomes in centrom-eres actually wrap it in reverse. “It has some re-ally profound implications,” Henikoff says. “All the interaction surfaces that are holding together that nucleosome are facing away from each other.” The idea that comes out of this finding is that it’s the wrapping pattern that’s causing the centromere to be so dif-ferent from the rest of the chromo-some.

Independent minds

Henikoff says it was the practice of his PhD advisor, Matt Meselson at Harvard, that showed him how important it was to let students carve out their own paths. “He gave us a lot of independence,” Henikoff says of his days studying Drosophila RNA in the late ‘70s. “I felt that that was great training to be self-reliant.”

In his own lab, Henikoff makes clear the benefits of interacting with colleagues while emphasizing the need to establish one’s own proj-ects. “I try to make the lab more a

community of indepen-dent scholars,” he says. “I don’t encourage at all team research.” Genom-ics as a field lends itself to the concept of team research, he says, but he believes a better ap-proach is to encourage collaborations while en-suring that each scientist is responsible for and in-vested in his or her own projects. “I think that’s

the best training,” he says. “After you leave your postdoc, you’re going to be out there on your own” and he wants to make sure his trainees leave the lab equipped to stand on their own feet. To that end, Henikoff avoids any impulse to micromanage. “I’m not going to look over anyone’s shoulder,” he says.

Another element of the Henikoff philosophy is to empower research-ers by reminding them not to rely on the tools at hand. Over the years, the lab has released a number of tools that became commonly used by the community, and the reason for that is Henikoff’s refusal to be constrained by what’s available. If a scientist in his lab wants to do an experiment but the tools don’t exist to perform it, Henikoff likes to see that person delve into building the necessary tools rather than abandon the research path in favor of some-thing that’s more in line with exist-ing technologies.

STEVEN HENIKOFF


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TAKEHITO FURUYAMAA current postdoc with Henikoff, Furuyama recently published a paper in Cell demonstrating a finding that the PI calls “the most exciting thing we’ve ever done” — that is, evidence that nucleosomes in the centromere wrap DNA in the opposite way that all other nucleosomes do. “We basically think that it’s the wrapping of the DNA that is responsible for all the differences that we see” in how centromeres behave and function, Henikoff says.

HARMIT MALIKNow the PI of his own lab at the Hutch, Malik did his postdoc with Henikoff from 1999 to 2003. His focus has been studying evolutionary signatures

of genetic conflict, Henikoff says, adding, “I learned more from him than he learned from me, that’s for sure.” Malik was awarded a Presidential Early Career Award for Scientists and Engineers by President Barack Obama this year.

CLAIRE MCCALLUMMcCallum was the brain behind TILLING, the tool that has become synonymous with Henikoff’s lab in the time since her graduate work there from 1996 to 2002. Her quest for the mutation of a known gene helped launch the method of mutagenizing all genes and screening them; it also led to a company she launched, which is now part of Arcadia Biosciences.

The original TILLING work “led to a very nice study, a nice story, a nice publication,” Henikoff says.

PAULINE NGDuring her years as a graduate student in Henikoff’s lab, Ng came up with the idea that deleterious nonsynonymous changes in protein sequence could be predicted based on evolutionary information. That work led to an algorithm called SIFT. After leaving the lab, Ng worked at Illumina and is now a senior scientist in genomic medicine at the J. Craig Venter Institute.

BAS VAN STEENSELVan Steensel, a postdoc with Henikoff from 1998 to 2000, helped get the lab into genome-wide profiling, Henikoff says. After his time at the Hutch, van Steensel went on to the Netherlands Cancer Institute, where he heads up his own lab.

>NAMING NAMESJust since 2000, the Henikoff lab has been home to some 25 trainees. Here are just a few of the students and postdocs who have earned their stripes there.

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A Grassroots InstituteAt the Institute for Genomic Medicine, reaching out to on-campus researchers and resources has helped it weather tough economic times. By Matthew Dublin

Sometimes you have to get by with a little help from your friends. Such is the case with the re-cently established Insti-

tute for Genomic Medicine at the University of California, San Diego, where a severely stricken state econ-omy and limited university budget have forced the institute’s executive committee to operate with the man-tra that no man — or institute — is an island.

To compensate for a lack of giant startup coffers, the institute’s found-ers have focused more on securing a brain trust from around the UCSD campus to form a strong foundation upon which to slowly build IGM. “We have had generous intellectual support from the school of medi-cine, and very broad-based support from the various UCSD campuses, the undergraduate biology depart-ment, and the school of engineer-ing,” says Joseph Gleeson, a profes-sor of neurosciences and pediatrics at UCSD, and a Howard Hughes Medical Institute Investigator. “UC-SD is a place that builds things from the grassroots up. We don’t have someone that guides things from the top down, so we haven’t identified a big source of funding to get the initiative going.”

Gleeson is also a member of IGM’s executive committee, which in-cludes institute director and UCSD professor of ophthalmology and human genetics Kang Zhang, and

Bruce Hamilton, director of the UCSD Genetics Training Program. Gleeson says that plans to construct a dedicated building for IGM have stalled slightly due to the poor state of the California economy. When plans are finalized, however, the group hopes to break ground by the end of this year and begin mov-ing in by 2012 or early 2013. Currently, the researchers are still distributed across the UCSD campus. Until the institute has its own in-house sequencing and data analysis gear, members will make use of the university’s Biomedical Genomics Laboratory core.

And while the institute is getting a certain amount of startup funding thanks to the powers that be at the university, when that runs out, the core membership will have to as-sume operational costs with shared grants and private donations.

Medical efforts

Despite a grim economic land-scape, the folks behind the new institute have not been deterred in their efforts to realize the potential of genomic medicine to change the way doctors will treat patients. IGM will initially focus on various forms of cancer, AIDS, and neuropsychiat-ric, developmental, and eye diseas-es. With the UCSD Medical Center nearby and a slew of investigators

taking a genomics approach to their own areas of disease research, suc-cess could be just a matter of put-ting all the pieces together in one location. “We have outstanding re-searchers in many disorders, and we’re all learning about genomics on our own and applying some tech-nologies in our own labs or maybe outside of the university,” Gleeson says. “We would really like to make a central place where we could all deposit the new technologies and be able to better take advantage of them.”

Its leaders hope the institute can ultimately deliver real-life solutions to common problems doctors and patients face every day. “We really want to be a part of bringing per-sonalized medicine to the people of San Diego and [to] the national scene. …. If we could make advanc-es in some of these targeted disease areas, we will be taken seriously by the rest of the genetics com-munity, and that’s our challenge,”

RENDERING OF THE INSTITUTE FOR GENOMIC MEDICINE

Under One Roof BASIC MEETS CLINICAL


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Gleeson says. For many involved, the establishment of IGM is seen as a coming-out party for the uni-versity as a significant genomics research site. “Unfortunately, UCSD has not really had much of a pres-ence in genetics. With the exception of a few people who have done some important work, we haven’t had a department of genetics or an insti-tute or anything like that,” Gleeson adds. “But we have certain unique strengths — a lot of our faculty is just out of their postdoc and excited to get something done.”

Eventua l ly, IGM researchers would like to perform genome-scale sequencing on every patient that comes through the doors of the Med-ical Center as well as the local chil-dren’s hospital. Some of the key areas the institute will focus on include whole exome sequencing and copy number variation — especially as they relate to particular disease enti-ties where UCSD has strong patient cohorts. “Our vision is we would like to perform genetic analysis on every patient ... and then we would like to work with the pharmaceutical companies to take advantage of that information in disease drug trials and by helping them look for outli-ers in their various clinical trials,” Gleeson says.

To that end, the institute is being pitched to university scientists with relevant patient cohorts as a place where they might be able to get more out of their data. “We’re trying to get all the researchers on campus who have unique patient cohorts together and say that IGM can be a place where you can bring your cohorts with your phenotypic data and think of ways you get them all genotyped with whatever platform would be most applicable, whether it’s copy number variation, high-density SNP arrays, and then let’s see what data falls out,” he says. “Whether it’s a pharmaceutical response or what-

ever, you can apply the richness of the genetic data to your particular problem.”

Getting started

IGM is currently building itself from the ground up with a core team of members from across the university. This initial group in-cludes several researchers from the Cellular and Molecular Medicine department as well as individual re-searchers with specialized skill sets, such as Trey Ideker, division chief of genetics and associate professor in the department of medicine and bioengineering at UCSD, who will lend his expertise in bioinformatics and genetic network analysis. Terry Gaasterland, professor and direc-tor of the nearby Scripps Genome Center, is now also spending a lot of time on the medical school campus

helping IGM plan for its bioinfor-matics infrastructure.

In addition to creating synergy among resources and researchers on the UCSD campus, equally es-sential is the role that other in-stitutes will play, particularly the J. Craig Venter Institute, which is right in IGM’s backyard. Albert La Spada, an IGM member and genet-ics chief in the pediatrics depart-ment at the UCSD Medical Center, has high hopes for on-campus and off-campus collaborations. “I think at UCSD and the affiliated insti-tutes there is incredible expertise in emerging genomics technologies, including next-generation sequenc-ing and, perhaps most importantly, computational biology and bioin-formatics,” La Spada says. Breaking through bioinformatics bottlenecks will also be facilitated by resources at the San Diego Supercomputer Center and the California Insti-tute for Telecommunications and Technology. “What is unique about UCSD is that we’re positioned to leverage this type of program based upon access to those resources and infrastructure … but we’re looking to partner with all types of organi-zations as the program grows and evolves,” La Spada adds.

He is looking forward to the institute working to elucidate the mechanisms of neurological disease — his current area of focus. La Spada would really like to have a better handle on the pathways responsible for neurode-generative processes, and it appears that for a number of these disorders, these pathways involve alterations in transcriptional function. “Being able to interrogate the transcriptome of neurons is an important and neces-sary approach that this institute will better allow in the future, so there are certain emerging technologies that could better position our group to have a leadership role in [that area],” La Spada says.


>THE INSTITUTE FOR GENOMIC MEDICINESan Diego, Calif.DIRECTOR: Kang ZhangESTABLISHED: 2009SIZE: There are currently about 16 researchers that have come aboard the institute, although this number will probably increase as more UCSD faculty start contributing to its ef-forts. FUNDING: Initially, IGM will garner the majority of its launch funding from money allocated by UCSD’s budget. Once the institute is up and running, grants and private funding from its core members will have to keep the institute afloat. FOCUS: IGM is intended to be a center point for all genomics efforts on the UCSD campus. It also aims to take part in collaborations with other genomics institutes with the goal of making personalized medicine a reality.


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Project AnnotationLetting students get involved in annotation projects can be great real-world experience — or it can open the doors to lots of errors entered in GenBank. What’s the best plan here?

Re s e a r c he r s who study well-docu-mented creatures like fruit flies or E. coli are blessed with

the most powerful tools of biology at their fingertips. Armed with data from genome sequences, transcrip-tomes, ontologies, and pathways, the goal of putting pieces together in a network of interacting genes can be addressed pretty quickly.

But what if you study something else, like corn or wheat? The outskirts of biology tell a different story. Once you venture away from the well-annotated references in the model organism world, the set of research tools gets sparse. The databases look less and less complete. Annotations, if you can find them, are more shady, and words like “hypothetical” and “putative” appear around every cor-ner. And those tools that we enjoy in the civilized world like GO ontolo-gies or KEGG pathways? Good luck.

Your genome sequence, if you have one, probably won’t even merit a track at the UCSC genome browser,

much less a current build. So what do you do? Work on some-

thing else and wait for your ’omics collection to catch up? Or is there another answer?

The student force

One strategy is to seek help. Some college instructors have realized that education and annotation can coex-ist. They’ve found that involving stu-dents can speed the data annotation process and train future biologists at the same time. Rather than waiting for database curators to catch up on an ever-growing mountain of work, researchers benefit when lots of stu-dents are added to the labor pool.

This summer, I attended the iPlant Genomics Education conference in St. Louis and listened to talks about students’ contributions to the world of annotating ’omics databases. In-structors spoke passionately about the results they saw from integrating

the realms of teach-ing and research.

We learned about many kinds of an-notation projects. Ch ar le s Hardnet from Spelman Col-lege showed electron micrographs of the phage that his stu-dents isolated and

annotated through their school’s partnership with HHMI. For the bac-terial projects, Derek Wood, Brad

Goodner, Daniel Rhoades, and Steve Slater from colleges across the US described a joint endeavor where students carried out functional an-notation by using bacterial mutants to test whether genes can correct deficiencies in nutritional pathways. Cheryl Kerfeld from the Joint Ge-nome Institute discussed a program where 65 bacterial and archaeal ge-nomes can be adopted and annotated by college classes. Representing in-sects, Sarah Elgin of Washington University discussed a national part-nership where students assemble and annotate genes from different species of Drosophila.

We also heard about annotation projects in plants. Brent Buckner from Truman State University de-scribed the use of yeast mutants to identify the functions of plant genes. Sue Wessler and Jim Burnette from the University of Georgia discussed annotating plant transposons. Iowa State’s Volker Brendl presented a

SANDRA PORTER

SANDRA PORTER My Take

O C T O B E R 2 0 0 9 G E N O M E T E C H N O L O G Y 2 5

Once you venture away from the well-annotated references in the model organism world, the set of research tools gets sparse. The databases look less and less complete.


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system where the entire community can use cDNA and EST evidence to evaluate and correct structural annotations that have been flagged as suspicious in the Plant Genome Database. And Uwe Hilgert of Cold Spring Harbor Laboratory presented a vision of the ultimate annotation pipeline.

Many iPlant attendees seemed to agree that the ultimate annotation pipeline would allow a biology class to check out a genome, review evi-dence, submit corrections, and give students some kind of visible credit so they could demonstrate their con-tribution to others.

The downside

Although the idea of combining useful work with directed studies might seem rather obvious, not ev-eryone shares the belief that engag-ing students in real annotation work is a good thing.

From the researcher perspective, the major concern with having stu-dents annotate gene sequences is quality. They anxiously point to past horror stories of poor quality or mis-identified sequences, like dinosaur DNA, contaminating GenBank. This group is wary of student work and they want the barriers high lest an incorrect annotation lead them down a wrong research path.

Certainly, these researchers are right to be wary, but this attitude shouldn’t keep students from con-tributing. After all, many of the sus-picious entries came from other re-searchers and were reviewed by their peers. The dinosaur entry (U41319), for example, was published in 1997 in Molecular Biology and Evolution. Further, many entries aren’t support-ed by experimental evidence; they’re predicted by algorithms.

If anything, teaching students how to review the evidence by having them annotate data could help de-

mystify the whole database business and make future researchers a little more skeptical. Students would learn that “buyer beware” and reviewing evidence with a critical eye are good policies to follow no matter where your data originates.

Given the number of students in some courses and the push for cost-effective solutions, some skepticism from the professional researchers might be justified. It is difficult to imagine that students in an under-graduate class with 200 or more stu-dents, five teaching assistants, and a very tight lab schedule would be able to finish annotation projects or make contributions that wouldn’t have to be double- or triple-checked. In fact, the National Science Foundation’s Vision and Change survey of under-graduate biology students conducted during the past two years found one of the most common complaints was that their schedule doesn’t include time for repeating labs or debugging mistakes. Perhaps a system could be adopted where professional curators would spot-check student work and assign reliability ratings (behind the scenes, of course) to classes from dif-ferent schools.

In another argument, some iPlant educators shared stories of peers, criticizing them for “using their students as technicians,” exploiting their students, and suggesting that they were allowing their students’ education to suffer by having them do research. Still other instructors worry about the competition for time. Research projects are time-intensive endeavors and there’s considerable pressure to pack as many topics in a course as possible. Would the time required to do a real project push other important topics out of the curriculum?

The concern about time is legiti-mate. Lab activities are often used to reinforce concepts from the lecture portion of the course. Some stu-

dents learn best through hands-on learning, and these students could suffer if certain kinds of activities are lost.

Does the possibility of a few mis-takes slipping by reviewers and con-taminating databases mean we keep students from participating in anno-tation projects? Does the possibility that their learning experience might change — or that change might be hard — mean we should keep things as they are? To paraphrase Paul Farm-er: this is not the end of the conversa-tion. This is the beginning.

The case for inclusion

One of the biggest drivers for in-cluding students in annotation proj-ects comes from the students them-selves. The NSF Vision and Change student survey found that students want more of an emphasis on apply-ing knowledge and problem-solving. They want more chances to do re-search and learn how research is done. They want to work with real data and practice evaluating scien-tific evidence. What they do not want are courses full of memorization that feel disconnected from “real world” science.

Although incorporating research means that learning opportunities will change, the benefits to students can be many. These projects can give students a chance to practice wet lab and bioinformatics techniques and give them better preparation should they pursue a career in life sciences or biotechnology. Students relish the chance to do something more mean-ingful than writing a lab report. They want to “publish” and contribute to the community. I’m glad there are instructors giving some of them a chance.

Sandra Porter, PhD, is president of the bioinformatics education company Digi-tal World Biology. Her blog is located at scienceblogs.com/digitalbio.



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Personal Supercomputers? Call them whatever you like, but HPC vendors are wasting no time in using current hardware to bring more processing power to the desktop than ever before. By Matthew Dublin

You’ve got to love marketing trends in the world of high-performance comput ing. Un-

less, of course, you’re stuck sift-ing through the hype to discern the best compute configuration for your lab or institute. Sometimes these trends become particularly slippery when categories of tech-nology are stretched to the point where their very description seems to be at best a misnomer or, at worst, nonsensical. Many a brow has furrowed over a recent trend that has picked up considerable momentum: “desk side” or “per-sonal” supercomputing. Manu-facturers like Cray, Nvidia, SGI, and HP have all gotten on the bandwagon of marketing HPC so-lutions geared toward the individ-ual researcher or small laboratory, which begs the question: Just what is “personal supercomputing”?

Andrew Jones, vice president of

consulting at the Numerical Al-gorithms Group, a nonprofit HPC software and services solution group, has argued that by defini-tion, a supercomputer is a com-

puter with data processing power beyond that which is commonly available. “There is always going to be a class of computing power that is much bigger than anything that will physically fit on your desk because if you can buy some-thing for $1,000 or $10,000 then there are going to be users that are prepared to buy hundreds of them for a million dollars,” Jones says. “And there’s always going to be something that is orders of magni-tude bigger than what most people can afford but the cheap stuff gets more powerful.” And that’s the point: good old Moore’s Law, along with improvements in hardware like GPUs, make that cheap and powerful stuff easily accessible for the rest of us.

Cray’s CX1

Supercomputer manufacturer Cray, which has since its inception more than 35 years ago focused

solely on mas-s i v e , h i g h - e n d supercomputers, unveiled the Cray C X 1 p e r s o n a l supercomputer a year ago. Unlike a ny t h i ng C r ay

created before, the CX1 can fit on or under a desk, draws its power from a standard 110 volt wall socket, requires no addition-al cooling infrastructure, and can

house up to 64 processing cores. The price tag starts at roughly $9,500, but in July, Cray released an even cheaper version called the CX1-LC (light configuration). And in an obvious effort to secure a customer base of individual re-searchers and small labs, both ma-chines come equipped with either the Windows HPC Server 2008 or the Linux-based Rocks+ operating systems.

Rico Magsipoc, chief technology officer of the Laboratory of Neuro Imaging (LONI) at the University of California, Los Angeles, School of Medicine, was tempted enough by the prospect of having a mini-supercomputer that he decided to purchase a CX1 unit for the re-searchers at his lab. Among other projects, LONI conducts cross-species brain function studies em-ploying complex algorithms that result in computationally heavy jobs. These jobs not only take sev-eral hours to run, but researchers were often subjected to additional wait time in order to gain access to the lab’s larger HPC resources. “We have quite an extensive HPC implementation in our facility here, but the problem is we have a large pool of processors for production, and a large pool of processors for development — but for the indi-vidual researcher, we don’t really have resources,” Magsipoc says. “With CX1 we were able to give a faculty member a machine with 32

Brute ForceHIGH-PERFORMANCECOMPUTING

“There is always going to be a class of computing power that is much bigger than anything that will physically fit on your desk.”


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CPUs, configured any which way, and he’s now a lot more nimble and agile with his research.”

Ultimately, eliminating the high cost of failure during the test-ing and tweaking phase of tool development is where Magsipoc sees the big win with personal su-percomputing. Before purchasing their CX1, all tools had to be tested on the lab’s development cluster, so if something turned out not to work as planned, it was costly in terms of energy usage and the time it took to queue up for access. Now, users can test tools to their heart’s desire without even set-ting foot in the cluster room. “We have a number of researchers here and I can envision each of them having their own CX1 and then when their tools are ready, we can deploy them on our larger cluster,” Magsipoc says.

Nvidia’s Tesla

GPU chipmaker Nvidia also has a desk-side supercomputer offering: the Tesla Personal Supercomputer, which is Linux 64-bit and Win-dows XP 64-bit enabled and comes loaded with a quad-core AMD or Intel CPUs, and up to four Nvidia

GPU cards. Nvidia encourages us-ers to construct their own units the same way gamers have done for years; still, preconfigured units are available through affiliated resell-ers, or one can just go to a local PC shop and have one built for you.

That’s exactly what John Stone, a senior research programmer at the

Theoretical and Computational Biophysics Group at the Univer-sity of Illinois, has done to facili-tate the development of molecu-lar visualization software without having to fork over a lot of money or deal with queuing up for time at a clus-ter. Stone currently uses a preconfigured quad-core Linux PC with three Nvidia GPUs that is capable of more than a teraflop’s worth of performance. “We actu-ally bought that from a local PC vendor, had them assemble the machines for us, and we got three of the Nvidia GPUs,” Stone says. “It was very easy and this is some-thing a lot of people can do.”

Stone’s personal supercomputer serves as a very real replacement for a cluster of PCs, and lets his team of researchers avoid some of the operational hassles asso-ciated with clusters. Currently, his lab has 20 such GPU-enabled PCs specifically equipped for vi-sualization tool development. Ul-timately, he says that what the personal supercomputing hoopla should really point to is the fact that for the first time ever, there

are commodity de-vices that are mas-sively parallel and have the same ag-gregate f loating point performance that just a few years ago would have required a room

full of typical PCs or server class machines.

In the case of Nvidia’s products, assuming you feel comfortable in the GPU programming world — which by steps is getting more and more attainable — you can get a level of performance that was not practical before with a machine

whose form factor would fit on or under your desk. “This is very ex-citing to me because I develop mo-lecular visualization and analysis software and this software is run

by a range of researchers, many of whom are not computer experts or hardware guys. They are wet lab scientists, so they are not compute savvy beyond the point of using the software to do what they need to do,” Stone says. “For them, the appeal is that they can very easily ask their local computer adminis-tration team and say ‘I need a new computer that has four GPUs in it and I will be able to run my work 100x faster’ which means they can do things they just couldn’t even do before.”

A few years back we might have called desk-side machines that were way beyond PCs’ processing power ‘technical workstations.’ Whether they really count as su-percomputers is beside the point — at the end of the day, mak-ing researchers aware of what’s out there is what really counts. “I don’t think there’s anything wrong with the term ‘personal supercomputing’ if it successfully gets a whole lot more people mak-ing use of the compute power that’s available,” Jones says. “It’s marketing, but it’s perfectly valid marketing, aimed at an audience that would normally not go any-where near large-scale supercom-puters. … HPC can do so much for people trying to do simula-tions and modeling that whatever we call it to get more people to using it, the better.”

“This is very exciting to me because I develop molecular visualization and analysis software.”

“I don’t think there’s anything wrong with the term ‘personal supercomputing.’”


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The language of technical computing

Accelerating the pace of engineering and science

Over one million people around the world speak MATLAB. Engineers and scientists in every fieldfrom aerospace and semiconductors to biotech, financial services, and earth and ocean sciences use it to express their ideas. Do you speak MATLAB?

Cells in mitosis: high-throughput microscopyfor image-based screens.Provided by Roy Wollman,Univ. California, Davis.

Article available at mathworks.com/ltc

©2009 The M

athWorks, Inc.


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GENE EXPRESSION

New Tools in NeuroscienceA brain atlas was once on the order of a coffee table book, known for its large,

glossy illustrations. Today’s brain atlases — led largely by the Allen Institute for

Brain Science — capitalize on localized gene expression and other data to truly

revolutionize the field of neuroscience.

BY MEREDITH W. SALISBURY

It’s been just three years since the Allen Institute released its mouse brain atlas — a free, publicly available online tool

that allows users to zoom in and out of a 3D brain, search by gene, and see expression data — but in that short time, this revo-lutionary look at the inner work-ings of a brain has dramatically changed the way neuroscientists do business.

Take Greg Foltz, for instance. A neurosurgeon at the Swed-ish Neuroscience Institute, Foltz studies glioblastoma mutliforme; for him, the glut of new data on this particular kind of tumor from the Cancer Genome Atlas project has been both an amazing resource and a cause of frustration. The “tremendous amount of sequenc-ing data available across hundreds of patients” — while a significant first step, Foltz says — doesn’t address a key issue in heterogeneous glioblas-toma tumors: location. In these types of tumors, knowing whether a gene is expressed at the core of the tumor or the leading edge of the tumor can be critical to deciding how to treat a patient.

Because of that, Foltz uses the se-quencing data and compares it to, of all things, the Allen Institute’s

brain atlas for mouse. He and his team have made extensive use of the atlas and believe that mouse brain is a fair approximation for what goes on in human brain, he says. Foltz can take the gene expression levels seen in the glio-blastoma-specific data and com-pare them to the mouse brain for a sense of “what genes appear to be expressed in an increased fashion or silenced,” he says. “That’s been really useful for us. If you think about it, we have no other way of making that comparison.”

Indeed, Foltz says that even that

level of information helps his team partition patients into groups based on likely treat-ment course and predicted outcome. Of course, what he really wants is to have a brain atlas for human — and one that would reflect the changes seen in glioblastoma patients.

Foltz is getting his wish. Thanks to a three-year, $2.1 million grant from the Ben and Catherine Ivy Foundation, Foltz will be teaming up with the Al-len Institute on the Ivy Glioblas-toma Atlas Project. The atlas will be based on tumor samples from 32 patients and will start with a focus on 300 genes selected “because they’ve already been known to have increased expres-

sion in glioblastoma,” Foltz says. He also plans for a comparison

to non-tumor brain, using around 20 samples from operations where patients with other neurological con-ditions, such as epilepsy, have had part of their brain removed. When the atlas is complete, it will include clinical information on the patients and the tool will be made freely available. “It is going to be absolutely fascinating to see,” Foltz says.

The human angle

Over at the Allen Institute, mean-while, the glioblastoma project


A BRAIN SLAB IS PREPARED FOR SECTIONING


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might be considered small com-pared to what these researchers have set their minds to: developing a human brain atlas.

This is no pie-in-the-sky goal. After more than a year of planning, insti-tute scientists are gearing up to begin the human brain project, which is expected to cost around $55 mil-lion, include two phases — the first a macro-level look and the second focusing more on the cellular level — and be completed in 2012, says institute COO Elaine Jones. The in-stitute is currently trying to raise $10 million to support the initiative from a variety of sources, including gov-ernment agencies, private sources, and philanthropies, she adds.

As most people are reluctant to give up their brains, the study will be per-formed on cadavers — anywhere from four to 10, with a mix of males and females, says Elaine Shen, manager of the human brain atlas project. She notes that the end result will be multi-modal, including magnetic resonance and classic histology information in addition to the microarray analysis and in situ hybridization data. “All of the gene expression data is going to be mapped back into 3D space,” Shen says. With all of that information in one place, she adds, the hope is that the new brain atlas will be far more useful to clinical researchers.

The human brain is approximate-ly 2,000 times the size of mouse brain, Shen says, which in itself has created major challenges for a pipeline designed around brain slices that could easily fit on a typi-cal laboratory slide. Other hurdles have come from using fresh frozen tissue: “So many of the stains have been optimized for fixed tissue,” Shen says. The brain sectioning process is typically easier in fixed tissue as well. As the institute has geared up for this project during the past year and a half or so, sci-entists there have become experts

in adapting protocols to work with fresh frozen tissue. The team also had to rebuild the informatics side of the pipeline to accommodate all the new clinical data as well as the microarray data. “The scale’s so much larger,” Shen says. “A project of this kind of scale and scope has not really been tried.”

In the first phase of the atlas proj-ect, researchers will collect about 1,000 samples per brain and per-form microarray analysis on them as a way to “systematically survey through the brain,” Shen says. The second phase will include the ISH part of the study and will “very likely concentrate on specific genes and specific structures.”

Shen notes that a key phase in plan-

ning for this project involved reach-ing out to the neuroscience com-munity. The goal was “to understand from them what they thought, one, would be needed [by scientists in the field], and, two, the challenges and expertise that would be required,” she says.

The choice of human brain for the institute’s next major project was no accident. According to Jones, the institute plans in three- to five-year phases, based in large part on the recommendations of its scientific advisory board. “We are looking at what’s the next big, high-impact proj-ect that we should be working on that will have a major effect on neu-roscience … that nobody else will touch,” Jones says.

MicroRNA Expression Sheds Light on Schizophrenia

A team of scientists at the Schizophrenia Research Institute in Australia have used studies of microRNA expression to determine that gene silencing appears to play a key role in patients with schizophrenia.

Murray Cairns, senior research fellow at the institute, worked on the project involving a cohort of postmortem samples from schizo-phrenia patients and controls. “After doing a lot of gene expression profiling, we noticed that

there was a general trend — more down-regulated … genes than upregulated. We thought maybe this was gene silencing.” That finding led to the current study, recently published in Molecular Psychiatry, in which “microRNA expression seemed to be globally elevated in the schizophrenia cases compared with the controls,” Cairns says.

To follow up on that, Cairns and his colleagues looked at the primary and precursor microRNAs of some of the differentially expressed microRNAs, finding that “the mature and precursor forms were … upregulated in schizophrenia but the primary transcripts didn’t seem to be altered,” he says. That suggested some kind of post-transcriptional alteration, which the team is currently investigating.The researchers are using microarrays and next-gen sequencing in their latest studies. “We’re looking at some other brain regions and we’re also trying to do some laser capture and identify the actual cell types,” Cairns says. They’re adding some functional genomics approaches as well to get a better sense of the patho-genesis of the disease.

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PGX

Companion Diagnostics Take OffPharma is realizing that it needs to collaborate with diagnostic

companies to stratify patients and to make safer, more effective drugs.

But obstacles remain in the path to full flight.


BY JEANENE SWANSON

As the saying goes, all good things must come to an end. And for ph a r m a, t h at means banking

on the one-size-fits-all model of drug development. Companion diagnos-tics, a relatively new concept that’s hitting the frontlines of drug discov-ery and development, is promising to change the way drugs are made and marketed.

With more and more biomarkers being discovered and validated, the field of companion diagnostics has more than a leg to stand on. Us-ing a companion test — whether it looks for genetic, proteomic, or gene expression markers — to pre-dict whether a drug will work in someone or what kind of dose that person should take is becoming more common and, according to experts,

will eventually become the norm. “It’s a new field, and it’s growing,” says Peter Tolias, executive director of the Institute of Genomic Medicine at the UMDNJ-New Jersey Medical School.

In the last five years most of the major pharmaceutical companies have adopted new programs to deal with companion diagnostic products. “In the olden days they never used to worry about who their drug was going to be functioning in, or who’s going to have an adverse effect and to actually support it with a clinical product in the marketplace,” Tolias says. “The tide has changed now and pharmaceutical companies are very interested in moving products onto [the] market where they can target safer and more effective products with companion diagnostics.”

Recently, the field has really heated up, and that’s due in part to increased awareness among pharma that in order to be more effective and save

“It’s going to take probably a generation for us to see a trans-formative change.”

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money, drugs will have to be more personalized. “The very important trend that’s emerged is the realization by the pharmaceutical industry that whether they like it or not, this is just how things are going to be, and once they realize that, that should be a re-ally big impetus in terms of moving things forward,” says Stephen Little, CEO of UK-based pharmacogenom-ics company DxS.

Taking off

While the anticipation in the field is that there will be a marked in-crease in the number of companion diagnostic products, it’s not going to happen overnight, says Tolias. “It’s going to take probably a generation for us to see a transformative change in the way that drugs are used, but clearly it’s already happening and there are tangible examples on the market today,” he adds.

The Personalized Medicine Coali-tion, a nonprofit advocacy group, reports that there are currently about 40 drugs in the US that have com-panion diagnostic tests associated with them — whether that means as a requirement to their being pre-scribed, a recommendation for use, or label information that lists genetic susceptibility relating to efficacy or dose.

While a number of pharma compa-nies have bought in, including Na-tional Pharmaceutical Council mem-bers Abbott, Pfizer, Bristol-Myers Squibb, Boehringer Ingelheim, and AstraZeneca, among others, it’s no-ticeably the diagnostics industry that has benefited financially. According to the PMC, the 200 companies in the diagnostics space reported $30 billion in sales in 2008. There are 65 publicly traded imaging diagnostic companies, and venture capital invested in 57 molecular diagnostic companies last year totaled $467 million.

The first test to be associated with

a drug debuted in 1998. Diagnostic company Dako launched HercepTest, an immunohistochemistry assay used to identify patients with HER2-pos-itive metastatic breast cancer, when it was discovered that patients with HER2 amplification responded better to Genentech’s breast cancer therapy, Herceptin. In August of this year, Ge-nentech and Dako agreed to submit for FDA approval both HercepTest and Dako’s HER2 FISH pharmDx

test for Herceptin in the treatment of advanced HER2-positive stomach cancer.

One leader in the field is DxS, which has partnered with some of the big-gest pharma companies to co-devel-op companion tests. In April 2007, the company launched TheraScreen, the first CE-marked diagnostic for detecting mutations in the epidermal growth factor receptor gene. The kit is used to select lung cancer patients who can be treated with tyrosine ki-nase inhibitors, since recent studies have shown that some patients with non-small cell lung cancer who have mutations in this gene respond better to tyrosine kinase inhibitors such as Roche/OSI Pharmaceuticals’ Tarceva and AstraZeneca’s Iressa. In 2007, DxS launched its K-RAS mutation de-tection kit, and in 2008 the company partnered with Amgen to develop a K-RAS companion diagnostic that can

be used to predict whether a patient with metastatic colorectal cancer will respond to Amgen’s drug Vectibix. The K-RAS test is also used to predict response to ImClone System’s Erbitux, which only works for patients whose tumors are not mutated.

“The uptake of [the K-RAS muta-tion diagnostic] has been really fast, and I’m sure part of the reason for that is that we don’t just have the diagnostic industry promoting the benefits of the assay, we have the pharmaceutical industry promoting the benefits of the assay as well,” says Little at DxS. Since the whole point of these tests is to identify patients who will do well, “you end up with better treatment for less money,” he adds. “It’s a very alluring prospect.”

Other notable collaborations are in the works, too. In July, Glaxo-SmithKline and Abbott announced that they would develop a companion diagnostic for GSK’s investigational MAGE-A3 immunotherapy. In Oc-tober 2008, Merck signed a two-year exclusive licensing agreement with Celera that gave the pharma access to up to 10 cancer targets for the devel-opment of RNAi-based therapeutics. Effectively, Celera can develop com-panion diagnostics for any therapeu-tics that Merck develops out of the licensed targets. In 2007, Merck inked a research collaboration agreement with Asuragen to develop a gene-ex-pression-based companion diagnostic for use in Merck’s clinical trials for an investigational cancer treatment.

Use in clinical trials is one of the reasons pharmas like to partner with diagnostic companies. Ac-cording to Carol Berry, head of the pharmacogenomic services division at Asuragen, “Our clients, which are pharmaceutical companies, mostly are looking at how can we develop assays — in other words, gene sig-natures — and then use those gene signatures in various phases of their clinical trials.” Indeed, most pharma

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giants look to companies like Asura-gen, for instance, toward the end of phase 2 or 3 trials when they are considering FDA submission. “The regulatory requirements drive them to solicit outside companies like ours that have the expertise and the know-how and the manufacturing facilities to be able to produce the diagnostic,” Berry says.

Working together

While most available companion diagnostics — whether molecular tests like those for the EGFR mu-tation or in vitro diagnostic tests like Oncotype DX’s test that looks for gene expression differences to measure susceptibility to breast cancer reoccurrence — have been developed separately from the drug they’re used with, the trend now is toward developing them together. And as more clinical trials include early biomarker tests for toxicity or efficacy screening purposes, it’s easy to springboard these into compan-ion tests, says Tolias.

“It’s pretty straightforward for us to design and develop a good quality assay, but to actually link that assay to drug response needs a clinical trial, and that needs the pharmaceutical industry’s buy-in,” says DxS’s Little. While that’s hap-pened over the last several years, the bigger challenge is getting pharma to start planning co-development agreements earlier in the clinical trials process. “I think the biggest challenge is often one of lack of fore-sight,” Little adds. “Oftentimes we’re involved with a drug company who requires a companion diagnostic, but they need it straightaway and they haven’t really given us time to develop that. What would be ideal would be if those co-development programs were initiated earlier.”

From the viewpoint of PMC, whose membership comprises a number of

different organizations from diag-nostics firms to pharma companies, there’s a more complex set of prob-lems. “The significance here is that the companion diagnostic can facili-tate the approval of a drug because it works in a large percentage of people,” says Director Ed Abrahams. “[Pharma has] understood for quite some time that they need to enrich the pool — so that they understand why a drug works and for whom

it works and so that they can pull the plug early if they’re seeing it’s not working. … But now they un-derstand, to get something onto the market, it can be useful to have the diagnostic joined to the drug.” But working together is not as simple as it sounds. Abrahams says one of the big hurdles to getting personalized medicine tests up and running is that of divergent business models, which do “not allow for easy part-nerships.”

A looming incentive for pharma companies to partner with a diag-nostic manufacturer is that submit-ting a diagnostic with a drug might increase the therapeutic’s chances of being approved. In the case of Novartis’ failed drug, Prexige, there have been whispers about the phar-ma resubmitting the drug to FDA for approval, but this time with a com-panion diagnostic test. If submitted

and approved, this would be the first time a drug has been resuscitated by a companion diagnostic.

Regulatory hurdles

Another big hurdle, according to Abrahams, involves regulatory is-sues. While FDA issued a draft Drug Test Codevelopment Concept Paper in early 2005 to lay out the initial guidelines for the regulatory pro-cess for drugs with companion tests, the document hasn’t been improved upon much since then. In 2002, the FDA created the Office of Combi-nation Products, which addresses companion devices and tests that don’t fit into the agency’s established pipelines. “Companion diagnostics don’t really fit into the current FDA paradigm of regulating diagnostic kits,” says PMC’s Amy Miller, public policy expert. The FDA has indi-cated that it may turn the concept paper into an actual guidance for industry, and the PMC is taking responsibility for collecting sugges-tions from the community on how to update it. They plan to publish those suggestions in late October, says Miller. However, she adds, “It’s really unclear how these products are going to be regulated.”

Felix Frueh, who used to lead the genomics review group at FDA’s cen-ter for drugs and now heads up research and development for per-sonalized medicine at Medco, is on the board of PMC and has helped compile the comments. “For one, the co-development draft guidance is still only talked about, but noth-ing has been written,” Frueh says. So far, he adds, many feel the cur-rent concept paper is too technical and doesn’t address the regulatory strategies that one could actually use in the co-development of a drug and companion test. “The last I heard is that the comments are going to be written up more or less as the white

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paper itself,” Frueh says, adding that he thinks FDA should focus the paper on teasing out the clinical and strategic issues involved in the process. “But I don’t know what FDA is currently thinking about — [whether they are] going to write a guidance, how that guidance is going to look, and what it’s going to say. … I know they want to do it, I just don’t know whether it’s going to happen or not.”

A significant incentive for drug makers to co-develop a diagnostic is not only for preventing drugs that will ultimately fail, but also because FDA approval might come more eas-ily. “The approval of the drug is potentially more imminent with a diagnostic because they can show it’s working,” Asuragen’s Berry says. However, matching up timelines and understanding the separate regulatory processes between drug manufacturers and diagnostic com-panies could prove daunting. “All of us are navigating through these various organizations and entities at the FDA and trying to understand what is the best way to develop a diagnostic test that could go with a drug,” Berry says.

That’s not to say that FDA hasn’t made inroads. Changing drug la-bels to include various types of pharmacogenetic information is becoming more prevalent. Of the 40 or so drugs that are associated with diagnostic tests, FDA requires a companion diagnostic test to be used for only about five. Some drugs have updated labels that include recommendations to use a test — warfarin being an example — while the majority only have updated in-formation about the possible genetic link to side effects and optimal dose. Peter Tolias says, “You’re going to see this trend increasing.” In fact, in July, FDA changed the labeling of colon cancer drugs Erbitux and Vectibix to be prescribed only to

people with non-mutated forms of the K-RAS gene.

It’s unclear, however, how use-ful updating labels with recom-mended or informational items will be. While warfarin labeling now includes FDA-recommended geno-typing for mutations in two genes that cause increased susceptibility to bleeding, the label doesn’t require it. Many industry insiders have said that stronger labeling is needed to make sure the tests are actually used to guide dosage when prescribing warfarin.

Down the line

While co-development strategies and regulatory issues are big wrin-kles to be ironed out, what eventually matters is whether or not doctors use the tests. And though development has taken off in terms of proving certain tests’ efficacy in clinical trials, proving real-world success isn’t as cut and dry. Frueh’s work at Medco involves this sort of outcomes re-search, for which the company just finished enrollment for two clinical trials. Research “focuses on estab-lishing the clinical effectiveness for the use of biomarkers to optimize

drug therapy,” Frueh says. “Our fo-cus is the translation of these tools into clinical practice,” he adds. “We want to know how they’re going to perform, not just in one or two highly skilled clinical settings,” but in the broader sense. This will be especially useful as more insurance companies start covering the tests — it’s hard to determine whether or not a company should cover a test with-out a true measure of its prevention of hospitalization, he adds.

Moreover, though uptake for re-quired companion diagnostics has been good, most doctors still don’t know enough about the field to feel comfortable ordering recommended tests. Medco recently conducted a nationwide physician survey that reached about 400,000 doctors. While 98 percent agreed that ge-netics is important for drug therapy, only about 10 percent said they felt adequately informed about it. Addi-tionally, about 12 percent said that they’ve been ordering a genetic test over the last six months and about 25 percent indicated that they’re planning to order genetic test. “So you see there is tremendous growth potential,” Frueh says. “It really all points to a lack of education, a lack of penetration with respect to get-ting the information about these tests.”

Little at DxS predicts a move from “cytotoxics toward targeted thera-pies” when it comes to cancer drug development, while Tolias see more protein markers being used. Now, it’s mostly genetic markers — tests that look for SNPs or some form of structural variation — but proteins could take the field much further. “What you ultimately want is not necessarily just something that pre-dicts risk but something that’s caus-ative, and a lot of these markers are risk predictors, but they don’t actu-ally tell you that you’re sick at that time,” says Tolias.

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SEQUENCING

Humans as HostParticipants are calling the Human Microbiome

Project a second Human Genome Project. The

massive global effort aims to get to the bottom

of the relationship between microorganism and

host, and disease and health.

BY CIARA CURTIN

The exact num-ber of bacte-ria living in or on humans isn’t known, though it is estimated to

be around a trillion. In any case, the number of microbial cells in the hu-man body outnumbers the human ones by a factor of 10. Those symbi-otic microbes endow humans with otherwise unattainable metabolic ca-pabilities, but also may contribute to human disease. What is certain, however, is that humans may really be classified as super-organisms — and ones that are mainly bacterial at that.

“There’s a huge amount of gene activity [in the human body] that’s being carried out by microbes,” says George Weinstock, associate director of the Genome Center at Washing-ton University in St. Louis. “There just has to be a very large impact of all of that microbial genetic activ-ity on both healthy body as well as when pathological conditions set in different parts of the body. I think

we’re right at the very, very begin-ning of an extremely exciting era where we’re going to make connec-tions between things that we waved our hands about in the past or didn’t understand or may not have even focused on.”

Researchers have been studying the flora living in and on the human body for decades. The problem, however, is that most of the bacteria that can be seen peering through a microscope stubbornly refuse to grow on Pe-tri dishes in microbiology labs. Still, scientists slogged through and man-aged to link these microorganisms to everything from cirrhosis to irritable bowel syndrome to autism. Recently, though, the human microbiome has been lavished with attention and funds. Now, genomics approaches are being applied to identify the bacteria lurking in and on the human body.

Knowledge from what is being called the “second Human Genome Project” will be able to inform clinicians pre-viously stymied by the cause of a dis-ease or a patient’s response to a drug treatment. Organizations around the world have poured money into this work — an international consortium

was formed to foster collaboration and data-sharing among member countries. In the United States, the National Institutes of Health recently launched a five-year, $140 million Human Microbiome Project, mod-eled after the Human Genome Proj-ect, to better understand how the human microbiome affects human health and disease.

This project had been in the wings for a while, Weinstock says, but tech-nology and tools hadn’t caught up to the idea. “Then, four years ago or so when next-generation sequencing methods started coming and they also became highly adaptable for microbial genomics, you had the development of the perfect storm where there was a large microbial project just waiting there to be done,” he says.

The known biome

Despite the lack of funding focus on the human microbiome until recently, researchers have been whittling away at the microbiome’s unknowns: How is it established? How similar is it between individuals? How diverse is it? How does it affect human health? “This was of great interest at least to me and my colleagues elsewhere prior to the NIH Roadmap Program,” says Stanford University’s David Relman.

In 2007, Relman and his colleagues followed 14 babies — including a set of fraternal twins — as well as their mothers and most of the fa-thers during the babies’ first year. The researchers profiled 16S rRNA sequences from the participants’ stool samples using a specialized micro-

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array and sequencing in an effort to determine how the microbiome is established. And it arises quickly. By the end of a week, Relman says, there are a surprising number of taxa present, and a prominent source of microbiota for each baby was its mother. At the end of a year, the ba-bies’ microbiome is adult-like and is, for the most part, distinct from each other and the adults. “The one pair of twins that we had in our group, they were shockingly similar at any given time during that first year, one to the other,” Relman says.

Relman and his colleagues, includ-ing the J. Craig Venter Institute’s Karen Nelson, also characterized the diversity of the adult microbiome. In 2005, they analyzed the 16S rDNA of mucosal and fecal samples from three healthy human adults, finding 244 novel bacterial phylotypes. Most of the organisms they found belonged to one of two phyla, the Firmicutesor the Bacteroides. “That work also pointed out that there was a lot of this micro-diversity within populations,” Nelson says. It’s been described as a tree with thick limbs that branch into tiny twigs at the ends.

Then in 2006, they kicked off the metagenomics age of microbial stud-ies by shotgun-sequencing the distal gut microbiome of two healthy adults — a study affectionately known as the HuPoop Project. “Using Sanger-based approaches, [we] could see a significant amount of microbial di-versity in those two samples,” Nelson says. “I think that everybody realized from that study that there’s a tremen-dous amount of diversity in human that has yet to be tapped into.”

Naturally, studies haven’t focused solely on the gut. The National Hu-man Genome Research Institute’s Julia Segre characterized the skin microbiome by taking samples from 20 different skin sites on 10 healthy people. Also from 16S rRNA, she and her colleagues found 19 bacterial

phyla living on the skin, though most belonged to Actinobacteria, Firmicutes,Proteobacteria, or Bacteroidetes. Like Relman and Nelson, Segre saw great-er diversity at the species level.

She also noted that some bacteria prefer certain body sites, such as se-baceous sites. “They are very different in terms of properties, whether they have hair, whether they have sweat glands, and it turns out that those factors end up really influencing what [is there],” Segre says.

By following up on five of the vol-unteers, Segre also found that the skin microbiome is fairly stable. The volunteers were significantly more similar to themselves than to the other participants.

In other research, Imperial Col-lege London’s Jeremy Nicholson has found that the microbiome affects how people respond to drug treat-ment. “The bugs make compounds that are actually competitive with drugs for metabolism,” he says.

Recently, in an August issue of PNAS, he and his colleagues found that the chemical p-cresol, produced by gut microflora, affects how people metabolize Tylenol as both p-cresol and acetaminophen undergo sulfona-tion. Some people have microflora that are more active in cresol produc-tion than others, and when they take acetaminophen, there isn’t enough

sulfur for acetaminophen to go down that metabolic pathway. “Even Tyle-nol is affected by your gut microbe activity,” Nicholson says.

Of course, some drugs are meant to affect the microbiome. Antibiotics act broadly on bacteria and disturb the microbiome. Last year, Relman and his colleagues studied the effect of a five-day course of Ciprofloxacin on healthy human gut communities. “What we saw was a return to es-sentially the same community after about four weeks of time, but there are some exceptions,” Relman says. “The exceptions might be important.” There were microorganisms that hadn’t returned by the end of four months and others that were more abundant than they had been. “It’s hard to say if that’s important or what the long-term consequence might be, but we’re now looking at longer time periods of follow-up,” Relman says.

As in-depth as the studies have been, they have merely skimmed the top layer of what’s to be found in the mi-crobiome. A deeper look is still ahead.

Sequencing the microbiome

One of the main tools being used in the Human Microbiome Project is the sequencer. The first phase of that project is to develop tools to support further research into the microbiome. For that phase, four sequencing cen-ters — Baylor College of Medicine, the Broad Institute, JCVI, and Washing-ton University — have been working on sequencing bacteria from healthy individuals and 200 bacterial refer-ence genomes.

That first prong was originally to take samples from 250 healthy vol-unteers between the ages of 18 and 40 at various body sites — 15 sites for men and 18 for women — to try to get a description of the human microbiome. Now, that number of volunteers has been upped to 750.

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“The first goal ought to be to have some description of human micro-biome that could be comparable to the working draft of the human ref-erence sequence,” Weinstock says. “That description of the human mi-

crobiome should go far beyond any-thing that has been done so far and to really help to answer some of the very basic questions about our different microbiome communities in different parts of the body and how they vary

between individuals.” According to Baylor College of Medicine’s James Versalovic who is coordinating the clinical efforts for this phase of the project, more than 150 people have been sampled.

The 12,000 samples from the par-ticipants are a mixture of bacteria, prokaryotic microorganisms, and vi-ruses; the sequencing centers want to do a sort of census to determine what microbes are there and in what quantities. One way to do a head-count of the bacteria, Weinstock says, is to sequence all the 16S rRNA in the mixture. “[16S] is the functional equivalent of a barcode for an organ-ism,” says Doyle Ward at the Broad Institute. That barcode can then be analyzed and compared against ref-erence genomes to determine what bacteria are present.

The centers have been working to-gether to establish rigorous methods for deeply surveying community com-position by sequencing and analyzing 16S sequence. In particular, Ward is developing methods to do this work on the 454 Titanium platform, as well as new analytical tools. One example is ChimeraSlayer, which detects chi-meras in 16S data. He is currently working on adapting it for 454 data.

However, looking at 16S rRNA doesn’t answer all the questions. Weinstock says that while 16S rRNA gives a good idea of a bacterium’s rela-tive abundance, it doesn’t take vastly different strains of the same bacteria into account. For example, he says that through 16S sequencing, E. coliall look the same. Some E. coli strains, such as the K12, are benign but others are not — in 1993, the O157:H7 strain killed four people who ate at Jack in the Box restaurants in the western US. In their gene content, those two strains differ by about 1,000 genes.

“Work that we’ve done looking at other environments has shown that organisms can have identical 16S se-quences, but have wide variation in

Is There a Core Human Microbiome?

Part of the Human Microbiome Project aims to determine whether there is a core human microbiome that all people share. Right now, whether there is one or not is a matter of some controversy. And then, if there is, there’s the matter of reso-lution — how far down the taxonomy ladder do you have to go? What percentage of people must have the group for it to be “common”? A few preliminary studies have suggested there is a core microbiome, but they are far from the full picture.

JCVI’s Karen Nelson isn’t convinced there is a microbiome common to all people. Early studies, she points out, were limited to North Americans. “I think that once we start to get out and do broader sampling, we will have a better feel,” she says.

“To some extent, the question is: how big is the core group of organisms?” saysGeorge Weinstock at Washington University in St. Louis. From years of medical microbiology, he says that “we know that for certain parts of your body, there are certain organisms that we’re pretty sure are going to be there.”

However, Baylor’s James Versalovic and Stanford’s David Relman add that there is not even a definition of “core” just yet.

RIKEN’s Todd Taylor says the issue depends largely on resolution. “If you are talking globally, at the strain level, I’d guess no. If you are talking more locally, say within Japan, at the strain level, maybe, at the genus level, almost certainly,” he says. “There are many factors that need to be considered in the core microbiome question, such as, one, are we talking about genes or species; two, if species, at what level: genus, species, or strain; or, three, if geographic, in what range: global, continental, country, state, local, or some other region?”

Versalovic says he thinks there is a core microbiome but agrees it is a matter of resolution. “When you say there is a core, does that mean that E. coli, for example, is present in more than 50 percent of people or does that mean that E. coli is pres-ent in 80 percent of people?” he says. “I take a somewhat liberal perspective on this. More than 50 percent is probably enough.”

Now with sequencing, more species can be found than before using culture plates. “The question then becomes: is the core just a handful of organisms, and then there’s a lot of variation after that, or are there really quite a few additional organisms that are non-culturalable that are also frequently found in body sites?” Weinstock says. Furthermore, he adds that there could be more than one core group for a particular body site, based on environmental factors.

Then for a particular body site, one set of people might have one group of organ-isms and another have a different set of organisms. “There might be more than one type of core that people can have,” Weinstock says.

“In some way, shape, or form, it would be nice to know what, if anything, we share that determines the ability of our communities to promote health or be as-sociated with health,” Relman says.



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their genome content,” Nelson adds.Shotgun analysis of the DNA sam-

ples, on the other hand, will catch those virulence factors and other genes of interest. Since assembling genomes from that mix is very hard to do, Weinstock says that each of those sequences is analyzed to determine what genes are present in the commu-nity. “That’s what allows you to detect toxins and things like that,” he says.

This approach also allows research-ers to determine whether any eu-karyotes or viruses are also present. “The metagenomic approach allows us to really delve into the question of how much genetic diversity there is in these populations,” Nelson says, adding that it also avoids introducing biases inherent to other approaches.

Data derived from those healthy volunteers then needs to be compared to something to tell just what their microbiomes contain. In addition to sequencing people’s microbiome, the four sequencing centers are also tasked with creating reference bac-terial genomes. “We are going to sequence, overall, about 1,000 mi-crobial references genomes,” Nelson says. Through the Human Micro-biome Project, JCVI has received $8.8 million in American Recovery and Reinvestment Act funding to do just that. Baylor received $3.7 million and WashU was awarded $16.1 million.

But which lucky microorganisms will be sequenced? “The centers in the consortium arrived criteria that we tried to apply to our selections,” the Broad’s Ward says. Those criteria emphasize phylogenetic uniqueness and whether or not related organisms have been sequenced, as well as its dominance or abundance within its niche and whether it is associated with health or disease. As the Broad has no microbiology lab, Ward says they also rely on the clinical exper-tise of their collaborators to deter-mine what would be interesting to sequence. Through the initial phase

and pilot programs, the Broad has sequenced 150 microbial genomes and recently received an award to sequence at least 200 more.

Data from these large-scale projects are continually being released and up-dated. “We actively try and release data as quickly as possible,” Nelson says.

Funding the smaller scale

With the first large-scale phase of the Human Microbiome Project un-der way, the second phase — smaller-scale projects — is now beginning. NIH has awarded $21.2 million for these demonstration projects, and program officially kicked off in June of this year. Many of these new proj-ects focus on health and disease, but some will also look into technology development. “Fifteen new principal investigators that are from different institutions in the United States are now funded by NIH to pursue spe-cific clinical projects,” says Baylor’s Versalovic, who is the clinical coor-dinator of these projects.

For his own work, Versalovic is studying irritable bowel syndrome in children between the ages of seven and 12 with his $750,000 grant. “We think that bacteria have a role to play — not only in the immune re-sponse, immunity inflammation, but

also in terms of pain perception,” he says. “There are some data that some bacteria that normally live within us actually affect the nervous system and the ways that, for example, transmis-sion of pain and reception of pain and pain signals may be processed.”

The University of Michigan’s Vin-cent Young and his colleague, mi-crobial ecologist Thomas Schmidt at Michigan State, have both been studying the gut microbiome for a decade; they received a $1 million grant to study ulcerative colitis, a bowel disease marked by abdominal pain, gurgling, and diarrhea.

Nelson is working with New York University’s Zhiheng Pei on esopha-geal cancer. “Our preliminary work has suggested that you can see a cor-relation with various microbial popu-lation and the onset and development of esophageal cancer,” Nelson says. She is also collaborating with NYU’s Martin Blaser to study psoriasis, a condition in which skin becomes salmon-colored, scaly, and raised.

Another project comes out of Segre’s lab at NHGRI and will be studying the relationship between the human immune system and the microbiome. “The NIH Clinical Center has a lot of patients who are immunocompro-mised. So we’re looking at patients who are immuno-deficient and see-ing how specific immunodeficiencies affect their microbiome,” Segre says. “We just don’t know that much about our relationship between our human cells and our microbial cells.”

On the tool development end of the spectrum, there is the University of Colorado, Boulder’s Rob Knight and the University of Maryland’s Mihai Pop. Knight has been given $1 mil-lion to develop computational tools. “What we have been doing is devel-oping ways to compare communities and individuals with [a] large number of sequences from each individual,” Knight says, as in the past few years the scale of the data has increased

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JULIA SEGRE

rapidly. He and his lab are developing tools to make a phylogenetic tree from 16S bacterial sequences and measure the distances between them.

Pop is working with Steven Salz-berg on a $780,000 grant to develop assembly and analysis tools for all the new data. “Essentially there is very little bioinformatics infrastructure for metagenomics data,” Pop says. “In particular, there is I would say zero software available for assembly. There are a lot of issues in gene find-ing and binning.”

Also, Young and Schmidt will be coming full circle and developing ways to “culture the unculturable,” particularly of organisms near the mucosal lining of the intestines that need low levels of oxygen. So far, they have been able to grow organ-isms that had only been identified through molecular surveys. “One of the reasons for doing that is that part of the Human Microbiome Project, they have a list of 600 organisms that they want to get full genome sequences, [but] they want more things to sequence,” Young says. “We thought that by doing this, we could generate more cultivars so that we can do full-genome sequencing to understand how different members of a microbiota make their living.”

The practice of medicine

The ultimate goal of diving into the depths of the human micro-biome is to make people healthier. If there is a core microbiome that most people have that keeps them healthy (see sidebar, p. 41), then, as the story goes, perturbations to that community could be tracked and correlated to disease. Then the microorganisms behind the problem could be targeted by therapies, or prebiotics or probiotics could pre-ventively encourage the establish-ment of a healthy microbiome.

“In my opinion, the ultimate goal

of this research is for us to under-stand how the meta-system — host, microbes, viruses, other organisms, metabolites, environment, et cetera — works as a whole and to be able to predict how perturbations in the sys-tem impact the various parts,” RIK-EN’s Todd Taylor says. “This research is still in its infancy. There is a long, unpaved road ahead, but with persever-ance, hard work, and innovation on the part of the research-ers involved, we will discover many fasci-nating things along the way.”

With these new tools, Segre says that the practice of medicine and diag-nosing and treating diseases will change. “Now that we have the tools to do it, we can start to look for disorders we previously hadn’t ex-pected to have microbial infections,” Segre says. Baylor’s Versalovic adds that they may be able to develop new diagnostic test.

However, Relman says it will be difficult to prove Koch’s postulates for a microbial community. Those postulates set the criteria that need to be fulfilled for an infectious agent to be the cause of a disease. Namely, the agent or microorganism has to

be present in all cases of the disease, isolated from someone with the dis-ease, cultured, and then cause dis-ease in a new host from which the agent is then recovered. “Causation is a really tough nut to crack,” Rel-man says. “What has emerged so far is a bunch of associations that no one can really be sure that the different-looking community is re-sponsible for, or whether it simply is a result of, disease.”

Instead, he says, longitudinal stud-ies will be needed in which people at risk for certain diseases, and their microbiomes, are followed over time. “You’re looking for an early change that predates the pathology,” Relman. “That’s going to be tough. It’s doable, but it’s going to take some really smart clinicians getting together with some willing subjects and good sci-entists and then being patient.”

In the long run, though, a swarm of prebiotics and probiotics could

be developed to encourage a healthy microbiome or to have an effect on a dysfunctional microbiome and bring the community into a better balance. “You might lack this important mi-crobe — and there’s some evidence now already that suggests there are some key elements missing in pa-tients with certain diseases — so we may have diagnostic tests that detect certain bacteria for human health and, when absent, indicate suscepti-bility to disease,” Versalovic says.

“I really think that this is a big deal and I think it is going to have a very big impact,” Weinstock says.

“The ultimate goal of this research is for us to understand how the meta-system works as a whole and to be able to predict how perturbations in the system impact the various parts.”



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F U N D E D G R A N T S

$282,202/FY 2009 $365,200/FY 2009METABOLOMIC INVESTIGATION OF BIOSIGNATURES OF CHRONIC COCAINE EXPOSURE Grantee: Chi Chen, University of Minnesota, Twin Cities Began: Sep. 1, 2009; Ends: Aug. 31, 2011In this work, Chen will use liquid chromatography/mass spectrometry-based approaches to identify small-molecule metabolites linked to chronic drug exposure or drug addiction. Chen and his colleagues will analyze changes to the metabolome due to chronic cocaine use to identify biosignatures in rats. Then, they will examine how treatment affects those biosignatures.

MARKERS FOR HCV-RELATED HCC: PLASMA PROFILING, TARGETED STRATEGIES AND VALIDATION Grantee: Laura Beretta, Fred Hutchinson Cancer Research Center Began: May 1, 2009; Ends: Feb. 28, 2014Using her new method to quantify a complex proteome, Beretta and her colleagues will look for proteins and protein isoforms that differ between patients with hepatitis C virus-related cirrhosis that have progressed to hepatocellular carcinoma and those with HCV-related cirrhosis without HCC.

PROTEOMONITOR

Grant Supports Proteomics Synchrotron Work

T h e C a s e Western Re-serve Univer-sity School

of Medicine announced it has been awarded a five-year, $4 million grant from the National Institutes of Health to fund the school’s synchrotron center, where, among other things, novel proteomics approaches are being developed.

While synchrotrons have historically been used in chemistry and physics, the life sciences, especially protein-related studies, are increasingly finding value in the technology. The grant, from NIH’s Nation-al Institute of Biomedical Imaging and Bioengineer-ing, continues a history of funding from the agency to the Case Center for Synchrotron Biosciences stretching back to 1995.

The Case center is based at Brookhaven National Laboratory in New York, where the National Syn-

chrotron Light Source, built in 1984 and operated by the US Department of Energy, is located.

Worldwide, there are about 60 synchrotrons with hundreds of beamline facilities. The Case center is one of six that receives NIH funding.

In the first year of the grant, the center will re-ceive about $1.1 million, and in each of the four remaining years, it will receive about $750,000.

In addition to paying for the eight employees at the center and three staffers who provide off-site sup-port from the university in Cleveland, Ohio, the first-year allotment includes funds for the purchase of a new detector for the cen-ter’s X-ray spectroscopy program for investigations into metal atoms in pro-teins at low concentrations and molecular structure around the metal, says Mark Chance, director of the center.

The funding from NIBIB supports technology in three technology cores at the center — the foot-printing core, based on the X28C footprinting beam-line, provides facilities for the study of protein and nucleic acid structure and function, including in vivo studies. Mass spec-based research, including novel proteomics approaches in-vented at the center, is also conducted at this core.

The center also has a macromolecular crystal-lography core based on the X29 undulating beam-line.

— Tony Fong

DATAPOINT

$828THOUSAND

FUNDING FOR AN AUSTRA-

LIAN PROJECT TO LOOK

FOR PROTEINS INVOLVED IN

MULTIPLE SCLEROSIS

Proteomics Notes

DENATOR, a Swedish sample prep firm, is heading up a consortium that received $427,000 from the EU EUROSTARS PROGRAMME to improve how human blood plasma samples are handled to help advance the discovery of blood-based protein biomarkers.

As part of the CHINESE HUMAN LIVER PROTEOME PROJECT,researchers have identified 6,788 liver proteins. In the Journal of Proteome Research, they also report a transcriptome data set of 11,205 genes.

BRUKER reports that it has received $10 million in orders from stimulus programs in the US, Japan, and Europe, and it expected more NMR, X-ray crystallography, high-end mass spectrometry, and other orders during the second half of the year.

PROTEOMICS Upstream



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$187,130/FY 2009 $232,500/FY 2009PHYLOGENETIC BINNING OFMETAGENOMIC SEQUENCE DATAGrantee: Eric Allen, University of California, San DiegoBegan: Aug. 24, 2009; Ends: Jul. 31, 2011Allen and his team will use this grant to “develop new computational methods for large-scale taxonomic clas-sification of metagenomic sequence data, applicable to raw reads as well as assembled contigs” and “develop software and protocols to use taxonomic data binning as a pre-treatment to increase efficiency of existing sequence assembly software,” the grant abstract says.

CROSS-SPECIES MICROARRAY-BASED GENOMICSELECTION: APPLICATION TO NONHUMAN PRIMATEGrantee: James Thomas, Emory UniversityBegan: Jan. 15, 2009; Ends: Dec. 31, 2009The plan for this grant is “to test and to demonstrate the capability of a newly developed genomic technology, microarray-based genomic selection” as a method to “use the available nonhuman primate genomic resourc-es as a springboard for population-based genomic se-quencing in a greater diversity of species,” according to the abstract.

INSEQUENCE

Complete Genomics Raises $45 Million in Series D

In late summer, Complete Genom-ics announced that it had raised $45

million in private equity from a Series D fund-ing round, which closed six months later than originally planned. As a result, the company, which anticipates reach-ing profitability next year, has pushed back its plans to launch its human ge-nome sequencing service from June 2009 to Janu-ary 2010. The funding adds to the $46 million that the company raised in three prior financing rounds.

The firm plans to se-quence 10,000 human ge-nomes next year using its proprietary sequencing technology. Previously, it was aiming to sequence 1,000 human genomes by the end of this year and 20,000 in 2010.

The “1,000 genome mark” has “slipped out”

by six months, and the company now expects to reach it by mid-2010, says Complete Genomics chairman, president, and CEO Cliff Reid. The firm is still targeting a price of $5,000 per human ge-nome for batches of ge-nomes when the service launches.

The six-month push-back is tied to the com-pany’s inability to raise new funding in a timely

manner, he says. In April, Complete Genomics first revealed that the closing of its Series D round was delayed, forcing it to cut costs.

“Our timing could not have been worse,” Reid says. “We started this fi-nancing the day that Leh-man Brothers failed and found that in Q4 and Q1, the private equity financ-ing world was really on hold.” Only in early April did those companies start to move toward making new investments again, he adds.

The funding will be suf-ficient to launch the com-pany’s human genome sequencing service in January and to build and scale up its commercial sequencing center, based in Mountain View, Calif., over the first six months of 2010 as the firm tran-sitions from an R&D to a services company, ac-cording to Reid.

Complete G enomic s, which currently has about 120 employees, also plans a “modest headcount in-crease.”

— Julia Karow

DATAPOINT

40NUMBER OF WORM

GENOMES RESEQUENCED

BY THE BEIJING GENOMICS

INSTITUTE TO DEVELOP A

GENETIC VARIATION MAP

FOR SILKWORM.

Sequencing Notes

LADATECH has filed suit against ILLUMINA,saying that the sequencing vendor’s Genome Analyzer and related products and services infringe a patent originally assigned to GENELABS and now held by LadaTech. The patent was issued in 2000 and covers a “method of amplifying a mixture of DNA fragments by repeated linker/primer replication.”

HELICOS BIOSCIENCES installed two systems and recorded $371,000 in revenue during the second quarter, according to its SEC filings. As of Aug. 14, the company reported having $5 million in cash and equivalents. According to Helicos President Steve Lombardi, in late summer the company had a total of seven instruments installed, including four “placements” by Helicos and three systems ordered by customers.

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RNAiNEWS

UMass, Whitehead Fire New Salvo in Tuschl IP Suit

T he University of Massachu-setts and the W h i t e h e a d

Institute for Biomedical Re-search returned fire against the Max Planck Institute and Alnylam Pharmaceu-ticals in their ongoing le-gal battle, counterclaiming that, among other things, Max Planck inappropri-ately sought to replace the Whitehead-appointed law firm overseeing prosecution of the intellectual property at issue in the case.

UMass further argued in its counterclaim that a key aspect of the disputed RNAi technology — the 3’ over-hangs commonly incorpo-rated into siRNAs — was an inherent feature of the RNAi molecules described in a patent application filed prior to another patent ap-plication from Max Planck that specifically claims the overhangs.

The litigation began in June when Alnylam and

Max Planck sued UMass, Whitehead, and the Mas-sachusetts Institute of Technology for allegedly misappropriating certain RNAi inventions, most notably the use of 3’ over-hangs on siRNAs, from the Tuschl-II patent family and included them in pat-ent applications from the Tuschl-I IP estate.

B o t h Tu s c h l - I a n d Tuschl-II generally relate

to the use of siRNAs, 21 to 23 nucleotides in length, to target specific mRNA degradation in mammals. However, Tuschl-II in-cludes claims on two- to three-nucleotide-long 3’ overhangs. Both are named after former Max Planck researcher Thomas Tuschl, an Alnylam co-founder who is now a researcher at Rockefeller University.

Alnylam acquired the ex-clusive therapeutic rights to the Tuschl-II family from the IP’s sole owner, Max Planck, but shares therapeutic rights to the Tuschl-I estate — invented at Max Planck, Whitehead, MIT, and UMass — with Merck subsidiary Sirna Therapeutics and, to a limited degree, RXi Phar-maceuticals.

Alnylam and Max Planck maintained in their law-suit that if any Tuschl-II inventions are included in Tuschl-I patents, Sirna, RXi, and any other compa-nies sublicensing Tuschl-I will “unfairly gain access to the Tuschl-II property without paying consider-ation for a license.”

— Doug Macron

DATAPOINT

$672THOUSAND

AMOUNT A SUBSIDIARY OF

NEW ZEALAND’S GENESIS

RESEARCH AND DEVELOP-

MENT WILL RECEIVE TO DE-

VELOP SINGLE-STRANDED

RNAI TECHNOLOGY

RNAi Notes

Australia-basedBENITEC received a notice of allowance from the US Patent and Trademark Office for its application for the use of multiple-promoter expression cassettes for simultaneous RNAi delivery.

SILENCE THERAPEUTICSand DAINIPPON SUMITOMO PHARMAare collaborating to work on an siRNA drug-delivery system. Silence will use its proprietary siRNA molecules with its in-house AtuPlex delivery technology.

SANTARIS PHARMAand British biopharmaceutical firm SHIRE will be using locked nucleic acid technology to develop drug candidates for rare genetic disorders. Shire will be doing most of the development as Santaris expands its therapeutic program.


$162,000/FY 2009 $282,600/FY 2009GLYCOBIOLOGICAL ANALYSIS OF PLASMODIUM-VECTOR HOST INTERACTIONSGrantee: Rhoel David Ramos Dinglasan, Johns Hopkins UniversityBegan: Apr. 1, 2009; Ends: Mar. 31, 2011To identify protein-glycan interactions between Plasmo-dium ookinete and the mosquito midgut, Dinglasan and his colleagues will use RNAi to knock down mosquito glycosyl- and sulfo-transferases and analyze midgut glycoconjugates during Plasmodium infection. They will also study the knockout proteome with mass spec.

DOUBLE-STRANDED RNA-MEDIATED SIGNALINGPATHWAY AND GENE SILENCINGGrantee: Yi Liu, University of Texas Southwest Medical CenterBegan: Apr. 1, 2009; Ends: Mar. 31, 2013With forward and reverse genetic approaches, Liu and his lab plan to characterize the signaling pathway of dsRNA-induced gene transcription. They will also study the role of DNA damage-induced small RNA. This “will reveal the role and the mechanism of RNAi in DNA repair and in maintaining genome stability,” says the abstract.

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$370,800/FY 2009 $181,024/FY 2009DEVELOPMENT OF RIP-CHIP METHODS AND TILEDARRAYS TO IDENTIFY FUNCTIONAL ELEMENTSGrantee: Michael Whitfield, Dartmouth College Began: May 1, 2008; Ends: Apr. 30, 2011Whitfield will use recombinant RIP-chip to study how RNA-binding proteins mediate gene expression on a genome-wide scale. He will identify the cis-acting regula-tory sequences in mRNAs bound by specific RNA-bind-ing proteins by using limited nuclease digestion and tiled mRNA arrays, and then will determine which miRNAs associate with the argonaute family of proteins.

NONPARAMETRIC ANALYSIS OF REVERSE-PHASE PROTEIN LYSATE ARRAY DATAGrantee: Jianhua Hu, University of Texas MD Anderson Cancer CenterBegan: Aug. 1, 2009; Ends: Jul. 31, 2011To enable more reliable analysis of protein lysate arrays, Hu will use a “monotone nonparametric response curve to all samples on the same array,” according to the abstract. This includes “modern shrinkage ideas in sta-tistics” to improve quantification and using “wild-boot-strap” to assess uncertainties in protein concentrations.

BIOARRAYNEWS

Affy Inks Deal with Beckman for Custom Tools

A ffymetrix and B e c k m a n Coulter have p a r t n e r e d

to create an automated tool and protocol for ge-nomic research that will pair Beckman’s liquid-handling instrumentation with Affy’s menu of array-based assays.

Under the terms of the deal, Affy and Beckman w i l l co - deve lop A f f y-specif ic configurat ions for Beckman’s Biomek FX Dual Arm Multichannel-Span 8 Liquid Handler. The companies claim that the combination of the Biomek with Affy’s exist-ing array cartridge plat-form as well its newer GeneTitan instrument will provide a standardized system containing all of the components necessary to run Affy genotyping and gene-expression assays.

According to Affy, the deal with Beckman will help fill a gap for custom-

ers performing higher-throughput studies.

It also comes at a time when other array vendors are looking to provide stan-dardized target-preparation options for their custom-ers as the size of projects increases. Agilent Tech-nologies, for example, said recently that it plans to launch an automated liquid-handling workflow in coming months.

Launched last year, the GeneTitan enables users to run expression-profiling assays in array plates de-signed to process 16, 24, or 96 samples. Now, the chip maker plans to launch next-generation genotyping assays for use on the system this fall. Unlike the gene-expression assays which contained legacy content, Affy will enable users to survey newly generated cat-alog and customizable con-tent using its genotyping assays as part of what both Affy and its rivals predict will be a second round of large genome-wide associa-tion studies.

Being able to streamline the front end of its as-say workflow is therefore “very important” for Affy, according to President and CEO Kevin King.

“With automated target prep robotics in front of our GeneTitan System, our customers will benefit from walk-away automa-tion from prepared sam-ples all the way through array processing and data generation,” King said in a statement.

– Justin Petrone

DATAPOINT

$6.2MILLION

NEW FUNDING RAISED

BY WAFERGEN

BIOSYSTEMS, MAKER

OF GENE EXPRESSION

AND GENOTYPING

SYSTEMS.

Microarray Notes

EXIQON plans to out-source the manufacturing of all of its research-related products, including its microRNA arrays, by the beginning of next year. The move is part of restructur-ing to cut costs and reach profitability.

KINEXUS, a 10-year-old proteomics company based in Vancouver, BC, will begin offering custom-ers the ability to screen kinases using its internally developed protein kinase chip. The microarray will include at least 200 differ-ent human protein kinases.

Researchers at the UNI-VERSITY OF DUBLIN’sSmurfit Institute of Genet-ics compared chimp and human protein and DNA sequences to identify three human genes that lack orthologues in other spe-cies. The work, published in Genome Research,suggests that the human genes evolved from non-coding DNA.

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$1,063,773/FY 2008 $135,000/FY 2009TEXT MINING INFRASTRUCTURE FOR THE ENTIREBIOLOGICAL LITERATUREGrantee: Gully Burns, University of Southern CaliforniaBegan: Sep. 1, 2009; Ends: Aug. 31, 2012This grant will fund the construction of SciKnowMine, a shared computational framework that “scales up processing large datasets across different communities through the automated mining of text, images, and other amenable media at the scale of the entire literature.” The system will support the actions of bio-curators through a generic set of Web services that can be specialized.

REPLICA EXCHANGE STMD FOR CHARMM: A POTEN-TIALLY LARGE ADVANCE IN BIOPHYSICAL COMPUTINGGrantee: Thomas Keyes, Boston University Began: Sep. 1, 2009; Ends: Aug. 31, 2011This award supports continued development of the CHARMM biosimulation application. The project aims to add the capability to use replica exchange statistical temperature molecular dynamics. The STMD algorithm and its extension to replica exchange “have substantially outperformed competing enhanced sampling algorithms in all tests,” the abstract says.

BIOINFORM

Pharma Calls for a Pre-competitive Approach

W hile large pharma-ceutical f i r m s

aren’t known for being generous with their data, a small group of pharma sci-entists is looking to change that perception with a call for pre-competitive bioin-formatics projects and en-hanced data sharing in the industry.

In an opinion piece pub-lished in the September is-sue of Nature Reviews Drug Discovery, computational biologists from AstraZen-eca, GlaxoSmithKline, and Pfizer argue that “high-quality, open and acces-sible data are the foun-dation of pre-competitive research, and strong pub-lic-private partnerships have considerable poten-tial to enhance public data resources, which would benefit everyone engaged in drug discovery.”

They add that many com-panies are already begin-

ning to embrace this idea, and that for some firms, “the focus has moved from the vigorous pur-suit of intellectual prop-erty towards exploration of pre-competitive cross-industry collaborations and engagement with the public domain.”

The paper comes in the wake of several initia-tives that aim to encour-age pharma scientists to

open up a bit, including the non-profit Sage Bionet-works, founded by former Merck scientists, which plans to build a pre-com-petitive platform for an-notated models of human disease; the cross-indus-try collaborative initiative Pistoia Alliance, which is developing standards for non-competitive aspects of the drug-discovery work-flow; and the European public-private Innovative Medicines Initiative, a col-laborative effort in which several pharmas are pool-ing resources in hopes of lowering the overall costs of drug development.

The borders around this emerging pre-competitive informatics space have yet to be defined, the authors of the Nature Reviews paper wrote, but noted that a first step is creating public-private partnerships that can expand on existing public resources to create “a series of foundational informatics resources.”

In addition, pharma firms need to explore new types of IT infrastructure and tool development.”

— Vivien Marx

DATAPOINT

$14.3MILLION

AMOUNT THE EUROPEAN

BIOINFORMATICS INSTI-

TUTE RECEIVED FROM THE

UK’S BIOTECHNOLOGY AND

BIOLOGICAL SCIENCES

RESEARCH COUNCIL

Bioinformatics Notes

SYMYX TECHNOLOGIES established a new software research and development center in Bangalore, India. The company plans to hire 30 to 35 staffers for the center.

CLINICAL TRIALS & SURVEYSCORPORATION, a privately held clinical trials management firm, is set to make raw and processed genomic data available to clinical researchers as part of its StudyCTMS database. Under the program, C-TASC will accept gene data from investigators in either raw or processed format for upload.

Scientists at VIRGINIA TECH will use a three-year, $1.4 million grant from the NATIONAL SCIENCE FOUNDATION to expand GenoCAD — a user-friendly software package that enables scientists to design genetic constructs using a genetic “parts list.”

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$390,000/FY 2009 $746,861/FY 2009METABOLOME AND PROTEOME PROFILES OF EMPHYSEMA AND AIRWAY DISEASEGrantee: Russell Paul Bowler, National Jewish HealthBegan: Apr. 9, 2009; Ends: Mar. 31, 2013NHLBI issued this grant to determine a possible molecu-lar basis for the different smoking-related phenotypes under the umbrella of chronic obstructive pulmonary disease. Bowler will use “proteomic and metabolomic approaches to identify new plasma biomarkers that are associated with COPD phenotypes” and then study those biomarkers further, says the abstract.

VALIDATION AND EXTENSION OF AN EXISTING RISK MODEL FOR LUNG CANCERGrantee: Carol Etzel, University of Texas, MD Anderson Cancer CenterBegan: Aug. 12, 2009; Ends: Jul. 31, 2011This NCI grant will allow Etzel’s team to build on an epidemiologic risk model for lung cancer by incorporat-ing a genetic biomarker and then assessing it in 1,000 cases and 1,000 controls. The assay to be studied, the cytokinesis-block micronucleus assay, measures chro-mosome damage and other cellular events.

PHARMACOGENOMICSREPORTER

Celera Hones Panel for Non-Small Cell Lung Cancer

C elera has vali-dated its mass spectrometry-based approach

for identifying circulating protein biomarkers that detect non-small cell lung cancer at all stages and is currently in the process of deciding whether to com-mercialize a prognostic as-say based on a six- or a nine-protein marker panel.

In collaboration with the New York University Langone Medical Center, Celera recently announced that it had replicated a “novel mass spectrometry-based approach to identify and validate circulating protein biomarkers that detect NSCLC in an inde-pendent cohort of individ-uals with lung cancer.”

Celera presented results from early studies in April at the American Associa-tion for Cancer Research annual meeting. Based on results from these studies, Celera said at the time that

it was “expediting” com-mercialization of its mass spectrometry-based lung cancer test.

Celera estimates the test would be launched by 2012. The test would have been launched much later were it not for these promising preliminary re-sults, which allowed the company to move up com-mercialization plans for the lung cancer test by as

much as one or two years.Accord ing to Celera

s p ok e s p e r s o n D a v i d Speechly, results from the most recent study involving the lung cancer diagnos-tic confirm the company’s “indirect” biomarker dis-covery approach by look-ing at lung cancer tissue from surgical resections, lung tumor cell lines, and the medium that the cell lines were grown in.

“Typically, in the detec-tion of markers that are present at higher levels in the serum, one would use mass spectrometry to in-terrogate the serum itself and compare the results from serum of lung cancer patients with serum from healthy smokers,” Speech-ly says. In contrast, Cel-era’s approach “provides much less complexity for the mass spectrometry analysis.”

Celera’s clinical analyses have resulted in the vali-dation of a nine-biomarker immunoassay on patient samples with Stage I NSCLC, which may be able to detect disease in the earliest stages.

— Turna Ray

DATAPOINT

2GENEUITY CLINICAL

RESEARCH SERVICES VALI-

DATED AND LAUNCHED

TWO ASSAYS TO SCREEN

PATIENTS FOR KIDNEY DAM-

AGE FROM DRUGS IN CLINI-

CAL DEVELOPMENT.

PGx & Molecular Dx Notes

A genome-wide asso-ciation study published in the Journal of the American Medical As-sociation reports that the CYP2C19*2 variant of the cytochrome P450 gene influences Plavix response and treatment outcomes. Researchers at the UNI-VERSITY OF MARYLAND SCHOOL OF MEDICINEstudied more than 400 Amish people to find genet-ic variants that affect drug response.

NANOSPHERE has filed a 510(k) application to the US FOOD AND DRUG ADMINISTRATION for marketing clearance of its Verigene SP Respiratory Virus Assay, which detects influenza and respiratory syncytial virus.

In a study of type 2 diabetes in central Indiana, BIO-SERVE will provide clinical biosample and other servic-es to the FAIRBANKS IN-STITUTE FOR HEALTHYCOMMUNITIES.

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Innovation Through ImagingSanjiv Sam Gambhir discusses how systems biology approaches and biomarker research are shaping the way imaging is used in detecting early-stage cancer.

Sanjiv Sam Gambhir is the director of the Molecular Imaging Program and the Canary Center for Can-cer Early Detection, both

at Stanford University. GT’s Jeanene Swanson spoke with him about how molecular imaging is changing the way disease is detected and treated. What follows are excerpts of that conversa-tion, edited for space.

GENOME TECHNOLOGY: What role does imaging play in early disease detection?SANJIV SAM GAMBHIR: We feel that molecular imaging will have a significant role in the early detec-tion of cancer. Right now, we see it as the three I’s: identify, isolate, and intervene. The ‘identify’ is a low-cost screening test that involves blood bio-markers or urine biomarkers. ‘Isolate’ is where imaging comes in, to isolate where in the body that disease is, if, in fact, the blood test was correct. Then you go to the third ‘I,’ which is to ‘intervene.’ You do it at such an early stage you’re able to much more effectively treat the disease.

GT: What new techniques are you working on?SSG: We’re developing several new strategies that are designed to detect much smaller disease foci than what is currently possible. One strategy is using ultrasound. You can inject into the body bubbles and the bubbles are targeted to blood vessels growing

in early cancer. The ultra-sound is imaging the lo-cation molecularly of new blood vessels that are feed-ing the cancer.

Another strategy we’re de-veloping is based on pho-toacoustic imaging. The idea here is that light goes in, interacts with imag-ing agents, and produces sound. The advantage of that is you now can develop imaging agents that can leave blood vessels and go and interact with molecular targets on the surface of cancer cells.

A third technique is Raman mo-lecular imaging. In Raman imaging, light goes to a target tumor site, interacts with an imaging agent that scatters the light, and we detect the Raman scatter. And that ends up being very sensitive. We can take ad-vantage of systems biology in that we can do multiplexing, we can target many different molecular events and see a separate signal from each one. One of the problems with molecular imaging is it’s not highly multiplexed — you can interrogate one thing at a time, maybe a couple things at a time. With Raman, we can interrogate 20 [or] 30 things simultaneously. In Ra-man, light gets scattered inelastically. Inelastic light scattering can allow you to interrogate different proper-ties of the tumor, for example.

The hope is that by syncing the low-cost screening through blood test-ing to highly sensitive, highly multi-

plexable molecular imaging strategies, one can really make a significant shift in earlier detection of disease.

GT: How does molecular imaging make use of bio-marker research?SSG: Molecular imaging is a lot like the field of drug development; that is, you

have to start with a molecular target. In order to build imaging agents spe-cific for that target, you [have] got to know what target to go after. Now, we don’t need the target to be able to control the cell because we just want to detect it — not treat it — but sometimes the targets are the same.

How do we go after different mo-lecular targets? We do our own biomarker discovery: we look for, in tissues, what biomarkers are on the surface of cells [or] within cells that make them unique from nor-mal cells. We sometimes leverage off of biomarkers being discovered by the pharmaceutical industry. In each case, the idea is that we’re able to find biomarkers that we can build imag-ing agents towards, and a lot of the same techniques — proteomics for discovering biomarkers in the blood — have been also used for finding biomarkers in tissue.

Systems biology and other pro-teomics techniques are helping us also to understand which biomarkers we should target from an imaging perspective.

Q&A: SANJIV SAM GAMBHIR Downstream

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CASE STUDY Downstream

The Peptide BlockadeScientists demonstrate that novel peptides can block HIV infection by targeting protein-protein interactions.By Jeanene Swanson

Sc ien t i s t s h ave u s ed molecular eng ineer-ing techniques and a follow-up cell-based as-say to block HIV entry

into cells. In their work, published in August in the Proceedings of the National Academy of Sciences, they took advantage of the fact that engi-neered peptides can stably interact with cell surface proteins to block HIV infection of cells. In the future, the technique could be used as an alternative to current therapies that rely on antibody-based drugs, says lead author Sam Gellman, a chem-ist at the University of Wisconsin, Madison.

For many viruses — including HIV, influenza, Ebola, and the se-vere acute respiratory syndrome vi-rus — protein-protein interactions between viral and host proteins are important for the virus to be able enter the cell it infects. In this study, Gellman’s team created a set of peptide-like molecules that were then used to successfully block HIV infection in human cells in an in vit-ro cell-based assay. The assay work was done by Gellman’s collabora-tors, John Moore and Min Lu at the Weill Medical College of Cornell University.

“If you look at biological systems at a molecular level, it’s clear that what nature tells us is you want big, folded molecules to do complicated tasks, not the small molecules that most organic chemists tend to work with,”

Gellman says. “For a number of years, we’ve been interested in try-ing to take inspiration from proteins to create new kinds of molecules, basically by using dif-ferent kinds of build-ing blocks, in our case

-amino acids instead of -amino acids.”

Their synthetic peptides, which they’ve named foldamers, make a modest tweak to the backbone of the amino acid that ends up having a large functional effect. Instead of one carbon at the heart of the mol-ecule, which is called an -amino acid and is the usual structure, they engineered the amino acid to have two carbons. These beta amino ac-ids change the shape of the result-ing peptide, which they then used to bind to a crucial HIV membrane fusion protein, gp41, locking it into place and preventing it from letting the virus enter the cell.

“So essentially there’s the potential for a parallel universe of beautifully complex, folded molecules of either pure -amino acids or mixtures of

- and -amino acids,” Gellman says.

In the past, attempts to prevent infection by interfering with host-cell protein-protein interactions have not had widespread success, he says. Because most drugs are small molecules, they’re not very effective at disengaging interactions between

macromolecules like proteins. Smaller pep-tides work better, but they’re broken down faster by enzymes in the body and so need to be administered of-ten and in large doses. Gellman’s foldamers are useful in that the two-stage design ap-

proach he employed — first creating a -peptide and then chemically “ri-gidifying” the backbone — created peptides that are more resistant to natural degradation.

In a cell-based assay using one T-cell-line-adapted strain and three primary isolates of HIV, the Cor-nell team showed that the peptides prevented infection of a TZM-bl cell line. Although it is not clear that the foldamers themselves could ever be used as anti-HIV drugs, Gell-man says, their study proves that using modified peptides to disrupt protein-protein interactions is a new way to think about designing mol-ecules for antiviral therapies and other biomedical applications.

He hopes that his method will both enlighten the field and be broadly applicable in the future. “Perhaps you could create things that would mimic the recognition surfaces dis-played by proteins and then use those things, as we use them in this [paper] — to block biomedically important protein-protein interac-tions,” Gellman says.

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Events MEETINGS AND DEADLINES


ConferencesDATE CONFERENCE ORGANIZER LOCATION CATEGORYOct 4-7 AIRI Annual Meeting Association of Seattle General

Independent Research Institutes

Oct 5-6 Critical Assessment Northwestern University Chicago, Ill. Bioinformatics of Microarray Data Analysis

Oct 5-7 Clinical Proteomic Technologies for NCI Bethesda, Md. Proteomics Cancer Annual Meeting

Oct 5-8 International MGED Meeting TGen Phoenix, Ariz. GenomicsOct 6-9 NIH Research Festival NIH Bethesda, Md. GeneralOct 17-21 Neuroscience 2009 Society for Neuroscience Chicago NeuroscienceOct 20-24 ASHG Annual Meeting American Society of Honolulu Genetics

Human GeneticsOct 27-30 Genome Informatics Cold Spring Harbor Cold Spring Bioinformatics

Laboratory Harbor, NYOct 29-31 11th International EMBL European Molecular Heidelberg, Student

PhD Student Symposium Biology Laboratory GermanyNov 2-4 Discovery on Target CHI Boston PharmaNov 9-10 Burrill Personalized Medicine Meeting Burrill & Company San Francisco Personalized

medicineNov 9-11 Northeast Regional Life Sciences Cornell University Ithaca, NY Core labs

Core Directors MeetingNov 16-17 The Science of Biobanking CHI Philadelphia ClinicalNov 18-19 Personalized Medicine Conference Harvard Partners Center Boston Personalized

medicineNov 19-22 AMP Annual Meeting Association for Molecular Kissimmee, Fla. Clinical

PathologyDec 5-9 ASCB Annual Meeting American Society San Diego Cell biology

for Cell Biology

2010Jan 4-8 Pacific Symposium on Biocomputing Big Island, Hawaii BioinformaticsJan 9-13 Plant and Animal Genome Meeting XVIII Scherago International San Diego GenomicsJan 11-15 PepTalk CHI San Diego ProteomicsFeb 3-5 Molecular Medicine Tri Conference CHI San Francisco TranslationalFeb 18-22 AAAS Annual Meeting AAAS San Diego GeneralFeb 24-27 Advances in Genome Gcorp Marco Island, Fla. Genomics

Biology and TechnologyFeb 28-Mar 5 Pittcon 2010 Pittsburgh Conference on Orlando Proteomics

Analytical Chemistry and Applied Spectroscopy

Mar 7-10 US HUPO US HUPO Denver ProteomicsMar 18-20 AUTM 2010 Annual Meeting Association of University New Orleans, La. Tech transfer

Technology ManagersMar 20-23 ABRF 2010 Association of Sacramento, Calif. Core labs

Biomolecular Resource Facilities

Apr 17-21 AACR 101st Annual Meeting AACR Washington, DC CancerApr 20-22 Bio-IT World Conference & Expo CHI Boston BioinformaticsApr 24-28 Experimental Biology AFMR Anaheim, Calif. General


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OCTOBER 1 Application deadline for the NIH grant, APPLICATION AND USE OF TRANSFORMATIVE EMERGING TECHNOLO-GIES IN CANCER RE-SEARCH. These funds will reward innovative, high-risk research to evaluate the performance of emerging technologies for studying cancer. The grant is part of NCI’s broader Innovative Molecular Analysis Tech-nologies Program.

OCTOBER 2 Application deadline for the NIH award, PILOT-SCALE LIBRARIES FOR HIGH-THROUGHPUTSCREENING. As part of the NIH Roadmap Molecu-lar Libraries Program, this money will support the generation of chemical libraries for high-through-put biological screening by the Molecular Libraries Probe Production Centers Network.

OCTOBER 7 Application deadline for the NSF grant,INTEGRATIVE, HYBRID & COMPLEX SYSTEMS,which is meant for re-search and development in nanosystems, among other things. Integrative devices could include system-in-a-package and system-on-a-chip technologies.

OCTOBER 9 Application deadline for the NIH grant, MODELING THE SCIEN-TIFIC WORKFORCE. This money will help develop computational models of

the dynamics of the scien-tific workforce in the US.

OCTOBER 15 Application deadline for the INSTI-TUTIONAL CLINICAL AND TRANSLATIONAL SCIENCE AWARD. These funds will support new re-sources for investigators to further advance basic and translational research.

OCTOBER 20 Applica-tion deadline for the NIH grant, REVOLUTIONARY GENOME SEQUENCING TECHNOLOGIES – THE

$1,000 GENOME. The money — for researchers, organizations, and small businesses — will support the development of new technologies for low-cost, high-throughput DNA sequencing, with a goal of sequencing a mammalian-sized genome for $1,000.

OCTOBER 21 Applica-tion deadline for the grant, 2010 NIH DIREC-TOR’S PIONEER AWARD PROGRAM. This grant will support scientists who propose “pioneering and

possibly transforming ap-proaches to addressing ma-jor biomedical or behavioral challenges.”

OCTOBER 28 Application deadline for the grant, 2010 NIH DIRECTOR’S NEWINNOVATOR AWARD PROGRAM. These funds will go to investigators who propose “bold and highly innovative new research ap-proaches that have the po-tential to produce a major impact on broad, important problems in biomedical and behavioral research.”

Deadlines

MEETINGS AND DEADLINES Events


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Blunt End HUMOR, WE HOPE

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Conquer the next wave of genomic discoveries:Visit booth #415 or www.axiom.affymetrix.comAnd attend our seminar:New Microarray Solutions for GWAS and CytogeneticsWed., Oct. 21, 11:30 A.M.–1:00 P.M., Room 314, Convention Center

Our next-generation genotyping technology allows you to leverage high-value markers from our proprietary data set, public databases, and your scientific collaborations to find new genetic associations. The Axiom™ Genotyping Solution includes array plates with unique genomic content, complete reagent kits, analysis software, and the new GeneTitan™

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The Axiom Genotyping Solution — Conquer the next wave of genomic discoveries.

Revolutionize life


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Revolutionize lifehmpdacc.org/doc/GT_20091001_Oct_2009.pdf2009/10/01 · Meredith W. Salisbury, Editor What do you think of Genome Technology? Let me know how we’re doing by e-mailing

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