thegenome...thegenome newtechnology nowtechnologyisallowingresearchersto address this complicated...
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n just one generation medicine willtake a huge leap forward. That is, ifresearchers are right about how datafrom the human genome can be
used to address disease. There has been a greatdeal of optimism about how sequencing thehuman genome might create new diagnosticsand new medicines.
Ten years ago, when we had our first lookat the human genome, it was thought that theera of personalized medicine was just aroundthe corner. In reality, it has proven to be muchmore difficult to take the discoveries stem-ming from the unraveled genome in the laband translate them to therapies.
Biology, it turns out, is far more compli-cated than first thought. Researchers have dis-covered there are plenty of disease-relevant
vance, says genomics, as a discipline, needs tobegin early in the development process.
“The goal of the human genome project(HGP) was to understand, sequence, and de-fine the human genome,” he says. “This goalwas met, absolutely. The HGP deliveredunder budget and before the actual deadline.Genomics as a science is only about 15 yearsold, and the real fruits of those initial forays ofapplying genomics to developing medicinesare just beginning to emerge.”
Dr. Turi says in retrospect, there was prob-ably a little too much hype around genomicsinitially; there was a lot of excitement and en-thusiasm from the scientific community thatgenomics could and would change the waydrug discovery and development would bedone.
Denise Myshko
targets available, but that doesn’t automati-cally mean a therapy can be developed to ad-dress that target.
“Identification of genetic changes that arecausing a disease doesn’t always lead to devel-opment of drugs that can cure or slow downthe disease progression,” says Sridaran Nate-san, Ph.D., scientific site head of R&D andhead of external innovation and parftnering atSanofi-Aventis. “The question remains: is thegene druggable? In other words, with thetools and technologies currently available, canwe develop small molecules or biologics thatcan modulate the function of the gene attrib-uted to the disease?”
Thomas Turi, Ph.D., VP, science and tech-nology, discovery and translational services,and VP, biomarker center of excellence, at Co-
Despite the promise of advancements inunderstanding the human genome, significantchallenges remain for bringing products to marketthat take advantage of this evolving discipline.
I
20 January 2011 � PharmaVOICE
TheGenome:TheNext 10Years
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The Genome
NewTechnologyNow technology is allowing researchers to
address this complicated science. New andbetter tools are being developed that canbring down the cost of gene sequencing, dothe sequencing faster, and provide ways formanaging and assessing the vast amount ofgenerated data.
Some industry experts are still optimistic,despite the initial setbacks, that the knowl-edge and insights gained from sequencing thegenome, as well as the technology advance-ments, will be truly transformative in the next10 to 20 years, and that there will be a greatdeal of investment in this area.
Panna Sharma, CEO of Cancer Genetics,says the advances that will be made in apply-ing genomic information to personalizedmedicine will be staggering.
“There is going to be a tidal wave in thenext 10 years to 12 years,” he says. “The last10 years were about putting all of the tech-nology, processes, and infrastructure togetherand ensuring that they worked consistentlyand reliably. The expectation that we wouldbe pumping out dozens of new drugs by nowwas not realistic. This is just not feasible giventhe number of years it takes to get a new drugto market and given the number of years ittakes to put a new, proven research and devel-opment infrastructure in place.”
Mr. Yousaf agrees that this is a revolution-ary period in the life sciences.
“Already there are pilot trials that are ana-lyzing the sequence of a tumor, the sequenceof the normal cells of the patient, and then re-searchers are looking at the metabolic vulner-ability of the tumor as a way to design a newdrug therapy,” he says. “Within 10 years, thistype of methodology should become routinein the treatment of cancer and genetic dis-eases.”
Mr. Sharma points out that the pieces arenow in place to move the discipline forward.
“We have a better understanding of thegenome’s nuances, and a number of companiesare making rapid strides in this area,” he says.“Technology is now robust in a way that was-n’t expected even five years ago. Costs arecoming down rapidly. And the regulatorybodies, the major pharma and biotech compa-nies, and government consortium are workingaggressively on initiatives to put some param-eters around how they can compare and syn-thesize genomic data and how this will im-pact clinical trials. All of the forces are comingtogether.”
Dr. Cohen says sequencing technology hasraced far ahead of our ability to synthesize andmake sense of the massive amounts of infor-mation generated.
“This requires sophisticated informationtechnology, a deep understanding of biology,and lots of creativity,” he says. “While ge-nomics has not yet fulfilled its promise, this isonly because of our simplistic assumption thatsimply having DNA sequence information
“ Itwas very simple at first: find genes.Later, the process becamemorechallenging.”
DR.THOMASTURI / Covance
ImplementingGenomic Strategies
» Begin by incorporating genomics or
genomic-based approaches early in
discovery and development programs. It
takes time to understand the biology and
variations within patients.
» In addition to identifying a gene’s
relevance to disease, identify the
pathways affected by a gene. If the gene
is not“druggable,”it may be possible to
develop a drug downstream or upstream
from a particular target.
» Work internally and externally with
partners who understand genomics and
how to apply that in the drug discovery
and development environment.
Source:PharmaVOICE
TIPS
“When we first entered into genomics per-haps there were some misconceptions abouthow easy it would be to go from a set of DNAsequences to a validated target to a fullylaunched drug discovery and developmentprogram,” he says. “We forgot that there wasa little something called biology in the mid-dle of the process.”
Additionally, Shaf Yousaf, president, ge-nomic analysis, at Life Technologies, says afterthe first genome was sequenced scientists did-n’t understand what it all meant, which led tosome initial disappointment.
“The number of genes in the genome was20,000 instead of the 100,000 that some ex-pected,” he says. “At the time, some thoughtthis was called ‘junkDNA’ simply because thedata weren’t well understood.”
To be fair, sequencing the human genomehas led to tremendous advances in knowledge.
“The list of clinically useful genetic markersis growing, and the list of drugs that are bestused with the aid of genetic information is alsoexpanding,” saysOrenCohen,M.D., chiefmed-ical and scientific officer at Quintiles. “Exam-ples includeHER-2 andKRAS testing to guidecancer treatment; cytochrome P450 testing toguide warfarin dosing and estimate the likeli-hood of response to clopidogrel; HLA typing toestimate the likelihood of developing abacavirhypersensitivity syndrome; and IL-28B testingto guide therapy for hepatitis C infection.”
Dr. Cohen says sequencing technologycontinues to advance at an astonishing rate.
“With today’s sequencing technology, itis possible to accurately sequence a humangenome in about a 1.5 days at a cost of lessthan a tenth of a penny per thousand basepairs,” he says. “This extraordinary pace oftechnological breakthroughs has enabled usto study genomics at a population and dis-ease-specific level. Although still in its in-fancy, we’re starting to be able to answerquestions about genetic markers of disease,prognosis, response to therapy, and drug tox-icity.”
“ Eventually, a genomic test is goingto be as routine as a blood test.”
DR.CLIFFORDREID / Complete Genomics
21PharmaVOICE � January 2011
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available would be sufficient to yield clinicallymeaningful insight, but the future is verybright indeed.”
The Economics of SequencingEfforts to sequence the genome have been
challenged by economic issues, says CliffordReid, Ph.D., chairman, president, and CEO ofComplete Genomics.
“When the first human genome was se-
quenced in 2000, there was a real groundswell of interest in understanding the geneticbasis of disease based on a working hypothe-sis that a very small portion of the humangenomewasmedically relevant to uncover themedical secrets and the rest was unimpor-tant,” he says. “This supposition turned outnot to be true. There is a significantly largefraction of the genome that has medical rele-vance. But the measurement tools available atthe time were too expensive. No researchercould go through these large portions of thegenome to determine the genetic cause of dis-ease and then conduct a study big enoughbased on the findings.”
Several promising technologies in devel-opment nowmaymake the “druggabilty” lessof an issue in the future, and if these efforts aresuccessful they will undoubtedly open thedoor for faster development of new classes oftherapies for a variety of diseases.
“The latest estimate is that in five years thecost to sequence a complete genome could bejust a few thousand dollars or less,” Dr. Nate-
san says. “This is going to help the pharma-ceutical industry significantly. There are a lotof diseases that we would like to understandin greater detail at the genomic level but thecosts have been very prohibitive; it used tocost hundreds of thousands of dollars to se-quence a human genome. Pharma companieswill be able to put efforts into undertakinglarger studies to understand disease mecha-
The Genome
“ Knowledge aboutdiseasebiology keeps changing, and ourunderstanding of diseasemechanisms keeps getting better.”DR.SRIDARANNATESAN / Sanofi-Aventis
Personalized MedicinesAre Shaping R&D
Personalized medicine development is lead-
ing companies to change their R&D para-
digms, including how they make go/no-go
decisions,according to a recently completed
study by the Tufts Center for the Study of
Drug Development.
TThhee ssttuuddyy ffoouunndd::
» The magnitude of resources required to
create personalized medicines means
developers must team with multiple
external partners, presenting challenges
for project stewardship and intellectual
property rights.
» Biomarkers increasingly are used to
better understand patient response, but
companies still cannot use biomarker
data to support approval until the
regulators’ capacity to evaluate the
information catches up to the science.
» Oncology leads other therapeutic areas in
the number of personalized medicines
on the market as well as in the pipeline
with the expectation that within the
decade all oncology drugs will have a
related diagnostic component.
» Other key therapeutic areas in which
personalized medicine is making
headway include: cardiovascular, central
nervous system, and immunologic
therapies. Personalized medicine
development is just getting started for
metabolic and respiratory therapies as
well as virology.
Source: Tufts Center for the Study of Drug Development. For more information, visitcsdd.tufts.edu.
“ The power of the newsequencing technologies is causinga revolution in genomics and itsapplication tomedicine.”
SHAF YOUSAF / Life Technologies
“ Pharma companies have been slow to fully adopt some genomic technologies and approachessimply because the small-molecule machine continues to work. ”PANNA SHARMA / Cancer Genetics
22 January 2011 � PharmaVOICE
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nisms if the whole genome sequencing costgets cheaper.”
Mr. Yousaf points out that the first genomesequence took about seven years to completeand cost about $300 million.
“We can now sequence a complete humangenome within about two weeks at a cost ofabout $6,000,” he says. “Now, many morehuman genomes have been sequenced, andthe role of DNA in disease is much better un-derstood.”
Kevin Hrusovsky, president and CEO ofCaliper Life Sciences, believes the cost of se-quencing will continued to decline.
“In the next few years, the cost will be$100 to $1,000,” he says. “There is already anevolution afoot. Next-generation sequencingtechnology is being developed. Current tech-nologies require a lot of PCR, which is an ar-tificial way to chemically amplify the DNAthat creates biases and false positives. Newertechnologies are attempting to reduce theamount of sample that is needed, perhaps evento a single molecule that is much longer.There is a fourth generation of sequencingtechnology being developed by IBM, called aDNA transistor, which might possibly reducethe cost to $10 to $100 per genome, but thistechnology is probably 10 years away.”
According to BCC Research, the world-wide market for sequencing products willgrow from an estimated $1.3 billion in 2010to more than $3.3 billion by 2015.
Life-sciences research and drug discoveryand development applications represent thetwo largest markets for DNA sequencing rev-
enue, accounting for about $920.1 million in2010. Analysts predict that these markets areforecast to grow at a compound annualgrowth rate of 13% to reach almost $1.7 bil-lion in 2015.
Translational EffortsDr. Reid sequencing the genome provides
a whole new set of addressable targets for thepharmaceutical industry to pursue.
“For the first time, researchers can tap hun-dreds of people with a disease using very high-accuracy sequencing tools and narrow downthe potential causes for the disease to either asingle gene or a handful of genes that are act-ing in concert,” he says. “In the case of cancer,for example, there is a need to sequence notjust one person but hundreds of people withthe same cancer. We also need to sequence pa-tients multiple times as the cancer evolves tosee the patterns of mutation and use that in-formation to change the course of drug ther-apy throughout the development of thetumor. This is how cancer will be treated inthe future.”
But Mr. Yousaf points out that at the mo-ment translational genomics is very much anart.
“The challenge is that there isn’t enoughbasic or even applied research available yetthat relates DNA variation to disease,” hesays. “We need two or three more years ofbasic research to try and work out some of thedisease mechanisms.”
Jerry Coamey, senior VP, practice leader,personalized healthcare, at CAHG, says two ofthe most critical challenges are the approvalgap and the knowledge gap.
“The combining of a diagnostic with atherapeutic is one of the greatest opportuni-ties in genomics-based medicine, but the cur-rent drug approval process is not set up forthat…yet,” he says. “The FDA has a great op-
portunity to identify, clarify, and simplify theprocess for parallel approval of a companiondiagnostic/therapeutic. To their credit, theagency has begun work in this area. The sec-ond challenge and opportunity is for industryto educate one of its most critical customers:the physician end-user of these new ge-nomics-based tests and targeted therapies. Asour landmark physician study reveals, theyacknowledge a critical need for education andinformation about all aspects of genomics-based medicine, but also acknowledge beingopen to receiving that knowledge from phar-maceutical and molecular diagnostic compa-nies, as well as their sales representatives.”
One company making great strides in thisarea is Sanofi-Aventis. The company had sig-nificant efforts in the use of high throughputgenomic technologies such as gene expressionprofiling to find targets for pharmacologicalmanipulation.
“We identified several novel targets for dif-ferent therapeutic indications and are cur-rently in the process of validating them,” Dr.Natesan says.
Dr. Natesan says going forward the thera-peutic departments in the company will doany large scale genomic studies instead of ded-icated genomic centers.
“We still have significant internal capabil-ities to do high throughput genomic studieswhen there is a need,” he says.
Mr. Hrusovsky cautions that companiesneed to also think beyond the genome.
“Companies may think genomics is theonly piece of puzzle,” he says. “In fact, thegenome itself is only half the equation. Thereare other factors that affect health. For the firsttime in U.S. history, a child born today has ashorter life expectancy than his or her parent.And the reason is obesity. There are so manyfactors in play that go beyond purely thegenome. That’s why we think the genome is
The Genome
CCAAGGRR%% AApppplliiccaattiioonn 22000099 22001100 22001155 ((22001100--22001155))
Research, drug $822.3 $920.1 $1,694.2 13.0%
discovery/development
Commercial 239.1 241.6 615.1 20.6
applications
Workflow solutions 108.2 139.4 497.2 29.0
Emerging applications 12.2 15.5 541.4 103.5
Total 1,181.8 1,316.6 3,347.9 20.5
Note: Dollars in millionsSource: BCC Research. For more information, visit bccresearch.com.
Global Value of DNA Sequencing Products by End-Use Application (through 2015)
“ Today, we are beyond what wasthought possible based on whatsequencing the genome hasmeant and the rate of next- generation technology advancements.”KEVIN HRUSOVSKY / Caliper Life Sciences
23PharmaVOICE � January 2011
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area, Mr. Hrusovsky has outlined several factorsthatwill be critical for healthcare going forward.“Eventually, when people are born they
will have their genome sequenced and thiswill provide information about what theirparticular mutations are that make themunique,” he says. “Additionally, biomarkerswill play an important role in discoveringthe various mutations that a patient has,which will allow drugs to be tailored to theindividual. About 40% of drugs coming tomarket have some type of genome marker orprotein marker related to them. It is ex-
traordinary to think that we are that faralong and have companion diagnostics withdrugs.”The third factor, Mr. Hrusovsky says, in-
volves diagnostic imaging.“Our theory is that over the course of time,
it’s not just about the DNA and what is goingon in the body, but the environmental factorsa person is exposed to,” he says. “Many timesenvironmental factors create conditions thatan image will help understand. Sometimes wecan see things with an image that we neverwould have been able to detect with agenome.” PV
The Genome
EXPERTS
“ We are starting to be able toanswer questions about geneticmarkers of disease and responseto therapy.”DR. OREN COHEN /Quintiles
just one of the three themes impacting health-care.We believe that biomarkers and imagingwill also play an extraordinary role.”In a review of the trends in the diagnostic
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READER TO ACCESSMORE ON THIS TOPIC.
“ The FDA has a greatopportunity to clarify andsimplify the process forapproval of companiondiagnostics/therapeutic.”JERRY COAMEY/ CAHG
24 January 2011 � PharmaVOICE
JERRY COAMEY.Senior VP,
Practice Leader,Personalized
Healthcare,CAHG,a healthcare
communications company and a
wholly owned subsidiary of Omnicom
Group Inc.For more information,visit
cahg.com.
OREN COHEN, M.D.Chief
Medical and Scientific Officer,
Quintiles, a fully integrated bio
and pharmaceutical services
provider. For more information,visit
quintiles.com.
KEVIN HRUSOVSKY.President
and CEO,Caliper Life Sciences, a
provider of tools and services for
drug discovery and life-sciences
research.For more information,visit
caliperls.com.
SRIDARAN NATESAN, PH.D.
Scientific Site Head of R&D and
Head of External Innovation and
Partnering,Sanofi-Aventis, a
global pharmaceutical company that
discovers,develops, and distributes
therapeutic solutions.For more
information,visit sanofi-aventis.us.
CLIFFORD REID, PH.D.
Chairman,President, and CEO,
Complete Genomics,which
provides high-throughput DNA
sequencing of human populations.For
more information,visit
completegenomics.com.
PANNA SHARMA.CEO,Cancer
Genetics Inc.,which offers prod-
ucts and services that enable
cancer diagnostics and
personalizedmedicine.For more
information,visit
cancergenetics.com.
THOMAS TURI, PH.D.VP,
Science andTechnology,
Discovery andTranslational
Services, andVP,Biomarker
Center of Excellence,Covance, a drug
development services company.
For more information,visit covance.com.
SHAF YOUSAF.President,
Genomic Analysis, Life
Technologies, a global
biotechnology tools company.
For more information,visit
lifetechnologies.com.
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The Genome
head of external innovation and partnering atSanofi-Aventis.
“It is difficult for pharmaceutical compa-nies validate the hundreds of targets thatcome out of ‘omincs’ research, and they havehad to rely on academia or biotech partners tovalidate most of these targets,” he says.
Shaf Yousaf, president of genomic analysisat Life Technologies suggests that new disci-
plines within medicine will be needed to de-termine how genomic data are analyzed,stored, and tied to patient clinical data beforethe information can be used by doctors fornew therapies.
Dr. Natesan says in addition to the largeamount of data being generated — whichcannot be easily interpreted — the reliabilityof the information is also an issue.
“There have to be better analysis tools de-veloped to make the data reliable,” he says.
Under the CloudCurrently, while there is no computing
power in place that can harness the vastamount of information being generated,Kevin Hrusovsky, president and CEO ofCaliper Life Sciences, says there are advancesbeing made in the computer industry, such ascloud computing.
“The cloud could significantly increase thepower needed, by as much as a hundred timesthe current level,” he says.
Denise Myshko
Managing data is one of the bigger technical problems associated withgenome sequencing. The answer might just be the cloud.
The ComplexTask ofManaging Data
THE GLOBAL BIOINFORMATICS
MARKET IS EXPECTED TO REACH
$8.3 BILLION BY 2014, A CAGR OF
24.8% FROM 2009 TO 2014.
Source: MARKETSandMarkets
FACT
“ Current Internet connections in mostinstitutions are relatively small. Movingvast amounts of data through these is likesucking the ocean through a straw.”
DR. PAUL ALDRIDGE / Genomic Health
he amount of data being gen-erated via genomic researchand gene sequencing is huge,so vast that the industry hasbeen unable to keep up.
The challenge of managing genetic infor-mation caught the industry by surprise, saysClifford Reid, Ph.D., chairman, president,and CEO of Complete Genomics.
“The old generation of tools produced verylittle data, and these data were well managedby a spreadsheet,” he says. “But as the cost ofgenerating data went down, the amount ofdata generated went up. In the last few years,we completely blew out the spreadsheetmodel of data management.”
The discipline of genomics and informaticsis very resource intensive, says Sridaran Nate-san, Ph.D., scientific site head of R&D and
T“ People think they can press the easybutton and the cloud works magnifi-cently, but the cloud still has complexityto it. In reality, the cloud is probably an‘easier’ button.”
DAVE POWERS / Cycle Computing
January 2011 � PharmaVOICE
DIGITAL EDITION — BONUS CONTENT(c
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putation burden is greater than its internalcomputing and storage capabilities.
“Rather than build a data center and buyservers and populate them, which can costtens of millions of dollars, we partner with atechnology company to extend our capabili-ties,” he says. “By using the cloud on demand,we only have to pay for the hours or days weuse. And when we are done, we can pull thedata back inside and work on the result.
“We’re a small company and we want tobe in the diagnostics business not in the datacenter business,” he adds. “The math and
computations that are required for some ofthe analysis we want to do are enormous. Wewant to be able to scale up that capability inthe cloud on demand.”
Dr. Aldridge says the one drawback isthat standards and technologies are stillemerging.
“We are still experimenting,” he says.“We’ve done some experiments that havebeen successful. The longer term issue is de-termining how we can seamlessly create ahybrid model with internal and external ca-pabilities.” PV
Cloud computing has the potential to ad-dress the data management/data storageneeds of genomics, says Dave Powers, busi-ness development at Cycle Computing.
“Cloud computing is a disruptive tech-nology, especially in large enterprises on twodifferent levels,” he says. “First, it reducesthe time needed from weeks to minutes.Second, there is transparency of cost. Com-panies know exactly how much it’s going tocost to launch those machines or use thismuch storage.”
Mr. Powers predicts that in five years asignificant percentage of a corporation’s in-frastructure will exist in the cloud, whetherthat consists of servers or storage.
Complete Genomics is addressing some ofthe issues; through an outsourced service thecompany can process raw data and provide asmall set of finished, medically actionabledata.
Paul Aldridge, Ph.D., chief informationofficer, Genomic Health, says his companyuses the cloud for those times when the com-
The Genome
EXPERTSPAUL ALDRIDGE, PH.D. Chief
Information Officer, Genomic
Health, which develops and
commercializes genomic-based
clinical laboratory services for cancer.
For more information, visit
genomichealth.com.
KEVIN HRUSOVSKY. President
and CEO, Caliper Life Sciences, a
provider of tools and services
for drug discovery and life-sci-
ences research. For more information, visit
caliperls.com.
SRIDARAN NATESAN, PH.D. Scientific Site
Head of R&D and Head of Exter-
nal Innovation and Partnering,
Sanofi-Aventis, a global
pharmaceutical company that
discovers, develops, and distributes
therapeutic solutions. For more
WORKFLOW SOLUTIONS, WHICH
INCLUDE SEQUENCE CAPTURE
AND BIOINFORMATICS, ACCOUNT
FOR $139.4 MILLION IN THE 2010
DNA SEQUENCING MARKET AND
ARE FORECAST TO REACH $497.2
MILLION BY 2015.
Source: BCC Research
FACT
PharmaVOICE � January 2011
DIGITAL EDITION — BONUS CONTENT
information, visit sanofi-aventis.us.
DAVE POWERS. Business Development,
Cycle Computing, a provider of
high performance computing
(HPC) and open source solutions
internally and via the cloud. For
more information, visit
cyclecomputing.com.
CLIFFORD REID, PH.D. Chairman, President,
and CEO, Complete Genomics,
which provides high-throughput
DNA sequencing of human
populations. For more
information, visit
completegenomics.com.
SHAF YOUSAF. President, Genomic Analysis,
Life Technologies, a global
biotechnology tools company.
For more information, visit
lifetechnologies.com.
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