Genomics era gives rise to new breed

of complex, cross-cutting projects
2 | The Academic Executive Brief - Volume 3, Issue 2 | 2013
I was a program director at the National Cancer
Institute for seven years before coming to the
Common Fund. One of the areas I was interested
in was Tuberous Sclerosis, which is a syndrome
that no one institute or center really owned
because the people have symptoms in all sorts of
different organ systems, and they often develop
cancer and epilepsy. The Common Fund was
designed to address important areas of science that
span the missions of several ICs.
Would you say the HMP
fits that model?
Mary: Yes. Especially as a concerted effort to do
what the HMP ended up doing, it would have
fallen between the missions. For us in the NIH’s
Office of Strategic Coordination, the HMP was
ideal for the Common Fund because there was
both a need and an opportunity. In the mid to
late 2000s, the decrease in cost for sequencing and
the increase in throughput suddenly put studying
the microbial community within reach. Common
Fund projects should be timely and catalytic,
and HMP was.
George, would you agree that
the time was ripe for the HMP?
George Weinstock: For those of us outside the
NIH, it made a great deal of sense. With Common
NIH Common Fund in position to foster collaboration

An interview with Mary Ellen Perry, Program
Leader for the Office of Strategic Coordination
at the National Institutes of Health, and
George Weinstock, Leader of the Human
Microbiome Project and Associate Director of
The Genome Institute at Washington University
Hundreds of researchers and multiple academic
institutions and NIH institutes participated in the
Human Microbiome Project (HMP) to sequence
and analyze microbial genomes, create resource
repositories, and examine the associated ethical,
legal and social implications. The National
Institutes of Health (NIH) Common Fund
contributed $143 million to the HMP over the
first five years (Phase 1), and $15 million to a
more limited Phase 2.
Mary, how did you become
involved in the Common Fund?
Mary Ellen Perry: The Common Fund was
established in 2006 to support research that
benefits more than one NIH Institute and Center
(IC). I became involved because I believe a lot of
important and interesting areas of research fall
between the missions of the ICs, and because of
the way the NIH is set up, they are sometimes less
well supported than they should be.
George Weinstock is Associate
Director of The Genome Institute
and Professor of Genetics and
Professor of Molecular Microbiology
at Washington University in St. Louis.
He has played leadership roles in the
Human Genome Project, the Human
Microbiome Project, and other
genome projects. His interest is in
applying large-scale genomics methods
to medical problems in infectious
diseases and human genetics.

Mary Ellen Perry is a Program
Leader in the National Institutes of
Health Office of the Director’s Office
of Strategic Coordination and oversees
the development, implementation
and assessment of several cutting-edge
Common Fund programs. Dr. Perry
was previously a Program Director
for the National Cancer Institute.
For unabridged author biographies, visit:
http://AcademicExecutives.elsevier.com.

http://AcademicExecutives.elsevier.com | 3
forth. All these areas really are crosscutting,
with the intersection point being the genomic
information that you just created. And so from
the very first genome that was sequenced, it was
almost immediately an interdisciplinary project.
The great thing is that everyone wants to be part
of that and wants to help in the analysis. In fact,
for many of the initial genomes we did, we would
put together big consortia of analysts who would
all do it for free just because they wanted to be
part of it. It became standard operating procedure
to put together people from different disciplines.
How does a project of this
magnitude begin?
Mary: Each year the Common Fund hosts an
open series of meetings to gather ideas. If an area
Fund support, all the institutes could then take
the information, resources, framework and
infrastructure from the HMP and use them to
start their own microbiome projects targeting
their own particular mission, which has in fact
happened. Now microbiome projects exist in
16 institutes.
What you are seeing here is the genome era
creating a multidisciplinary type of project that
has been played over and over again. To really
maximize the utility of the sequencing information,
you have to bring in lots of different specialists.
You need to involve not only people who under-
stand the biology of the organism, but people
who understand metabolism, the regulation of
gene expression, bioinformatics, population
genetics, evolution, comparative biology and so
“What you are
seeing here is
the genome era
creating a
multidisciplinary
type of project
that has been
played over and
over again.”
PUBLICATION COUNT
CAGR 2008-2012 = 69%
JOURNAL CATEGORY COUNT
CAGR 2008-2012 = 28%
Using a keyword search of
“human microbiome,”
the figure shows a compound
annual growth rate (CAGR)
of 28% for journal category
expansion, and 69%
for number of publications
between 2008–2012.
Source: SciVal custom analysis
Figure 1: Growth in human microbiome publication diversity
Publication Count Journal Category
4 | The Academic Executive Brief - Volume 3, Issue 2 | 2013
“The Human
Microbiome
Project had clear
and valid goals
that were very
timely and
important for
everybody.”
Genomics era gives rise to new breed... continued
community, but more so medical specialists who
worked on infectious diseases, microbiomes,
microbial ecology, and specific organs and tissues.
Together, we were able to provide input to help
the Common Fund frame a program proposal
for the HMP.
How successful was
the HMP in carrying out
this shared mission?
George: For the HMP, the NIH really did a great
job of bringing together very different health areas.
The NIH staff member who led the sample
collection was from the National Institute of
Dental and Craniofacial Research. Grantees from
the National Institute of Allergy and Infectious
Diseases played an important role in defining
organisms to look for and sampling mechanisms.
Researchers from the National Institute of
Diabetes and Digestive and Kidney Diseases,
is identified as having promise, then we try to
home in on the possibilities by having subsequent,
targeted workshops. Many of the types of leaders
we would invite are apparent, but we do like to
balance out the group, going so far as to get
someone in the room whom we would call a
skeptic. We also need to determine how much
interest or potential there is for NIH staff to foster
a trans-NIH program. For the HMP, this meant
reaching beyond the National Human Genome
Research Institute, which was organizing the
effort, to the National Institute of Dental and
Craniofacial Research, the National Institute of
Allergy and Infectious Diseases, and the National
Institute of Diabetes and Digestive and Kidney
Diseases, as well as others.
George: I was at, and chaired, a couple of those
workshops. And as Mary said, they not only
brought together people from the genome
Figure 2: HMP Data Analysis and Coordination Center Source: http://www.hmpdacc.org/
http://AcademicExecutives.elsevier.com | 5
“All these areas
really are
crosscutting,
with the
intersection
point being
the genomic
information that
you just created.
And so from
the very first
genome that was
sequenced,
it was almost
immediately an
interdisciplinary
project.”
Genomics era gives rise to new breed... continued
and share data, yet they were ultimately
competing for funding. So we put them between
a rock and a hard place and we didn’t intend to.
We also found that one year was a pretty limited
time to put together and inspire a team. We didn’t
need to be that stringent.
George: There is a happy ending to some of those
stories. At least two of those projects that didn’t
get continued funding via the HMP put in for
R01s, and both got funded. So it wasn’t like they
died on the vine. It actually did initiate projects
that would not have been initiated otherwise due
to the tenacity of the investigators.
The HMP was a large, complex project,
and throughout its lifespan resources were being
added — much more so than we had anticipated
at the beginning. There is a much smaller HMP2,
but it might have been good after the fourth year
to envision a wider scope as certain things were
getting off the ground. Much work is being
taken up in some ways by different institutes,
but some areas cut across all the institutes and
really shouldn’t be the responsibility of one
or the other.
In general, our biology projects are getting so
huge we may want to stand back and think about
whether models used successfully in the past are
scalable and whether there might be new things
to consider to tackle even larger projects. n
who study a lot of GI tract issues, made a list of
organisms and outlined other tasks the group
should do, and so it went. We covered far more
parts of the human body and far more organisms
than any other project has even come close to.
That could not have been done without this
wonderfully coordinated and broad-based input
from the expertise embedded in the different
NIH institutes.
What were the key ingredients
in the success of an effort of
this magnitude?
Mary: The earlier on that everyone is consulted,
the earlier they feel part of the effort. When they
have had input into the goals, the goals become
their own and their contributions reflect that
ownership. The clarity of the goals is also key.
If an effort gets off the ground and it’s still a little
unclear exactly where it’s going, then people get
confused and disgruntled. Eventually they will
give up and move on.
The HMP had clear and valid goals that were
very timely and important for everybody. Every IC
staffer and researcher said, “Yes, I can see this would
be important for me, but even if it’s not for me, it’s
important for the field.” It really got a lot of buy-in
and enthusiasm and a lot of collaboration.
Is there anything you would
have done differently?
Mary: In one area, we set up demonstration
projects and gave investigators one year to
demonstrate feasibility. We asked them to talk
to each other, come up with common approaches,