Genetics, Genomics & Proteomics

Faculty Retreat

Summary Minutes

May 15, 2002

Gaithersburg, Maryland

Overview

The first Genetics, Genomics & Proteomics (GGP) Faculty Retreat was held
on May 15, 2002, at the Gaithersburg Hilton in Gaithersburg, Maryland.
Drs. Jeff Strathern and Steven Chanock, GGP Executive Committee members,
coordinated the day's events. The morning session of the retreat
featured two scientific lectures, brief presentations from
representatives of six National Cancer Institute (NCI) core facilities,
as well as the Cancer Genome Anatomy Project (CGAP) and the Division of
Cancer Epidemiology and Genetics (DCEG); and an informational session
regarding the Office of Science and Technology Partnerships (OSTP). In
the afternoon, there was a poster session, presentations from the Office
of Training and Education, the Office of Technology and Industry
Relations (OTIR), and the Technology Transfer Branch (TTB), and,
finally, an overview of the GGP Web site. In addition, Dr. J. Carl
Barrett, Director of the Center for Cancer Research (CCR), and Dr.
Joseph Fraumeni, Director of the DCEG, addressed the GGP Faculty and
answered questions. At the end of the day, Dr. Chanock encouraged
interested participants to join the GGP Steering Committee (SC).

Welcome and Introduction

Jeff Strathern, Ph.D., Chief, Gene Regulation and Chromosome Biology
Laboratory, CCR, welcomed participants to the GGP Faculty Retreat. He
mentioned that over 25 percent of Principal Investigators (PIs) in the
NCI were members of this faculty, and speculated that a higher
percentage of PIs use genetics, genomics, or proteomics in their
research. He also stressed that the GGP Faculty is still in the planning
stages; therefore, participation from the members today would determine
the structure and direction of the faculty.

Stephen Chanock, M.D., Acting Director, Core Genotyping Facility, stated
that the overall goals for this retreat were to formulate long-range
plans for the faculty and establish a core membership. He stated that
the mission of the GGP Faculty is to advance research and promote
interactions between members of the NCI who have common interests in
classical genetics, high-throughput genomics, and proteomics. The
challenge, he declared, was to promote collaborations and the sharing of
expertise between NCI investigators. Dr. Chanock also explained that the
GGP Faculty is not intended to be a funding mechanism or an additional
level of peer review. He then stated the following GGP Faculty goals:
(1) to encourage interaction between Faculty members; (2) to encourage
the use of technical platforms and core facilities; (3) to foster ties
to other Faculties; and (4) to establish an educational program that
includes a technology and educational series, as well as access and
oversight of graduate and postgraduate students. Next, he defined the
long-term challenges for this faculty. They are to promote the use of
available technology by both basic and clinical researchers, integrate
data from these technologies (e.g., microarray combined with
proteomics), foster educational programs and mentorships, and encourage
the use of model systems. Dr. Chanock speculated on how to engage people
outside of biology who have experience in analyzing large data sets,
(e.g., scientists from the National Aeronautics and Space
Administration).

Dr. Chanock then presented detailed information about the GGP Faculty SC
guidelines. The SC comprises 11 members, who may serve a maximum term of
five years. Dr. Chanock encouraged interested individuals to volunteer
for SC membership. Next, he stated that the GGP Faculty could use more
members, a program committee for lectures and workshops, an educational
series, ideas for collaborative projects and forming close associations
with NCI faculties, and an e-mail coordinator. Dr. Chanock then
described the educational program. It would involve a series of
platform-driven workshop-oriented sessions beginning in the fall of
2002. He envisioned that there would be three related 20-minute talks,
followed by a 30-minute discussion. He mentioned that another component
of the educational program is to provide mentoring of graduate students
at NCI and assist in their selection of a laboratory. Continuing, Dr.
Chanock highlighted the plans for a Faculty Speaker Series. The series
would span an academic year (September to May), and the site of the
speakers would alternate between the Frederick and Bethesda campuses. He
explained that the speakers would be selected from individuals who have
either an innovative/visionary, or a technical/scientific focus. Next,
he briefly touched on how an e-mail group could be useful for announcing
GGP Faculty events such as the speaker series, for finding reagents, or
for establishing collaborations. In addition, Dr. Chanock hoped that the
GGP Faculty would encourage the use of technology by identifying the
technical issues, finding ways to access, evaluate, and encourage
collaborative projects using appropriate technology, and providing
resources for technology support and transfer. Finally, Dr. Chanock
outlined a set of criteria for judging the success of this Faculty: (1)
development of a sustained educational program; (2) enhanced utilization
of the core facilities; (3) development of a new programmatic direction;
(4) ability to interface with other Faculties; (5) development of a
training program that capitalizes on Faculty strengths; and (6)
increased publications by collaborative Faculty members.

Scientific Presentations

*Dr. Neal Copeland*, "*Mouse Cancer Genetics Program"*

Neal Copeland, Ph.D., Chief of the Mouse Cancer Genetics Program (MCGP),
CCR, presented information regarding the MCGP. Dr. Copeland stated that
the goal of this program is to expand NCI's research efforts in the
field of mouse cancer genetics. Mouse models are important for
elucidating the origins of human cancer, especially in the post-genome
era. The focus of the program is to identify cancer genes and their
place in various pathways; produce and study different cancer models;
study cancer modifiers by breeding mice onto different genetic
backgrounds; and conduct translational research. He explained that
Frederick was chosen as the site for this program because of the quality
of animal facilities already located there, availability of expansion
space, and the presence of a well-established mouse genetics program.
Dr. Copeland emphasized that he wants to attract world-class researchers
who are willing to tackle high-risk, high-return projects, and these
resources are designed with that goal in mind. The facilities encompass
12,000 square feet of newly renovated space and state-of-the-art
transgene and knockout facilities, including 20,000 mouse cages. The
costs for making transgene and knockout mice are fully subsidized by the
NCI. Dr. Copeland mentioned other attractions of the MCGP to
investigators. These include access to the National Institutes of Health
(NIH) Clinical Center; a high-throughput genetics core facility for
genotyping, sequencing, microarrays, bioinformatics, proteomics, and
imaging; and a critical mass of scientists with diverse and cutting-edge
expertise in mouse cancer genetics. Dr. Copeland stated that the MCGP
was in the process of recruiting 50 people for eight new research groups
over a 4-year period. Next, he discussed the progress made on the
facilities. He stated that two-thirds of the space has been renovated,
and the first two tenure-track investigators have been hired. The
tenure-track investigators are Dr. Karlyne Rielly, who will be studying
mouse central nervous system tumor models and Dr. Brad St. Croix, who is
an expert in the tumor angiogenesis field. Other established
investigators at the MCGP include Drs. Nancy Jenkins (Head of the
Molecular Genetics of Development Section), Lino Tessarollo (Head of the
Neural Development Section), and Shyam Sharan (Head of the Genetics of
Cancer Susceptibility Section).

Dr. Copeland then presented some of the ongoing research within the
MCGP. One technique that he and Dr. Jenkins have been using is
retroviral insertional mutagenesis (RIM) to identify novel cancer genes
in inbred strains of mice. He explained that RIM causes an integration
event in the mouse genome. This could affect the genome in two ways: the
integration could occur near a protooncogene to turn on an oncogene, or
it could inactivate a tumor suppressor gene. The integration site can
then be cloned and the disease-causing gene identified. Dr. Copeland
noted that with the available mouse strains, they can model a variety of
hematopoietic cancers. Next, Dr. Copeland explained a technique called
inverse polymerase chain reaction (IPCR). Using IPCR, he and his
colleagues can clone thousands of integration sites in a couple of
weeks. Dr. Copeland hopes to have a retroviral integration site database
operational soon. Identification of relevant genes is performed by
blasting these sequences against the mouse genome sequence database from
Celera Genomics. Dr. Copeland stated that he had blasted 1336 sequences
and found that 95 percent of the mouse sites could be positioned at some
point on the mouse genome. Forty-one percent of these were at common
integration sites, and 113 novel cancer loci were discovered. Of the 149
candidate genes discovered, 19 have already been implicated in human
disease. Nine others have been implicated in human cancer, and another
nine are related to various human cancers. Dr. Copeland identified the
next challenge as understanding the biology of the unidentified genes.

Dr. Copeland then reviewed some of the other research projects at the
MCGP. Because many tumors contain more than one integration site, the
identification of cooperative genes is important. This is accomplished
through a retroviral tagging process. Dr. Copeland explained that in
this process, sensitizing mutations could be introduced into mice
infected with retroviruses. He acknowledged two limitations to this
method: (1) there are presently no solid tumor models available to
study, and (2) oncogenes are the primary target uncovered in this
technique. To overcome these limitations, scientists in the MCGP are
investigating other systems of insertional mutagenesis, such as that
using Sleeping Beauty (SB) elements that act as classical transposons.
Dr. Copeland noted that another technique is the generation of mice who
have a high frequency of mitotic recombinations. These mice are then
bred onto a leukemia background. This process provides a tag for tumor
suppressor genes. Another interesting project involves the use of the
Cre/loxP system for inducing mitotic recombination. Dr. Copeland stated
that this method is used to find recessive genes. He indicated that
testing of this system would be done in whole animals soon; currently,
this work is only performed in embryonic stem cells. The final model Dr.
Copeland presented is an example of the kind of integrated research the
MCGP is interested in promoting. The technique is called
"recombineering" and is used to manipulate cloned DNA in *E*. *coli* by
homologous recombination. Dr. Copeland explained that it is possible to
introduce insertions, deletions, and point mutations into plasmids,
P1-derived artificial chromosomes (PACs), or bacterial artificial
chromosomes (BACs). Recombineering has allowed researchers to produce
targeting constructs in 2 weeks.

Dr. Copeland concluded with a listing of the future priorities of the
MCGP. These include completing the renovation; defining the research
priorities for the MCGP, perhaps with suggestions from the GGP Faculty;
facilitating interactions with the clinical programs; and attracting
researchers who are interested in developing new technologies that have
a high impact on cancer research. He then identified some ways to foster
interactions with members of the intramural programs, including direct
collaborations, identifying shared scientific interests, promoting
access to core facilities, and attending joint meetings, seminars, or
retreats. Dr. Copeland also advocated interactions with the Mouse Models
of Human Cancer Consortium. This group is developing technology that
could be of use to cancer researchers, such as a mouse repository in
Frederick. The repository would primarily include cancer models,
especially those that are new or in high demand. Finally, Dr. Copeland
noted that a Web site is currently under development to facilitate
access to this repository.

*Dr. Javed Khan, "Genomic Approaches to Cancer Research"*

Javed Khan, M.D., Principal Investigator, Pediatric Oncology Branch,
CCR, discussed how genomics can be applied to cancer research.
Microarray analysis is used to identify differentially expressed genes,
which are used to identify clinically relevant targets and improve the
diagnosis and prognosis of cancer. He illustrated this process by
describing a case study. A child came to the clinic with small blue
round cell tumor (SBRCT) diagnosed as lymphoma, but which was not
responding to conventional treatment. Dr. Khan noted that Ewing's
sarcoma (EWS), rhabdomyosarcoma (RMS), Burkitt's lymphoma (BL), and
neuroblastoma (NB) all are SBRCTs and that they are hard to diagnose. To
differentiate between these cancers and make a correct diagnosis, Dr.
Khan and colleagues used differential gene expression and neural
networks. Dr. Khan stated the hypothesis for the artificial neural
networks (ANNs) in this study: There exists a signature or pattern
within the gene expression profiles of each cancer that is specific to
the diagnosis of the biological behavior of that particular cancer. He
defined ANNs as recognition algorithms that function like the brain;
that is, through error minimization and learning. Dr. Khan described the
input for the system as any type of numerical data, and the output as
any given number greater than or equal to one. ANNs are currently used
in voice recognition software and the interpretation of
electrocardiograms, for example. He explained that neural networks first
require "training" to reduce any background noise. In this case, Dr.
Khan and his colleagues took a training set of 63 tumors and split it
into thirds, using two-thirds for training the ANN, and one-third to
test it. They assigned four diagnostic outputs for each tumor type (EWS,
RMS, BL, and NB) from zero to one. By their definition, the perfect
output for an EWS tumor reads 1,0,0,0. Dr. Khan then presented data to
demonstrate that the classification rate with this system was 100
percent. Next, he illustrated how to identify the most relevant genes
from this analysis. Dr. Khan began this study with 6000 genes, but
wanted to find 96 significant genes whose expression changes in these
four tumors. He demonstrated how this classification takes place. The
change in output with respect to gene expression is graphed. A lower
slope indicates a lower sensitivity, and therefore, a lower rank of
significance. A higher slope, however, means that the expression of this
gene is more sensitive and is assigned a higher rank. Dr. Khan explained
that now the top 96 genes could be clustered by disease type to show
which genes are important to which disease. He and his colleagues
identified some of these genes, and they hope to convert the knowledge
learned from these genes into diagnostic tools. Dr. Khan then retrained
the network with the 96 samples and tested a number of blinded samples
at the same time. He presented results indicating that there was 100
percent specificity and 93 to 100 percent sensitivity in this
experiment.

The next phase of this study is to identify which patients will respond
to treatment. Again, the analysis must be performed at the molecular
level because there are no biologically detectable differences between
these tumors. Once the gene expression is profiled, tumor DNA is
extracted for comparative genomic hybridization (CGH) on microarrays.
Dr. Khan explained that CGH is a great tool for this type of study
because it allows the direct identification of amplified or deleted
regions of the gene with small (2 to 10 g) amounts of DNA. Next, he
illustrated the procedure. Cellular RNA is harvested and labeled using
Cy5 dye for cancerous cells and Cy3 for the control cells. The RNA is
incubated on a microarray slide that contains cDNA targets identified
from the gene expression profiling. If a gene has a normal expression
level in a noncancerous cell, but low expression and little
amplification in a tumor cell, then it is likely a tumor suppressor
gene. However, if the normal expression is low, but the gene is
amplified and overexpressed in the tumor, then the gene is probably an
oncogene. By identifying which genes are expressed in a particular
cancer, Dr. Khan hopes to pinpoint better targets for therapy. CGH can
also be used to study the mechanism of drug actions. Dr. Khan noted that
the effect of Gleevec on specific cell lines has been studied this way.
Once candidate genes are identified, single nucleotide polymorphism
(SNP) analysis is performed to determine the mutation. Dr. Khan
explained that the next step is to validate the targets for potential
therapeutic intervention. Both normal (noncancerous) and malignant
tissues need to be studied. Dr. Khan concluded his presentation by
summarizing the future directions and challenges for microarray, ANN,
and CGH technology. First, he feels that there ought to be a unification
of the methods used in this research. There are numerous microarray
platforms, scanners, protocols, and data analysis methods in use, and
some standardization would ensure similar results between different
researchers. Second, he is working with several members in the
bioinformatics area to generate databases of all of the information that
is being discovered and make some of these tools more accessible to
researchers. Third, he mentioned that he is developing genomic arrays
with Drs. Ilan Kirsch, Tom Ried, Peter Fitzgerald, and Jonathan Wiest.
Fourth, he is developing chip-based promoter arrays with Dr. Kevin
Gardner. Finally, he is coordinating a project with the National Human
Genome Research Institute (NHGRI) to validate all of the targets being
discovered using cell array technology.

Infrastructure: Core Facilities

*NCI Microarray Facility*

Ernest Kawasaki, Ph.D., Director of the NCI Microarray Facility at the
Advanced Technology Center (ATC), presented information regarding the
services offered through this facility. He listed the goals of the
facility: 1) to manufacture quality microarrays for complex gene
expression, SNP, and CGH analysis; 2) to provide up-to-date training,
protocols, and technical support for microarray users; 3) to develop new
microarray technologies and applications; 4) to form research
collaborations with investigators whenever possible; and 5) to print the
entire human gene complement on two slides. The facility includes three
Gene Machine arrayers and one biorobotics arrayer enabling the staff to
read 200 to 400 slides per week. Scanners that cover most fluorophores
in the range of 500 to 700 nm are also available. Dr. Kawasaki stated
that 10K panels of human and mouse sets are being printed onto slides
(the mouse sets are being printed in Frederick). To make the process
faster, the cDNA arrays are being converted to oligonucleotides. Dr.
Kawasaki envisions determining gene expression through oligonucleotides
and Affymetrix gene chips. He noted that there was a complete set-up,
including the latest software available through the ATC, at several
locations on campus. Dr. Kawasaki concluded by announcing that
microarray laboratory courses are held at the ATC once a month.

*Comparative Molecular Genetics Core Facility*

Ilan Kirsch, M.D., Chief, Genetics Branch, CCR, stated that the purpose
of this facility is to study structural genome anatomy, such as
chromosomal reconfigurations (e.g., translocations and inversions),
numerical changes, or gene dosage changes. The technologies supported at
this facility include fluorescent *in situ* hybridization (FISH),
spectral karyotyping (SKY), CGH, and chromosome flow sorting. Dr. Kirsch
noted that these technologies are available for human samples;
processing of samples from mouse and other species is under development.
To access these facilities, an investigator needs to fill out an
application found at the core facility's Web site (See Appendix 1). Dr.
Kirsch emphasized that the ability of this core facility to provide
services to the intramural community is based on demand for it, and that
these services are highly subsidized. He briefly reviewed the use of
each type of available technology. Dr. Thomas Ried developed the SKY
technique. SKY is useful for identifying every single chromosome with a
unique color since the chromosomes are differentially labeled. The color
differences aid the identification of recombinations. Dr. Kirsch
explained that total chromosome CGH is offered at this facility, with a
resolution of 10 kb. This technique is useful in defining changes in
gene dosage across the genome to distinguish tumor types, or normal
cells from malignant cells. He hopes to have a genomic CGH array using
BAC clones set up in 4 months. Other future projects include converting
the data in the CCAP (cancer chromosomal aberration project) to virtual
CGH, developing a mouse CCAP, finding tools for identifying orthologous
maps of chromosomal aberrations, and identifying tools for the
comparison of gene expression profiles with chromosomal aberrations.

*NCI Core Genotyping Facility*

Dr. Chanock introduced this core facility, which is also located at the
ATC. Requests for use are accepted from researchers in the CCR and the
DCEG. He described the center as driven by bioinformatics. Special teams
oversee sample handling, assay validation, production, quality control,
and production. He emphasized that this facility analyzes only human
samples. Dr. Chanock stated that the goals of the facility are to
establish a high-throughput genotyping facility, address the needs of
the intramural program, conduct candidate gene studies, perform sequence
analysis for SNP and haplotype characterization, and assess different
assays and technologies. There is also a series of technology
development programs for DNA pooling, which can be used to estimate
allele frequency as a screening tool. To assist researchers with this
technology, Dr. Chanock announced that individuals at this facility are
developing an on-site course. Furthermore, he announced that there is an
individual holding office hours to answer questions. Dr. Chanock noted
the SNP500 cancer database as an important resource for this faculty.
One of the projects being coordinated is the analysis of 102 individuals
from four ethnic groups. He stated that the genotypes and allele
frequency would be published as soon as the data are analyzed. Next, he
identified Dr. Andrew Bergen as the individual who coordinates the
laboratory and inventory systems. Dr. Bergen is in the process of
selecting a contractor to assist with this task. Finally, Dr. Chanock
highlighted a series of partnerships with companies and intramural
branches that this facility is working with to provide a wide range of
assays and data analysis systems. To access the facility, Dr. Chanock
recommended calling or sending an e-mail message to Dr. Jim Vaught, who
is the coordinator through DCEG.

*Protein Expression Laboratory (PEL), Dr. James Hartley*

James Hartley, Ph.D., Director of the PEL, summarized the services
offered at the PEL. They are vector engineering and recombinant protein
expression, large-scale production of recombinant proteins, and protein
purification. He expects *in vitro* transcription and translation to be
available soon. Dr. Hartley explained that the PEL encompasses the
entire process from cloning to expression (in either microbial or
eukaryotic cells) to purification. The PEL is divided into four
specialized teams: cloning and expression optimization, fermentation
group, eukaryotic cell production, and protein purification. Dr. Hartley
mentioned that the cloning and expression group performs PCR, Gateway
recombinational cloning technology, and sequencing. The fermentation
group is capable of shake-flask and 60-liter fermentation. The
eukaryotic cell production group cultures mammalian and insect cell
lines for recombinant protein and antibody production. He noted that the
protein purification laboratory is responsible for recombinant proteins
of native or tagged cell types, and the purification of these proteins
by various methods (e.g., affinity columns, ion exchange columns).
Finally, Dr. Hartley summarized the future directions for the PEL,
including the development of new hosts and vectors; *in vitro*
translation; purification and expression of membrane proteins and
insoluble proteins; and finding instrumental approaches to test parallel
expression states. He envisions the ability to study up to 48
combinations of vector promoter, vector fusion tag, *E. coli* strain,
growth temperature, and induction condition in parallel to maximize gene
expression, solubility, and protein activity.

*Laboratory of Molecular Technology (LMT)*

David Munroe, Ph.D., Director of the LMT, presented information
regarding this core facility. It is located off-campus in Frederick, and
he invited everyone to an open house of these facilities on May 31,
2002. He stated that the mission of the LMT is to access and develop new
genetics technologies and make these technologies available to NCI
researchers through core facilities and collaborations. An additional
function of the LMT is to support independent cancer research projects.
Dr. Munroe listed the services available at the LMT. These include
sequencing, microarray, genotyping, custom automation, oligonucleotide
synthesis, and molecular diagnostics. He explained that the sequencing
group is split into two units: one with standard, slab gel sequencing on
the ABI 377, and the other with high-throughput capillary sequencing on
the ABI 3700. He noted that samples could be submitted in individual
tubes or in 96- and 384-well plates. He estimated that they read 25,000
sequences per month. Dr. Munroe also highlighted a database that
researchers can use to request sequencing jobs and access the data once
the sequencing is completed. Next, he stated that the microarray core
consists of two BioRobotics MicroGrid III instruments and two Axon
GenePix scanners, and they run 300 to 400 arrays per month. The
molecular diagnostics core is Clinical Laboratory Improvement Amendments
(CLIA) certified, and he mentioned that they run a variety of assays.
Dr. Munroe then addressed the functions of the oligonucleotide synthesis
core. This facility is on the main campus, but will be joining the other
LMT facilities towards the end of the year. He noted that researchers
could obtain standard, modified, and purified oligonucleotides, as well
as peptide nucleic acids (PNAs). The LMT produces 3500 oligonucleotides
per month. Next, Dr. Munroe mentioned that a genotyping core facility
based on the TaqMan platform is opening in July 2002. He also stated
that a variety of custom automation services is available through the
custom automation facility. In addition, a robotics system is being set
up in collaboration with Beckman-Coulter. To conclude, Dr. Munroe
highlighted the future projects for this core facility. These include
developing a whole-genome yeast two-hybrid system, studying DNA
methylation changes during mouse ovarian development, and studying
prostate tumor gene expression and loss of heterozygosity (LOH) events.

*Biomedical Proteomics Program (BPP) and Mass Spectrometry (MS) Center*

Timothy Veenstra, Ph.D., Director of the BPP and MS Center, described
the services available at these facilities. His philosophy is that all
available tools should be used when studying proteins to obtain as much
information as possible from a cell. He introduced the two groups in the
mass spectrometry (MS) center that prepare the samples and that are
involved with separation technology. An example of sample preparation
includes laser-capture microdissection with clinical tissue samples.
Next, Dr. Veenstra summarized the types of procedures used by the
protein isolation and fraction group. They include immunoprecipitation,
one-and two-dimensional polyacrylamide gel electrophoresis (PAGE),
capillary electrophoresis, reverse-phase liquid chromatography, and
chemical modifications of proteins (e.g., isotope-coated affinity tags).
The facility also identifies proteins through MS and Edman sequencing.
Dr. Veenstra listed all of the MS tools they have available, including
four LCQ Deca XP ion traps, a quadrupole time-of-flight (TOF)
instrument, Matrix-Assisted Laser Desorption (MALDI)-TOF/TOF,
Surface-Enhanced Laser Desorption/ionization (SELDI-TOF) analysis, and a
"metabonomics" group. He emphasized that all types of proteins, from
peptides to entire proteomes, could be analyzed at this facility. Next,
he discussed the BPP that is being established at NCI. The goal of this
program is to characterize proteins that play a key role in the
development and progression of cancer. He is integrating several other
programs into the proteomics facility, including the Image Analysis
Laboratory, LMT, Protein Chemistry Laboratory, PEL, and the Advanced
Biomedical Computer Center. To have a protein analyzed, researchers are
asked to submit a proposal through the group's Web site (see Appendix
1). Finally, Dr. Veenstra stated that the most important function of
these facilities is to assist in the diagnosis and treatment of
patients.

Infrastructure: Resources

*Cancer Genome Anatomy Project (CGAP)*

Lynette Grouse, Ph.D., Scientific Project Manager, Office of Cancer
Genomics, introduced the resources available through CGAP and the
Mammalian Gene Collection (MGC). The director for both of initiatives is
Dr. Robert Strausberg. She stated that the goal of CGAP is to determine
the gene expression profiles of normal, precancerous, and cancerous
cells to improve detection, diagnosis, and treatment for cancer
patients. She emphasized that all of the project resources are
accessible to the public. Dr. Grouse described the CGAP's strategy for
supporting gene discovery. A core component is the UniGene database,
which is used to analyze expressed sequence tags (ESTs). This database
is composed of a series of algorithms that clusters related EST
sequences together so that each cluster represents a unique gene. Dr.
Grouse clarified that for CGAP purposes, the word "gene" is based on the
structure of these unique clusters. Next, she explained how to access
information on the CGAP Web site. She noted that they tried to approach
this site from a biological perspective, so the portals are categorized
into genes, tissues, chromosomes, and pathways. Dr. Grouse then
discussed several gene analysis tools available through CGAP under the
heading of "genes." These include a gene finder, which is designed to
let users know in which tissues their gene of interest is located. There
is also a nucleotide Basic Local Alignment Search Tool (BLAST) that
searches only genes clustered in the UniGene database (unlike the NCBI
BLAST searches). She also mentioned the SNP500 and SNP Gene Viewer
databases. Under the "Tissues" heading, Dr. Grouse explained that there
are tools available to determine whether the tissue under study has been
used to make a library. By using the cDNA xProfiler, a researcher can
identify genes that are expressed in two different libraries, such as
normal breast tissue and breast cancer tissue. A researcher may learn
which genes are unique to a tissue or common to both tissues. A future
tool at the CGAP Web site is a technology for serial analysis of gene
expression (SAGE) called the SAGE Genie. It will include 80 to 100
libraries in a variety of tissues. She stated that the project is
focused on the reliability of a SAGE tag related to a gene of interest.
Every SAGE tag will be verified in the laboratory and given a confidence
level. In the "pathways" section of the Web site, researchers can click
on a particular disease and find all of the genes implicated in that
pathway. Dr. Grouse explained that clicking on an individual gene
reveals other pathways related to the gene of interest. Finally, Dr.
Grouse discussed the MGC. She stated that the MGC is an NIH directive
for obtaining full-length clones for every human and mouse gene. The MGC
contains about 9000 full-length human and 6000 full-length mouse clones.
Clones can be ordered from the MGC Web site (see Appendix 2) and are
obtained from the American Type Tissue Collection or Research Genetics,
Inc.

*Division of Cancer Epidemiology and Genetics (DCEG)*

Jim Vaught, Ph.D., Biorepository Coordinator, DCEG, discussed the
available biospecimens for performing population-based studies. The DCEG
is organized into seven branches and is a national resource for
population-based studies to identify environmental and genetic
determinants of cancer. Dr. Vaught stated that there were 250 to 300
active projects at the DCEG and that over 7 million samples have been
collected in the repository. The number of participants in these studies
varies from less than 100 to over 10,000. The biorepository contracts
the collection, processing, and storage of the samples. He noted that
the biorepository program emphasizes quality control and growth
management in specimen collections. The majority of the samples are
stored in Frederick and with the Boston Biomedica Inc. (BBI) Biotech
Research Laboratories in Gaithersburg. BioReliance in Rockville stores a
small quantity of samples as well. Dr. Vaught stated that there are over
80 specimen types in this collection, including hair, dust, and blood.
Buccal cells are the fastest-growing specimen type and are used for DNA
extraction and genotyping. He expects about 80,000 specimens in the
queue for this year and next year. He also noted that there are 35,000
samples in the queue for genotyping studies; some of these will be
performed at the CGF and some will be contracted. Dr. Vaught concluded
his presentation by summarizing the various assays run on the samples.
These include genotyping, virus detection, pesticide analysis, and
micronutrient analysis, and total one million assays for 40 projects in
25 studies.

Infrastructure: Technology Interface

*Office of Scientific and Technology Partnerships, (OSTP), CCR*

David Goldstein, Ph.D., CCR, discussed the new OSTP at the CCR. He
stated that the mission of the OSTP is to provide CCR investigators with
opportunities to access advanced technologies and scientific resources.
This mission is accomplished by identifying new technologies,
facilitating partnerships with government, industry, and academic
organizations, and introducing new technologies through the NCI core
facilities and Research Training Program (RTP). In short, this office
connects the CCR to other NCI intramural programs and the private
sector. Dr. Goldstein mentioned new gene and protein profiling
approaches, high-throughput systems for protein-protein interactions,
and technology for molecular target discovery and drug development as
examples of the technology the office is pursuing. Dr. Goldstein then
explained some other functions of the OSTP. They cooperate with the NCI
Technology Transfer Branch (TTB) to formalize collaborative
partnerships. They liaison with the OTIR to educate companies about the
variety of opportunities for collaboration with the CCR. Finally, they
sponsor the Program for Industrial Partnerships for Accessing Emerging
Technologies. He related an example of such a partnership with
Pharmingen for the Tissue Proteomics Initiative. He explained that
Pharmingen has agreed to provide any antibody to the NCI for this
initiative. In addition, NCI scientists are working with Pharmingen to
develop new antibodies to targets identified at NCI. He explained that
through this partnership, Pharmingen obtains the potential for new
products and an opportunity for marketing their technology, and NCI
acquires access to new technology. Finally, Dr. Goldstein discussed the
RTP at Frederick. The mission of the RTP is to provide expertise and
advanced technologies in the areas of gene discovery, proteomics,
analytical technologies, animal sciences, imaging, and computation to
support scientific initiatives and programs at the NCI. He displayed a
book entitled, "NCI Core Resources 2002" that contains a comprehensive
listing of the NCI core facilities. He noted that all NCI investigators
should have received a copy of this book and that more are available
from the OSTP.

Education

Jonathan Wiest, Ph.D., Associate Director for Training and Education,
CCR, presented information regarding the Office of Training and
Education. He stated that the mission of the CCR Office of Training and
Education is to have a programmatic impact on the overall training
experience of the basic scientists and clinical fellows in cancer
research. He estimated that there are 121 Clinical Fellows, 661
recipients of postdoctoral Cancer Research Training Awards (CRTAs) and
Visiting Fellows, 175 predoctoral CRTAs, and 226 summer interns at the
NIH. He highlighted a couple of programs sponsored by this office, such
as the annual postdoctoral retreat, the K22 career development awards,
the CCR senior clinical research awards, and the Graduate Partnership
Program (GPP). Dr. Wiest then addressed the graduate program at the NIH.
There are 14 university partners, and his office is working to develop
11 more partnerships. There are 130 to 140 investigators participating
in the GPP at the NCI and 36 GPP students in NCI laboratories. He stated
that the first year of a student's training is supported by the GPP and
that years two through five are supported by predoctoral CRTA
mechanisms. He also explained that investigators need approval from the
scientific director before they can be involved in this program. Next,
an affiliation is arranged with a specific institution, and then the
investigator helps develop collaborative projects. Dr. Wiest noted that
there is a new Request for Application (RFA) pilot program designed to
increase student-training opportunities and broaden university
partnerships. The focus of the RFA is to recruit students within
underserved areas in biomedical research, such as chemistry,
bioinformatics, and cancer epidemiology. According to the RFA, the
student spends the first two years completing coursework and preliminary
examinations at the university. This is supported by NCI extramural
funding. Then, students spend years three through five on the NIH campus
supported by a CRTA mechanism.

Dr. Wiest then discussed recruiting efforts for postdoctoral candidates.
There are two Web sites to assist in the recruiting efforts (Appendix
2). One site is designed for postdoctoral fellows so that they can find
open positions and submit their CVs online. The other site is for PIs so
that they can search the CVs posted by interested postdoctoral fellows.
Next, he introduced some of the mentoring issues this office addresses.
He encourages postdoctoral fellows to be more proactive with their
careers by presenting data, taking advantage of all of the research
resources available at NIH, and getting involved in mentoring summer or
pregraduate students. This office has implemented the annual review of
postdoctoral fellows, which is a program designed to improve
communication between investigators and fellows. Every year, the
postdoctoral fellow meets with his or her mentor to discuss research
goals, career development, professional networking, NIH courses, and the
writing and presenting of research results. Finally, he noted that his
office is also working to provide regular salary increases for
postdoctoral fellows.

Faculty Session

J. Carl Barrett, Ph.D., Director, CCR, briefly covered five functions
that are important to the CCR, and ultimately, the GGP Faculty. Their
functions include scientist training, technology development,
translational research, partnerships, and communication. He stated that
the concept of the NCI Faculties is to bring together different research
communities within the CCR. He described technology development as key
to the success of the Faculties. To assist with the goal of technology
development, Dr. Barrett also noted that the OSTP is designed to
facilitate NCI outreach to companies. He noted as a concern the issue of
how to improve interactions between Faculties. He suggested that the GGP
Faculty and the Bioinformatics, Biostatistics, and Computational Biology
Faculty are natural partners. To improve communication between the NCI
intramural and extramural research communities, Dr. Barrett noted that
NCI now sends intramural representatives to the extramural Specialized
Programs of Research Excellence (SPORE) programs. He also identified
translational research as a priority for the CCR. Dr. Barrett concluded
by asking for suggestions for improving communication within the CCR and
NCI.

Joseph F. Fraumeni, Jr., M.D., Director, DCEG, remarked that the NCI has
the resources and talent to support unparalleled research opportunities
in genetics, genomics, and proteomics. He then highlighted some of the
initiatives taken by the DCEG. They include the development of a cohort
consortium with large-scale cohorts from around the world; the promotion
of collaborations, such as the large scale family-based genetic studies;
and the ability to leverage extramural resources such as the Cancer
Genetics Network and the Cancer Family Cooperative. He stressed that the
large case-controlled studies are necessary to replicate findings of
studies addressing gene-environment or gene-gene interactions. In
addition, they also improve the ability of investigators to perform and
interpret complex statistical analyses.

In a subsequent question-and-answer session, the following points were
raised:

-   Information regarding the function and existence of Faculties should
    not be limited to PIs. Dr. Barrett noted that in the discussions
    regarding the formation of the Faculties, there were mixed views as
    to whether membership should be limited to PIs or opened to all
    interested NCI staff. Because no consensus was reached, the NCI
    leadership decided that each Faculty would decide the rules for its
    membership. Dr. Barrett encouraged the Faculties to be as inclusive
    as possible.

-   These Faculties rely on collaborations between investigators, but
    that idea conflicts with the PI-based system present at the NCI and
    other institutions. Reconciling these two ideas seems to have
    occurred within the DCEG; perhaps this should be a model for other
    divisions. Dr. Barrett agreed that the system of an individual
    investigator is derived from the academic tradition and is not the
    only way to perform modern scientific research. Indeed, the depth
    and breadth of technology and information requires investigators to
    form collaborations. Dr. Barrett wants to encourage both team-based
    and individual-based research without penalizing either approach.
    Dr. Fraumeni added that there are similar issues at academic
    centers. He emphasized the importance in any research approach of
    considering the impact of the project on the disease of cancer.

-   Core facilities are a great idea, but they do not seem to be
    designed for small projects. Dr. Chanock added that one of the goals
    of the GGP Faculty would be as an advocate for small users. Dr.
    Barrett stated that there is always a debate as to whether core
    facilities should be full-service or self-service entities. On the
    one hand, do laboratories want to commit a postdoctoral fellow to
    learning the intricacies of a microarray? Alternatively, do the core
    facility managers want researchers to run a microarray without
    really understanding the science behind it? The complex data
    analysis required for some of the technologies is an added problem.
    Dr. Barrett is forming a core oversight group to address some of
    these issues.

Office of Technology and Industrial Relations (OTIR)

Leslie Alexandre, Dr.P.H., described the functions of the OTIR. The
mission of the OTIR is to help accelerate the progress of cancer
research. She explained that is happens in two ways: (1) by encouraging
development and dissemination of new technologies, and (2) by promoting
and facilitating development of scientific collaboration with the
private sector. Dr. Alexandre noted that there are several efforts
promoting the development of new technologies. These include the
Innovative Molecular Analysis Technology grants, the Unconventional
Innovations Program for expensive, high-risk projects, and the Strategic
Technologies Seminar Series. The purpose of the seminar series is to
introduce to NCI investigators individuals from the private sector that
are interested in NCI collaboration. Dr. Alexandre then described a few
of the industrial relations functions of the OTIR. One is to educate
biotechnology or pharmaceutical companies about the funding and
collaboration opportunities available at the NCI. Another function is to
act as the first point of contact for companies entering NCI and
matching those individuals with interested investigators. She stated
that the third function is to interface with the private sector. This
happens through the coordination of specialized programs, such as
becoming beta test sites for new technology. The OTIR also handles some
technology transfer issues by handling requests from companies who
desire formal collaborations or who are interested in patenting or
licensing certain technologies. She emphasized that allowing OTIR to be
part of the process as early as possible is advantageous to everyone
involved. Dr. Alexandre concluded her presentation by referring to a
brochure from the OTIR designed to educate groups outside the NCI on how
to access the research and technology available at the NCI. She
encouraged any interested GGP Faculty members to call her about
receiving a copy of this brochure if they are interested.

Technology Transfer Branch (TTB)

Kevin Brand, J.D., identified the TTB as the first point of contact for
investigators when dealing with institutions or companies outside the
NIH. He described three principal TTB services: (1) consulting and
assistance on issues of inventions, patents, and technology transfer
policies and procedures; (2) negotiation of agreements with the private
sector; and (3) trademark registrations and limited assistance for
copyright issues. Mr. Brand explained that the essential document
investigators need to be aware of is the Employee Invention Report
(EIR). The purpose of the EIR is to memorialize inventions made by
Public Health Service (PHS) employees and to track these inventions for
potential licensing. He noted that this form is available through the
TTB office and must be signed and witnessed. He added that co-inventors
from outside the NCI may be included on this form, but they do not need
to fill out the NCI's form. Mr. Brand stated that EIRs should be
submitted as soon as investigators feel that they have an invention. A
common time to do this is after the investigator has completed an
abstract. He explained that processing the forms takes about 3 months.
He warned against disclosing any relevant information regarding the
invention at this time because any oral or written disclosure may have a
negative effect on the ability of the idea to be patented or marketed.

Mr. Brand then outlined the process of evaluating an EIR. First, the EIR
is reviewed to determine the marketability of the invention and
consistency with NIH policies. The NIH Office of Technology Transfer
then prepares a patentability report, which is reviewed by outside
counsel. In many cases, a patent is filed with United States Patent and
Trademark Office and on occasion, with foreign patent agencies. Once the
patent is issued, the technology is licensed. Mr. Brand clarified that
even if something cannot be patented, it can still be licensed. Two
examples he mentioned were cell lines and knockout mice. Next, he
addressed why government-sponsored investigators should patent their
inventions. First, patents provide an incentive to commercial
development, and second, they can provide a source of income for
inventors. He also stated that although the research funds are supported
by taxpayers, patents do return to the public after a number of years.

Mr. Brand also defined some of the typical agreements used in
negotiations with the private sector. A Confidential Disclosure
Agreement (CDA) is used when an investigator and a company want to share
confidential information, such as unpublished data. He warned that
investigators are sometimes unintentionally bound to these agreements,
especially when an agreement originates outside of the NIH. These
situations can be avoided by seeking TTB assistance at the beginning of
the agreement process. If an investigator wants to share materials with
another (usually not-for-profit) institution, a Material Transfer
Agreement (MTA) is used. An MTA prohibits commercial or clinical use of
the product. He explained that sharing material that is intended for use
in clinical trials requires a Clinical Trials Agreement (CTA). This is
also used to determine which party may use the resulting data. Next, he
defined a Cooperative Research and Development Agreement (CRADA), which
is used to formalize ongoing collaborative work. He explained that it
gives the collaborators rights to future inventions resulting from the
collaboration. A related document, the materials CRADA, is valid for a
term of one year and does not require a formal collaboration.
Furthermore, Mr. Brand presented information regarding a simple letter
agreement (SLA), which is a "bare bones" agreement used to facilitate
transfer to the NIH. He emphasized that all agreements are negotiable
and that the TTB works to expedite every agreement. Mr. Brand stated
that an investigator may approach the TTB with an idea for a specific
collaboration, or the TTB may advertise for a collaboration. In both
cases, the investigator is required to fill out conflict of interest and
fair access forms. These agreements are also subject to TTB review. In
conclusion, Mr. Brand urged the GGP Faculty members to contact the TTB
with any questions. He reiterated that an early start to the agreements
and patent procedure ensures an easier process for the investigator.

Steering Committee (SC) Membership

Drs. Strathern and Chanock requested volunteers to serve on the GGP
Faculty SC. Dr. Strathern envisioned structuring the Faculty in such a
way as to foster interactions. He stated that the job of SC members is
to contribute to the operation of the Faculty and contact the necessary
individuals (e.g., speakers, technology experts) who could help
accomplish Faculty goals. Dr. Chanock wanted to incorporate
investigators from a variety of scientific disciplines and points of
view. Drs. Samir Khliet, Ernest Kawasaki, Javed Khan, and Narayan Bhat
indicated that they are interested in serving on the SC.

GGP Faculty Web site

Joan Hanley-Hyde, Ph.D., presented an overview of the features of the
GGP Faculty Web site. Her role is to coordinate Web sites for all of the
NCI faculties. She noted that the current features on the GGP Faculty
Web site include a schedule of events, membership information, a reading
room for recent publications, and a news section. Planned features for
the Web site include a bulletin board and display of the listserv. She
stated the Web site is open to the public, but that certain segments
(e.g., the bulletin board) can have restricted access. Dr. Hanley-Hyde
hoped that the Web site would become a place to share materials,
reagents, expertise, and projects. She suggested that GGP Faculty
members also use this Web site to publicize Faculty plans and goals,
advertise meetings, share interesting scientific papers, help members to
find one another, and define common needs, such as a new core facility
or piece of equipment. Finally, Dr. Hanley-Hyde challenged the GGP
Faculty members to think about what they want the Faculty to accomplish
and how this Faculty could advance certain areas of cancer research. She
asked members to send her an e-mail at <jhhyde@mail.nih.gov> if they had
information they would like posted on the Web site.

Appendix 1

NCI Core Facilities Resource Page

The general core facility Web site is
[http://ccr.cancer.gov/resources/core_facilities.asp](http://ccr.nci.nih.gov/resources/core_facilities.asp)

The site contains links to all of the core facilities mentioned at this
retreat, as well as other facilities that may be useful.

NCI Microarray Facility

Ernest Kawasaki, Ph.D., Director

David Peterson, Manager

Phone: 301-435-7898

<petersed@mail.nih.gov>

[http://nciarray.nci.nih.gov](http://nciarray.nci.nih.gov/)

Comparative Molecular Cytogenetics Core Facility

Ilan Kirsch, M.D., and Thomas Ried, M.D.

Roscoe Stanyon, Ph.D., Manager

Phone: 301-402-2208

<stanyonr@ncifcrf.gov>

<http://web.ncifcrf.gov/core/cytogenetics/index.asp>

NCI Core Genotyping Facility (CGF)

Victor Llaca, Ph.D., Scientific Director

Contact phone: 301-435-7619

<llacav@mail.nih.gov>

Protein Expression Laboratory (PEL)

James Hartley, Ph.D.

Contact phone: 301-846-7375

<hartley@ncifcrf.gov>

<http://web.ncifcrf.gov/rtp/PEL.asp>

Laboratory of Molecular Technology (LMT)

David Munroe, Ph.D.

Contact phone: 301-846-1773

<mtlseq@ncifcrf.gov>

<http://web.ncifcrf.gov/rtp/lmt.asp>

Mass Spectrometry Center Analytical Chemistry Laboratory (ACL)

Timothy Veenstra, Ph.D.

Contact phone: Tom Conrads, 301-846-7353

<veenstra@ncifcrf.gov>

<http://web.ncifcrf.gov/rtp/labs/ACL/ACL.asp>

Biomedical Proteomics Program (BPP)

Timothy Veenstra, Ph.D., Director

<http://ccr.cancer.gov/tech_initiatives/bpp/default.asp>

Appendix 2

Other Web sites mentioned at the GGP Faculty Retreat

Center for Cancer Research:
[http://ccr.cancer.gov](http://ccr.cancer.gov/)

Division of Cancer Epidemiology and Genetics:
[http://dceg.cancer.gov](http://dceg.cancer.gov/)

SNP500 database (dbSNP) Web site:
[http://bumper.nci.nih.gov](http://bumper.nci.nih.gov/)

Cancer Gene Anatomy Project Web site:
[http://cgap.nci.nih.gov](http://cgap.nci.nih.gov/)

Mammalian Gene Collection:
[http://mgc.nci.nih.gov](http://mgc.nci.nih.gov/)

Graduate Partnership Program: [http://gpp.nih.gov](http://gpp.nih.gov/)

Online application system for postdoctoral candidates:
[http://generalemployment.nci.nih.gov](http://generalemployment.nci.nih.gov/)

Investigator access to CVs posted on that site:
[http://stargazer.nci.nih.gov](http://stargazer.nci.nih.gov/)

Office of Technology and Industrial Relations (OTIR):
[http://otir.cancer.gov](http://otir.cancer.gov/)

Technology Transfer Branch (TTB):
[http://ttb.nci.nih.gov](http://ttb.nci.nih.gov/)

NCI Faculty Web site:
[http://faculties.nci.nih.gov](http://faculties.nci.nih.gov/)

GGP Faculty Web site: <http://faculties.nci.nih.gov/ggp/index.html>