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Untitled Document Workshop on Defining the Epigenome

National Cancer Institute (NCI), Division of Cancer Biology (DCB)

Workshop on Defining the Epigenome: Addressing the Value and Scope of a Human Epigenome Project

 

November 28–29, 2005

 

Andrew P. Feinberg and Peter A. Jones, Co-Chairs

Grace Ault, NCI Organizer

 

 

Epigenetics is the study of modifications of DNA, other than the primary DNA sequence, plus associated protein factors, that have information content and are maintained during cell division. Unlike genetic information, the epigenome, or sum of genome-wide epigenetic patterns, distinguishes and defines one tissue from another, stem cells from somatic cells, and aged from young cells. We now appreciate that age, diet, inflammation, gender, genotype and drug exposures can alter the epigenome and cause disease, with the cancer epigenome being the best studied example. Two compelling influences are driving epigenomics research today—the appreciation that epigenetics changes are likely to mediate many human disease, and recent technical advances that allow genome-wide studies of epigenetic regulation.

 

Recognizing the importance of the field of epigenetics, the National Cancer Institute convened a workshop on defining the epigenome on November 28-29, 2005, attended by 25 distinguished scientists in epigenetics, representing diverse research interests including cancer, environmental health, neuroscience, aging, developmental biology, model organisms and basic research in chromatin. This international convocation of epigeneticists was prompted by the recognition by the community of an urgent need to establish a foundation for systematic epigenomics research. In particular, while great progress has been made in understanding epigenetics at the single gene/single cell level, little is known of the comprehensive epigenome, or of the variations in the epigenome that distinguish one cell type from another, or normal from diseased tissue. Prior to the meeting, there was a consensus among investigators that defining the epigenome would require an organized effort, to ensure both cost efficiency and maximal translational impact.

 

The Workshop responded to a recommendation from the Think Tank in Epigenetics organized by the NCI Division of Cancer Biology in May 2004, and followed a Conference on an Epigenome Project held by the American Association for Cancer Research in June 2005. The purpose of the current workshop was to answer three questions: (1) What would be the value of a comprehensive organized Epigenome Project, over that which can be done by regular investigator-initiated research? (2) What would be the scope of an Epigenome Project, i.e. what did the group feel needs to be defined? (3) What are the tools that can be brought to bear toward this effort, and in particular are they mature enough for such a project to be launched? The purpose was to incorporate the responses to these three questions in a draft outline of how a Human Epigenome Project could be structured—not necessarily to produce a final polished plan but to come up with a first draft.

 

The Workshop developed consensus support for an Epigenome Project, endorsing its value, addressing its scope, and defining the types of tools that could be applied toward this goal.

 

(1) Value of an Epigenome Project

 

During the session devoted to assessing the value of an epigenome project, it was clearly agreed that a comprehensive approach to defining the epigenome is critical to understanding stem cell biology, aging, development, and important diseases that have been relatively resistant to therapy, including cancer and psychiatric illness. Understanding the epigenome and knowing how it works in an integrated fashion would have major public health implications across NCI and NIH. Benefits of an Epigenome Project identified by the panelists include:

 

·        The need to discover the unexpected: we simply do not know the landscape of most of the epigenome. A comprehensive Human Epigenome Project will reveal the loci and patterns of modifications on which the broad community of researchers can focus in studying human diseases. This comprehensive approach will allow studies of the normal function and role in disease of modifications whose existence we would not otherwise know. Traditional epigenetics research is directed at what we already know or suspect, and a comprehensive epigenomics approach will open windows into the unknown, including:

o       A window to understanding the mechanism of cellular reprogramming, and the maintenance of stable patterns of transcriptional activation and repression.

o       A foundation for regenerative medicine, since epigenetics is fundamental to the difference between stem cells and somatic cells

o       Fundamental insights into the mechanisms of aging, a problem which is still almost completely opaque.

o       The role of the environment and nutrition in disease, as both have been shown to alter the epigenome.

o       A much better understanding of mental retardation, since several important common syndromes are caused or mediated by epigenetic changes.

o       Fundamental insights into psychiatric diseases, some of which show parent of origin effects, or respond to epigenome modifying compounds, yet the epigenetics of the brain are essentially unknown.

 

In addition, an Epigenome Project will provide:

 

·        Shared and standardized resources, such as good monoclonal antibodies and normal reference tissues for analysis.

·        Cost efficiency from economy of scale, and downward cost pressure from the Project itself.

·        The development of new technologies to allow more comprehensive and cost-efficient whole-genome epigenomic analyses.

·        The ability to integrate epigenetic information across experimental platforms, across types of epigenetic modification, and with phenotypic data such as pharmacological responses.

·        Creation of a bioinformatics infrastructure defining a data exchange format for epigenomics data.

 

The large amount of noncoding sequence, and epigenetic variation: Aravinda Chakravarti pointed out that a surprise from the human genome project is the comparison to other organisms reveals that only 5% of sequence is under natural selection and conserved, and, of that, while 1.5% is structural (protein-encoding), 3% is regulatory and the target of epigenetic processes. Hence epigenetic modification is crucial to understanding the genetic code itself. There is a growing realization that epigenetic information provides regulatory complexity that to a great extent accounts for human organismal complexity that seems disproportionate to the relatively small increase in gene number in humans compared to other mammals, or mammals compared to other vertebrates. Steve Henikoff discussed the importance of variant histones in understanding epigenetic reprogramming and development and as a means of identifying transcriptionally-active regions of the genome.

 

Epigenetic variation and the environment: Kazu Ushijima discussed the value of comparing the epigenome among populations with differing environmental exposures. In aging research, Manel Esteller noted the huge age-dependent changes in DNA methylation and chromatin in humans, apparent in the study of older versus younger monozygotic twins. He also stressed the importance of considering hypomethylation as opposed to hypermethylation, given the data from his and other labs. Steven Warren emphasized the importance of epigenetics in mental retardation, with several paradigm syndromes being epigenetically based or mediated, namely Prader-Willi syndrome, Angelman syndrome, and Fragile X. In the latter case, there is a close link between genetic and epigenetic change, specifically an expansion of a trinucleotide repeat which triggers chromatin modification that extends beyond the repeat. He stated that epigenetics is where the environment meets the genome, and we should think about genetic lability and environmental influence, as in twin studies. He noted that high dose interferon, even a single dose, triggers depression in a large fraction of patients, which persists in 4-5% of individuals, and he is looking for an epigenetic basis. Randy Jirtle suggested that for many diseases other than cancer, there may be a first hit involving genetic change, and a second that is a cytosine methylation rheostat. An example is the IAP insertion in the mouse agouti locus, in which dietary modification leads to stable silencing and a coat color change that can be transmitted to offspring.  He also suggested that imprinting is involved in intellectual development in evolution, pointing out the differences in imprinting of the mannose-6-phosphate receptor in brain, for example. He also discussed an October conference he chaired, sponsored by Duke University and the NIEHS that was attended by 450 scientists, although the initial solicitation called for only 150.

 

Value for stem cell biology and cancer: Speakers during this session included Steven Baylin, Andrew Feinberg, and Thea Tlsty, all of whom emphasized the importance of understanding the epigenetics of stem cells, in order to understand the epigenetics of cancer. Steve Baylin pointed out that cancer genes are useful models to understand chromatin generally. In cancer in particular, it is critical to identify epigenetic changes in normal cells that control stem cell function, and likely precede the development of mutations, and genetic changes. Andy Feinberg pointed out that the normal tissue of cancer patients frequently shows epigenetic alterations that likely precede and contribute to tumor development. Thus a comparison of tumor and normal tissue, while useful, may miss critical determinants of cancer that one would find be comparing the normal tissue of cancer patients to the normal tissue of patients without cancer. Thea Tlsty made the same point in breast cancer. She also pointed out that one could use epigenetic information to get a handle on another treatable target, such as COX2 inhibitors downstream of p16 methylation in breast cancer risk. Tim Huang noted that he finds widespread epigenetic changes in normal cells within 1-5 cm of tumors.

 

(2) Scope of an Epigenome Project

 

This session addressed the substrates for analysis, discussion of levels of resolution, and model organisms.

 

Substrates for analysis: Since there are many epigenomes and they vary according to developmental stage, age, etc., a key concept to emerge was that it would only be possible to perform comprehensive analyses for a limited number of epigenomes to begin with. By studying embryonic stem cells and a panel of differentiated cells from humans, focusing on samples acquired from young individuals to control for age effects, the variability of the epigenomic landscape will be captured. One thing that all agreed was that understanding the epigenome in embryonic stem cells would be critical, since these really represent the ground state of the epigenome.  Significantly, ES cells were appealing as a baseline because they are relevant and useful to all areas of research and all organ systems. Convincing cases were also made for the use of mouse embryonic stem cells since they can be experimentally manipulated so that alterations in the epigenome with respect to differentiation can be better understood. In this regard this project would have strong overlap with ongoing projects funded by the European Union which are mostly focused on the mouse. It would also be feasible, and indeed highly desirable, to define the epigenome in a human embryonic stem cell line. It will be critical to agree on a single stem cell line so that the data obtained can be integrated across studies.  With respect to human differentiated tissues, human epidermal keratinocytes and dermal fibroblasts obtained from newborn foreskins are a promising system that could provide a useful source of information allowing for comparisons to be made between differentiation lineages.

 

Ben Tycko noted the importance of defining normal tissue very carefully, requiring expert panels in the selection of each tissue type that will be analyzed. He also noted that an additional value of studying stem cells is that it helps to clarify the differences that distinguish one differentiated tissue type from another. Thea Tlsty emphasized that we should include all known marks, all “players” in the epigenetic program with no preconceived notions. She defined a set of requirements for sample collection: ample material, easy to sample, easy to visualize, easy to genetically and chemically manipulate. They should behave in a reproducible fashion, provide insight into key questions, with defined differentiation models (normal to disease, or ES to differentiated cells). Ideally, one would want to be able to do tissue reconstruction, so the in vitro situation faithfully recapitulates in vivo growth.  She suggested dermal keratinocytes, or dermal fibroblasts, and hematopoietic cells (B lymphocytes). There are models for skin growth, e.g. culture for burn victims, and these are easy to sample. For lymphocytes, there are excellent in vitro systems and in vivo correlates, and many relevant diseases. Keratinocytes and fibroblasts together would give insight into epithelium and stroma relationship, and might easily be obtained from newborn circumcisions. Another source of material she suggested is the HMEC (human mammary epithelial cells) system, which would allow comparison of epigenomic with known genomic and gene expression data, as well as the relationship to in vivo tumor progression.

 

Finally, it was agreed that expert committees must be assembled to recommend those human tissues to be studied as normal references for comparison with cells from patients with diseases, and to set the standards by which the samples will be defined.

 

Levels of resolution: It was agreed that the eventual goal of an epigenome project should be one base pair of resolution of DNA methylation, similar to the human genome project. The consensus was that it would be best to start with analysis of the selected reference epigenomes at the currently-feasible lower level of resolution (between 100 - 1,000 base pairs) to enable focused single-locus studies in the near term. Meanwhile, a major focus of the project would be to encourage the development of technology and methodologies capable of high level resolution.   

 

Peter Jones pointed out that unlike the human genome sequencing project, more material will be needed for the reference epigenome samples, because of the need to examine primary cells rather than cloned libraries.  He also stressed the importance of model organisms. As he pointed out, we must deal with imperfect materials, because there is no perfect reference epigenome. We also must do this work comprehensively across the genome, like the human genome project was done, or we will miss critical information. He made the point that a “reference” should start with normal tissue so as to form the basis for understanding the changes in each cancer.  After some number of normal tissues are done as reference epigenomes, less intensively evaluated epigenomes to reflect age, diseases, other tissues, etc, can be layered on top. A large scale project to produce this baseline can be complemented by R01-funded projects that provide these additional layers.

 

Model organisms: Several speakers convincingly argued for the necessity of including key model organisms. Model organisms provide a means of getting from correlation to causality by intervening experimentally in ways not possible in humans, testing the functional consequences of gene knock-outs or substitution of mutant copies as well as over-production of gene products. Shelley Berger pointed out that yeast is an outstanding developmental model. One could use a process for a reference, such as transcription as a model of changes over time, e.g. GAL1/HIS3. Questions would be asked such as, is there epigenetic similarity among members of a group of coordinately regulated genes?  Are there epigenetic differences profound or subtle between groups of coordinately regulated genes? One could also examine DNA damage (UV/IR induced), to look at changes over time. We could learn how broad are the regions of alteration around the breaks. Does the extent vary depending on chromosomal location? Are there permanent changes? An intriguing example is sporulation (gametogenesis), a developmental epigenetic state. Aging is another, as yeast has a finite life span.

 

The participants concurred on the short-term feasibility of understanding the yeast and Drosophila epigenomes particularly since both genomes are relatively small and neither of these organisms have substantial cytosine methylation. However, understanding how chromatin functions on a genome-wide level in these organisms would have considerable impact for understanding the human epigenome. Sarah Elgin discussed the advantages of including Drosophila as a developmental model. Advantages include the high quality genome sequence  and heterochromatin analysis being done in D. melanogaster, similar gene organization (intron/exon patterns), good annotation (FlyBase), a complex organ-based body plan (>70% human disease genes have orthologues), on-going work on insulators, and the accessibility of polytene chromosomes.  Past work has also made Drosophila a model for population and quantitative genetic approaches.. ChIP on chip is already established as a method, as well as nucleosome mapping using tagged histones, DNase hypersensitive site mapping has been done for specific genes, and should be possible on a genome-wide basis. She raised the question of the organization of the genome and presence of repeats. This could have great relevance to understanding epigenome regulation, as the type of repeats, rather than density of repeats appears to be important in epigenetic regulation in flies.

 

Laurie Jackson-Grusby noted the importance of focusing on the mouse stem cell. She noted that there is readily available scalable ES cell technology for studying genetically marked ES cells and various primary cell type derivatives. ES cells can also accelerate transgenesis and be used to model complex epigenotypes. To this end, one can generate a tetraploid embryo by applying current to fuse blastomeres of a 2 cell embryo. The tetraploid embryo goes on to become a blastocyst, and one can introduce embryonic stem cells into the blastocyst. The resulting mouse is entirely ES-cell derived (i.e. 2n), and faithfully retains the genotype and epigenotype of the injected ES cells. Epigenetic changes in donor ES cells can also be propagated by nuclear transfer. She also noted the recent genome-wide model for loss of imprinting, and the relevance to BWS, AS, PWS, and transient neonatal diabetes. Brad Bernstein observed that the high redundancy among histone modifications suggests that a small subset of the 100+ histone modifications would suffice for an initial reference epigenome draft. He noted that there may be coinciding trithorax and polycomb protein binding early in development, with loss of one or the other mark during differentiation, and that this is a compelling reason to include stem cell analysis. He also noted that the initial epigenetic state in embryonic stem cells appears to be to a large extent defined by DNA sequence, so epigenetic information must be closely associated with the DNA sequence in the epigenome project. Bing Ren has examined a variety of mouse tissues and compared them with mouse ES cells by ChIP on chip analysis, and found considerable overlap in marks among different tissues but a specific catalog of promoters with active marks in each tissue.

 

(3) Tools for Epigenome Analysis

 

The unanimous opinion of the Workshop participants was that the tools for epigenome analysis are available now for a pilot project. Peter Jones noted that bisulfite conversion can be followed by locus-specific PCR and possibly shotgun sequencing. The major limitation at this time is cost, although Steve Henikoff noted that in some ways methylation sequencing is simpler than DNA sequencing since it involves a resequencing effort, and only cytosines followed by guanines need be interrogated, and there are only two possible bases at these sites, C (if methylated prior to bisulfite treatment) and T (if unmethylated prior to treatment). The major limitation to bisulfite sequencing of all of the reference genomes is cost, although that will likely be driven down substantially by the project itself, similar to the history of DNA sequencing. Furthermore, the panelists agreed that we should not specify one particular method over another, as emerging technologies may drive the cost down further.

 

Largely because of the cost issue, the group felt that a lower resolution (1 kb) analysis should be performed immediately. At this level for DNA methylation studies, several exciting and workable technologies were discussed. These included restriction enzyme based platforms, as described by John Greally (Hpa II and Msp I based) and Jared Ordway (McrBC based). These methods are approaching the capacity of examining up to 14.5 million features in a single hybridization. Joe Costello described an integrated genomic and epigenomic analysis of human tumors, emphasizing that most epigenomic alterations in tumors are independent of the loci affected by genetic changes.  He concluded that a cancer genome project without an epigenetic component will not detect most of these genes. John Weinstein, an intramural scientist observer, noted the possibility of integrating even low resolution epigenomic information with genetic and pharmacologic data, as in the NCI60 cancer cell lines.

 

Peter Laird described the robustness and low cost of techniques such as MethylLight, but emphasized that rather than choose a particular approach, there is a wealth of technology to choose from. Another approach that might be used for the CpG island component is hybridization-based array analysis, as described by Tim Huang. John Greally noted the importance of computational methods in understanding epigenomic data. For example, he has found that a CG cluster analysis improves promoter/repeat detection ratio compared with current definitions of CpG islands. He noted that existing annotations are misleading, which is an argument against using CpG island microarrays to represent the genome, for example, another argument for a comprehensive approach to the epigenome. Along these lines, he has found that 80% of the change in DNA methylation in a mouse breast cancer model is not at promoters or CpG islands. He also stressed the short-term need to create a data exchange format for epigenomic information, as diverse data generated at multiple locations will need to be integrated, requiring in turn the creation of common identifiers, standards and common data elements for epigenomic information, akin to but much broader in scope than the MAGE/MIAME/Gene Ontology paradigms for gene expression microarrays.

 

Finally, Bing Ren noted that ChIP on chip technology is fairly mature and productive in complex genomes already, in studying both cell lines and tissues. He noted that 50% of known promoters have RNA Pol II in a set of 5 tissues examined, and 5% in only 1 tissue, but novel promoters show Pol II binding in only 1 tissue in 36% of cases. There is also relatively low CpG island content in tissue-specific genes, supporting the idea that many tissue-specific genes are normally methylated at their promoters. The bottlenecks are antibody quality, data analysis tools, standards, the large amounts of materials, and the costs of genome-wide tiling arrays, all of which would be ameliorated if not eliminated by a comprehensive epigenome project.

 

(4) Ongoing Epigenome Efforts and Relevant Projects

 

A special session was held to hear from other interested and related groups, in the hope that an Epigenome Project would be broadly connected to the community, as well as to ongoing research efforts. Paula Kim, a patient advocate, emphasized the importance of reaching out to many constituencies, through patient education, research committees, public policy/advocacy, and direct funding.  Translating Research Across Communities (TRAC) is an organization that she founded to harness the scientific/industrial/social will to accelerate discoveries into accessible and meaningful clinical applications. Another organization with a similar goal is the AACR scientist-survivor program. She stressed that we must emphasize the discoveries that are relevant to patient care, and how the Epigenome Project will get us there.  Kazu Ushijima (Japan) pointed out that although there is considerable interest and expertise in the field of epigenetic research in Japan, as yet there is no coordinated epigenome project. Japanese scientists have, however, recently organized a meeting entitled “Genome-wide Epigenetics” held at the University of Tokyo which brought Japanese investigators in this field together with international scientists to popularize this area of research. Efforts are being made to interest the Japanese scientific establishment and decision makers in the development of this exciting project. Patrick Varga-Weisz (European Epigenome Network of Excellence) described four ongoing epigenomic projects funded in Europe. One is a human epigenome project centered at the Sanger Center at Cambridge which is involved in the bisulfite sequencing in one base pair resolution of several defined loci. In this regard Europe is clearly a center of excellence for epigenomic research.

 

Peter Jones, as the President of AACR, described how AACR has played a significant role in the development of the field of epigenetics. It has organized three special conferences on cancer epigenetics and recently sponsored a workshop held at Landsdowne, Virginia on a human epigenome project. The proceedings at that workshop were in press in Cancer Research at the time of this workshop, in an issue that also included an editorial and cover photograph. The AACR has formed a task force which will be charged with continuing the development of the Human Epigenome Project. The immediate charges to this task force are: to finalize the approximate number of epigenomes to be defined at high resolution; to specify which histone modification marks should be included in the initial definition of the epigenome; to constitute subcommittees to discuss specific tissues which could be investigated at a high level of definition; to define a series of tissues and pathological states such as cancer which could be investigated at a lower level of resolution with respect to histone modification marks and DNA cytosine methylation patterns; to develop cost estimates and stages for the project, based on current and anticipated technology, including emerging sequencing platforms; and to promote the project in the scientific, patient advocacy and lay community.

 

Bing Ren described the overlapping goals of the ENCODE project in the areas of conserved sequence, transcribed, DNase hypersensitive, transcriptional regulatory elements, chromatin structure, and DNA methylation (including ChIP-on-chip). The focus of ENCODE has been on identifying the DNA sequence elements, not a reference epigenome. However, there have been intense discussions in NHGRI Council and the ENCODE scientific advisory committee on identifying biological functions for each of the functional elements being studied. Thus there could be considerable overlap in the interests of ENCODE and the epigenome community going forward. For example, both groups recognize the need for standardized reagents (antibodies, in particular) and bioinformatics infrastructure. The ENCODE Project is considering issues of scale-up, and one aspect of scale up is the question of which cells should be examined.  Certainly a dialogue on this issue between the two groups would seem useful.  Given the financial strictures of the times, it would seem worthwhile to try to construct these projects to support the congruence of interests where that is possible. 

 

Daniella Gearhart (NCI) discussed the Human Cancer Genome Project pilot, a 3 yr / $100M effort that will be focused on clinically important but biologically not too complicated tumors. There is discussion of examining one solid tumor and one liquid tumor. There is also an RFA to be issued on biospecimen availability. The focus will be on gene targets as well as regulatory sequences, chromosomal regional changes, and the integration of biological information.

 

(5) Next Steps

 

There was unanimous consensus among the workshop participants of the necessity for a Human Epigenome Project, and that the technology and rationale exist now to move forward. The Epigenome Project is critical for understanding the nature of stem cells, the differences among tissues during development, and many pathological states including cancer, neurological and psychiatric disease, and aging. The National Institutes of Health should take the lead in international efforts to develop scientifically and organizationally a Human Epigenome Project.

 

The Workshop participants agreed on the following mission statement for the Epigenome Project:

 

  • The long term goal is to achieve 1 bp resolution of DNA methylation, and a comprehensive analysis of chromatin, including modifications (such as H3K9 and H3K4 methylation), chromatin factor binding (such as polycomb, HP1), and structural change (such as DNase hypersensitivity), to be performed on normal human embryonic stem cells, fibroblasts and epithelial cells derived from newborns, and a panel of 10 normal tissues, corresponding to targets of common human disease, to be selected by experts in the tissue biology.
  • The short term goal is to analyze DNA methylation and chromatin (as defined above) in the same target tissues at a 1kb resolution.
  • Much added value would come from a comparative epigenomics arm to the project to harness the power of model organisms, specifically mouse, including mouse ES cells, Drosophila and yeast. The project will develop cross-organism investigator groupings and an organizational structure for cross-fertilization, rapid application to model organisms and back to human and translational biology.
  • The project should develop new tools for epigenome analysis, including reference reagents such as validated monoclonal antibodies for chromatin, and bioinformatics tools to allow information generated by multiple investigators to be assembled and compared for quantitative multi-platform epigenome analysis.

 

 


List of Participants

 

 


Andrew P. Feinberg, M.D., M.P.H. (Co-chair)

King Fahd Professor of Medicine, Oncology, and Molecular Biology & Genetics

Director, Johns Hopkins Genome Center in Epigenetics

720 Rutland Avenue, Ross 1064

Baltimore, MD 21205

Phone: (410) 614-3489

Fax: (410) 614-9819

E-mail: afeinberg@jhu.edu

 

Peter A. Jones, Ph.D (Co-chair)

Director

USC Cancer Center

1441 East Lake Avenue

Los Angeles, CA 90033

Phone: (323) 865-0816

Fax: (323) 865-0102

E-mail: jones_p@ccnt.hsc.usc.edu

 

Stephen B. Baylin, M.D.

Ludwig Professor of Oncology

Chief, Cancer Biology Division

The Johns Hopkins University School of Medicine

1650 Orleans Street

Suite 541

Baltimore, MD 21231

Phone: (410) 955-8506

Fax: (410) 614-9884

E-mail: sbaylin@jhmi.edu

Shelley L. Berger, Ph.D.

Associate Professor

The Wistar Institute

3601 Spruce Street, Room 207

Philadelphia, PA 19104

Phone: (215) 898-3922

Fax: (215) 898-0663

E-mail: berger@wistar.upenn.edu

 

Bradley Bernstein, M.D., Ph.D.

Assistant Professor

Massachusetts General Hospital and Harvard Medical School

146 Larch Road

Cambridge, MA 02138

Phone: (617) 256-5520

Fax: (617) 495-0751

E-mail: bbernstein@partners.org

 

Aravinda Chakravarti, Ph.D

Professor and Director

The John Hopkins University

733 North Broadway, Suite 571

Baltimore, MD 21205

Phone: (410) 502-7525

Fax: (410) 502-7544

E-mail: aravinda@jhmi.edu

 

Joseph F. Costello, Ph.D.

Associate Professor

Comprehensive Cancer Center

University of California, San Francisco

2340 Sutter, Room N225

San Francisco, CA 94143

Phone: (415) 514-1183

Fax: (415) 502-6779

E-mail: jcostello@cc.ucsf.edu

 

Sarah Elgin, Ph.D.

Professor of Biology

Washington University in St. Louis

One Brookings Drive

Biology Department, CB-1229

St. Louis, MO 63130

Phone: (314) 935-5348

Fax: (314) 935-5125

E-mail: selgin@biology.wustl.edu

 

Manel Esteller, M.D., Ph.D.

Director, Cancer Epigentics

Centro Nacional de Investigaciones Oncologica

Melchor Fernandez Almagro, 3

Madrid, Spain E-28029

Phone: +34-91-224-6940

Fax: +34+61-224-6923

E-mail: mesteller@cnio.es

 

Margaret Foti, Ph.D., M.D.

Chief Executive Officer

American Association for Cancer Research

615 Chestnut Street

17th Floor

Philadelphia, PA 19106

Phone: (215) 440-9300

Fax: (215) 440-9322

E-mail: foti@aacr.org

 

Thomas R. Gingeras, Ph.D.

Vice President Biological Research

Affymetrix Laboratories

3380 Central Expressway

Santa Clara, CA 95051

Phone: (408) 731-5069

Fax: (408) 481-0422

E-mail: tom_gingeras@affymetrix.com

 

Michael Goggins, M.D.

Associate Professor of Pathology, Medicine and

  Oncology

The John Hopkins University

632 Ross Building

720 Rutland Avenue

Baltimore, MD 21205

Phone: (410) 955-3511

Fax: (410) 614-0671

E-mail: mgoggins@jhmi.edu

 

John M. Greally, M.D., Ph.D.

Assistant Professor

Albert Einstein College of Medicine

1300 Morris Park Avenue, Ullmann 911

Bronx, NY 10461

Phone: (718) 430-2875

Fax: (718) 824-3153

E-mail: jgreally@aecom.yu.edu

 

Steven Henikoff, Ph.D

Professor

Fred Hutchinson Cancer Research Center

4711 51st Place

Seattle, WA 98116

Phone: (206) 667-4515

Fax: (206) 667-5889

E-mail: steveh@fhcrc.org

 

Hui-Ming T. Huang, Ph.D.

Professor

Human Cancer Genetics, Medical 

  Research Facility

420 West 12th Street, Room 514

Columbus, OH 43210

Phone: (614) 688-8277

Fax: (614) 292-5995

E-mail: tim.huang@osumc.edu

 

Laurie Jackson-Grusby, Ph.D.

Assistant Professor

Children's Hospital Boston, Harvard

  Medical School

300 Longwood Avenue

Boston, MA 02115

Phone: (617) 919-2104

Fax: (617) 730-0168

E-mail: laurie.jackson-grusby@childrens.harvard.edu

 

Randy Jirtle, Ph.D

Professor

Duke University Medical Center

4904 Montvale Drive

Durham, NC 27705

Phone: (919) 684-2770

Fax: (919) 684-5584

E-mail: randyjirtle@mac.com

 

Paula Kim

President

Translating Research Across Communities

10720 Columbia Pike #500

Silver Spring, MD 20901

Phone: (866) 261-2295

Fax: (310) 388-1524

E-mail: paulakim@cox.net

 

Peter W. Laird, Ph.D.

Associate Professor

University of Southern California

1441 Eastlake Avenue

NOR 6418, MC 9176

Los Angeles, CA 90089

Phone: (313) 865-0650

Fax: (323) 865-0158

E-mail: plaird@usc.edu

 

Jared M. Ordway, Ph.D.

Scientist

Orion Genomics

4041 Forest Park Avenue

St. Louis, MO 63108

Phone: (314) 633-1847

Fax: (314) 615-6975

E-mail: jordway@oriongenomics.com

 

Bing Ren, Ph.D

Assistant Professor

Cellular and Molecular Medicine

University of California, San Diego

9500 Gilman Drive #0653

La Jolla, CA 92093

Phone: (858) 822-5766

Fax: (858) 534-7750

E-mail: biren@ucsd.edu

 

Thea D. Tlsty, Ph.D

Professor

University of California, San Francisco

513 Parnassus Avenue  HSW-451

San Francisco, CA 94143

Phone: (415) 502-6116

Fax: (415) 502-6163

E-mail: ttlsty@itsa.ucsf.edu

 

Benjamin Tycko, M.D., Ph.D.

Associate Professor of Pathology

Columbia University

630 W. 168th St.

New York, NY 10032

Phone: (212) 851-5280

Fax: (212) 851-5284

E-mail: bt12@columbia.edu

 

Toshikazu Ushijima, M.D., Ph.D.

Chief

National Cancer Center Research Institute

5-1-1 Tsukiji

Chuo-ku Tokyo, Japan 104-0045

Phone: 81-3-3547-5240

Fax: 81-3-5565-1753

E-mail: tushijim@ncc.go.jp

 

Patrick Varga-Weisz, Ph.D.

European Epigenome Network of Excellence

Babraham Institute

Cambridge, United, UK CB2 4AT

Phone: (011) (44) 1223 496 434

Fax: (011) (44) 1223 496 22

E-mail: patrick.varga-weisz@bbsrc.ac.uk

 

Stephen T. Warren, Ph.D.

Professor of Human Genetics

Emory University School of Medicine

Whitehead Biomedical Research Building

615 Michael Street., NE., Suite 301

Atlanta, GA 30322

Phone: (404) 727-5979

Fax: (404) 727-3949

E-mail: swarren@emory.edu

 

Bernard E. Weissman, Ph.D.

Professor

University of North Carolina

Lineberger Center

102 Mason Farm Road

Chapel Hill, NC 27599

Phone: (919) 966-7533

Fax: (919) 966-9673

E-mail: weissman@med.unc.edu

 


 

 

National Institutes of Health Attendees

 

 


Grace S. Ault, Ph.D. (NCI Organizer)

Program Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

EPN 5000

Rockville, MD 20852

Phone: (301) 435-1878

Fax: (301) 480-0864

E-mail: ga5k@nih.gov

 

Anthony D. Carter, Ph.D.

Program Director

Division of Genetics and Developmental Biology

National Institute of General Medical Sciences

National Institutes of Health

45 Center Drive

Room 2A5-25R, MSC 6200

Bethesda, MD 20892

Phone: (301) 594-0943

Fax: (301) 480-2228

E-mail: cartera@nigms.nih.gov

 

John S. Cole III, Ph.D.

Program Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

Suite 5000

Rockville, MD 20852

Phone: (301) 496-1718

Fax: (301) 496-2025

E-mail: jc121b@nih.gov

 

Jennifer Couch, Ph.D.

Program Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

EPN 5004

Bethesda, MD 20892

Phone: (301) 435-5226

Fax: (301) 480-2854

E-mail: couchj@mail.nih.gov

 

Elise Feingold, Ph.D

Program Director, Genome Analysis

National Human Genome Research Institute

National Institutes of Health

5635 Fishers Lane

MSC 9305

Bethesda, MD 20892

Phone: (301) 496-7531

Fax: (301) 480-2770

E-mail: ef5j@nih.gov

 

Daniela Gerhard, Ph.D

Director

Office of Cancer Genomics

National Cancer Institute

National Institutes of Health

31 Center Drive

Room 10A07

Bethesda, MD 20892

Phone: (301) 451-8027

Fax: (301) 480-4368

E-mail: gerhardd@mail.nih.gov

 

Peter Good, Ph.D.

Program Director

National Human Genome Research Institute

National Institutes of Health

5635 Fishers Lane, Suite 4067

Bethesda, MD 20892

Phone: (301) 496-7531

Fax: (301) 480-2770

E-mail: goodp@mail.nih.gov

 

Mark S. Guyer, Ph.D

Director, Extramural Research

National Human Genome Research Institute

National Institutes of Health

5635 Fishers Lane

Suite 4080

Bethesda, MD 20817

Phone: (301) 496-7531

Fax: (301) 480-2770

E-mail: guyerm@exchange.nih.gov

 

Kevin Howcroft, Ph.D.

Program Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

EPN 5060

Rockville, MD 20852

Phone: (301) 496-7815

Fax: (301) 480-2844

E-mail: howcrofk@mail.nih.gov

 

John Ilekis, Ph.D

Program Director

National Institute of Child Health and Human Development

National Institutes of Health

6100 Executive Boulevard

PPB, Room 4B0C

Rockville, MD 20852

Phone: (301) 435-6895

Fax: (301) 496-3790

E-mail: ilekisj@mail.nih.gov

 

Carol MacLeod, Ph.D.

Program Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

EPN 5066

Rockville, MD 20852

Phone: (301) 435-1878

Fax: (301) 480-0864

E-mail: cm465d@nih.gov

 

Susan McCarthy, Ph.D.

Program Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

Room 5058

Rockville, MD 20852

Phone: (301) 594-8785

Fax: (301) 480-2844

E-mail: mccarths@mail.nih.gov

 

Anna McCormick, Ph.D

Branch Chief

National Institute on Aging

National Institutes of Health

7201 Wisconsin Avenue, Suite 2C231

Bethesda, MD 20892-9205

Phone: (301) 496-6402

Fax: (301) 402-0010

E-mail: mccormia@nia.nih.gov

 

Judy Mietz, Ph.D.

Branch Chief

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

EPN 5028

Rockville, MD 20852

Phone: (301) 496-9326

Fax: (301) 496-1224

E-mail: jm166o@nih.gov

 

Suresh Mohla, Ph.D.

Branch Chief

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

EPN 5038

Rockville, MD 20852

Phone: (301) 435-1878

Fax: (301) 480-0864

E-mail: mohlas@mail.nih.gov

 

Allan R. Mufson, Ph.D.

Branch Chief

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

EPN 5062

Rockville, MD 20852

Phone: (301) 496-7815

Fax: (301) 496-2844

E-mail: rm2300@nih.gov

 

Paul Okano, Ph.D.

Program Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Excutive Boulevard

Suite 5000

Bethesda, MD 20892

Phone: (301) 496-9326

Fax: (301) 496-1224

E-mail: po8k@nih.gov

 

Brad Ozenberger, Ph.D.

Program Director

Division of Extramural Research

National Human Genome Research Institute

National Institutes of Health

5635 Fishers Lane

Suite 4080

Bethesda, MD 20817

Phone: (301) 496-7531

Fax: (301) 480-2770

E-mail: bozenberger@mail.nih.gov

 

Jane Peterson, Ph.D.

Associate Director of Extramural Research

National Human Genome Research Institute

National Institutes of Health

5635 Fishers Lane

Suite 4080

Bethesda, MD 20817

Phone: (301) 496-7531

Fax: (301) 480-2770

E-mail: petersonj@exchange.nih.gov

 

William C. Reinhold

Biologist

Division of Genomics and Bioinformatics Group

National Cancer Institute

National Institutes of Health

9000 Rockville Pike

Building 37, Room 5056

Bethesda, MD 20894

Phone: 301-496-9572

Fax: 301-402-0752

E-mail: wcr@mail.nih.gov

 

Neeraja Sathyamoorthy, Ph.D.

Program Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

Suite 5000

Rockville, MD 20892

Phone: (301) 435-1878

Fax: (301) 294-5030

E-mail: sathyamn@mail.nih.gov

 

Dinah Singer, Ph.D.

Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

EPN 5044

Rockville, MD 20852

Phone: (301) 496-8636

Fax: (301) 496-8656

E-mail: ds13j@nih.gov

 

John Sogn, Ph.D.

Deputy Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

Room 5050

Rockville, MD 20852

Phone: (301) 594-8782

Fax: (301) 496-8656

E-mail: sognj@mail.nih.gov

 

Daniel J. Sussman, Ph.D.

Program Director

Division of Cancer Biology

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

Rockville, MD 20892

Phone: (301) 435-1878

Fax: (301) 496-8656

E-mail: sussmand@mail.nih.gov

 

Susan T. Taymans, Ph.D.

Program Director

National Institute of Child Health and Human Development

National Institutes of Health

6100 Executive Boulevard

Room 8B01

Rockville, MD 20852

Phone: (301) 496-6517

Fax: (301) 496-0962

E-mail: taymanss@mail.nih.gov

 

Frederick L. Tyson, Ph.D.

Scientific Program Administrator

Suspectibility and Population Health

National Institute of Environmental Health Science

National Institutes of Health

79 T.W. Alexander Drive

MD EC-21

Research Triangle, NC 27709

Phone: (919) 541-0176

Fax: (919) 316-4606

E-mail: tyson2@mail.nih.gov

 

May Wong, Ph.D.

Program Director

Cancer Etiology Branch

National Cancer Institute

National Institutes of Health

6130 Executive Boulevard

Room 5010, MSC 7398

Bethesda, MD 20892

Phone: (301) 496-1953

Fax: (301) 496-2025

E-mail: mw132k@nih.gov

 

John N. Weinstein, Ph.D.

Senior Investigator

National Cancer Institute

National Institutes of Health

37 Convent Drive

Bethesda, MD 20892

Phone: (301) 496-9571

Fax: (301) 402-0752

E-mail: jw4i@nih.gov


 

 

 

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