The Unsorted BBS Collection/thegreatunsorted.tar/thegreatunsorted/texts/txtfiles_misc/human_ge.pro

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Table of Contents

Foreword and Preface

Introduction
     History of the Human Genome Project
     DOE-NIH Coordination
     Scientific Five-Year Goals of the U.S. Human Genome Project

Highlights of Research Progress
     Mapping
     Informatics
     Sequencing
     Activities Addressing Ethical, Legal, and Social Issues Related to
      Human Genome Project Data
      Technology Transfer and Industrial Collaboration

Human Genome Center Research Narratives
     Lawrence Berkeley Laboratory
     Lawrence Livermore National Laboratory
     Los Alamos National Laboratory

Program Management Infrastructure
     DOE OHER Mission
     Program Management Task Group
     Field Coordination
      Human Genome Coordinating Committee
      Human Genome Management Information System
      Human Genome Distinguished Postdoctoral Fellowships
     Resource Allocation
     Interagency Coordination
      Joint DOE-NIH Activities
           Joint Mapping Working Group
           Joint Informatics Task Force
           Joint Sequencing Working Group
           Joint Working Group on Ethical, Legal, and Social Issues
           Joint Working Group on the Mouse
     Other U.S. Genome Research
      U.S. Department of Agriculture
      National Science Foundation
      Howard Hughes Medical Institute

International Coordination
     HUGO: Worldwide Genome Research Coordination
     UNESCO: Promoting the Interests of Developing Countries

Search Abstracts of DOE-Funded Research

      You may search by Author Name, Address, or any word that appears
      in the abstract.  You may narrow your search by using the boolean
      operators (and. or, not) or by phrase searches (".....").
      For example - if you want to see all the mouse work funded by the
      DOE Genome projuct simply search for

      mouse

      But if you want to see only the mouse projects that have proposed
      to use Fluorescence In Situ Hybridization (FISH) search for:

      mouse and fish

      this will narrow the results dramatically.


Appendices
     A. Primer on Molecular Genetics
     B. Conferences, Meetings, and Workshops Sponsored by DOE
     C. Members of the DOE Health and Environmental Research
      Advisory Committee
     D. Members of the DOE-NIH Joint Working Groups
     E. Glossary

     Index to Principal and Coinvestigators Listed in Abstracts
     Acronym List



Foreword

Acquiring complete knowledge of the organization, structure, and
function of the human genome_the master blueprint of each of
us_is the broad aim of the Human Genome Project. It is a new kind
of program in biology, both in its size and focus on a limited
set of goals and in its dependence on the development and use of
technology. The coordinated U.S. Human Genome Project was
officially initiated by the Department of Energy (DOE) Office of
Health and Environmental Research and the National Institutes of
Health (NIH) National Center for Human Genome Research (NCHGR) in
FY 1991 with the publication in April 1990 of Understanding Our
Genetic Inheritance; The U.S. Human Genome Project: The First
Five Years 1991-1995. The DOE effort, which began very modestly
almost 4 years before, is now over 5 years old. Taking stock of
what has been done and what remains to be done is particularly
appropriate at this time.

That the ambitious scientific goal of the Human Genome Project
can now be imagined is the result of the revolution occurring in
biology during the last 20 years. Modern biological science has
achieved a profound but still quite incomplete level of
understanding of how the diversity of all living things is
determined. This insight, along with scientific and technical
advances in other fields, has brought unprecedented power both in
being able to analyze and manipulate genetic structures and to
use and store large quantities of genetic information. DOE is
uniquely positioned to bring together expertise in physics,
chemistry, engineering, and computer science to help solve
fundamental biological problems and to exploit exciting
opportunities presented by the Human Genome Project. Genome
research will also contribute to the department's role in
providing the scientific foundation for understanding the health
effects of radiation and of chemical insults to the genome.

The DOE program stresses mapping, the development of sequencing
technologies and instrumentation, and informatics. Informatics
refers to computational approaches in acquiring, storing,
distributing, analyzing, and manipulating vast amounts of mapping
and sequence data that will result from the project. Another
important program component studies the ethical, legal, and
social issues arising from use of the generated data,
particularly in the privacy and confidentiality of genetic
information. Cutting across all DOE biological and environmental
research programs are several science education activities.

The Human Genome Project is a closely cooperative activity
between NIH and DOE. NCHGR is an important and essential
participant. Internationally, the formation of the Human Genome
Organization and the establishment of national genome projects by
an increasing number of countries indicate the fascination and
promise of this effort on the collective imaginations of many
nations. In addition to the inherent excitement about increased
knowledge of human life, the project offers the promise of many
new opportunities for benefiting humanity through the development
of new diagnostics, pharmaceuticals, and therapies for a
multitude of human diseases; a wide range of improvements will
flow from other biotechnology advances. Further expected benefits
include improved risk assessment for individuals and populations
exposed to agents that impact genetic material, as well as
possible applications of the data to environmental and
remediation issues.

To be successful, the program must continue to focus on clear
objectives for mapping and sequencing and to incorporate the flow
of technological developments into the efforts of all working
laboratories. Strategies must be planned carefully and in a
comprehensive fashion as the next phase begins, in which mapping
and sequencing results proliferate and technologies mature.
Planning must be project-wide and include interagency planning at
ever-earlier stages.

This report describes the status of the DOE Human Genome Program
and its accomplishments to date. Research highlights are noted
from the program as a whole and from the three principal DOE
human genome centers at Lawrence Berkeley Laboratory, Lawrence
Livermore National Laboratory, and Los Alamos National
Laboratory. These national laboratory facilities of DOE have been
especially successful because they are organized to focus
efforts, foster interdisciplinary projects, and use advanced
technologies, some developed for other purposes, toward program
goals. Essential work is also reported from 41 different research
universities. Remarkable progress has been made in advanced
instrumentation and informatics.

A further indication of the increasing development of the DOE
program is the simple statistic that the 1989-90 report had 157
pages and included 57 abstracts of work involving 211 scientists.
The current program report contains over 240 pages and includes
more than 150 abstracts of work involving over 400 investigators,
essentially a doubling of DOE program size.

The Human Genome Project ultimately will create scientific
resources for the next wave of advances in biology and medicine.
As the project is completed, accomplishments will dwarf those
that have occurred in the biological sciences since the advent of
recombinant DNA technologies. By the same token, the ethical and
social consequences of the uses of this new knowledge must be
considered as the knowledge is acquired; if this knowledge is
responsibly obtained and applied, the next decade of biological
research will be history's most fruitful and rewarding by any
measure.



David J. Galas, Associate Director
Office of Health and Environmental Research
Office of Energy Research
U.S. Department of Energy

Preface

This is the third report summarizing the Department of Energy
(DOE) Human Genome Program, its content, progress, and
accomplishments. Since the program's conception in 1986 and
initiation in 1987 by the DOE Office of Health and Environmental
Research (OHER), its broad objectives have rapidly gained both
national and international support. The program has made
important strides in the development and application of
technologies and tools that are required for the cost-effective
characterization of the molecular nature of the human genome.

This country's Human Genome Project is jointly administered by
OHER and the National Center for Human Genome Research of the
National Institutes of Health. A successful effort to
characterize the molecular nature of human inheritance will
require continuing international cooperation involving scientists
from many countries. A number of other nations have begun
substantial efforts to map and sequence the human genome and
those of key model organisms. Although intellectual property
issues threaten some aspects of international cooperation,
increasing exchange of information has led to more involvement of
the international community in discovery, acceleration of the
pace of the research, and increased cost-effectiveness.
International communication is facilitated by regular meetings to
update the maps of individual chromosomes and by contributions to
databases such as the Genome Data Base and nucleic acid sequence
databanks. Through such databases a worldwide data aggregation
and distribution system is being developed to exchange
information regarding the genome.

Aided by funding from the Human Genome Project, serious study is
under way on ethical, legal, and social issues that are becoming
more urgent because of the rapid growth in knowledge of human
genetics. It is important to develop and disseminate deeper and
more widespread understanding of these dynamic issues and of the
choices available for families, the law, and society. An educated
public is required to make intelligent choices in this area. The
national genome project is now the largest provider of funds for
study of such issues.

A key to the long-term success of the program is the initial
phase of intensive resource and technology development that
requires input and involvement from many scientific and
engineering disciplines. Exciting contributions have already been
made to biomedical knowledge and biotechnology, and such advances
are certain to continue at an ever-increasing rate. Announcements
of discovery of important disease genes have become commonplace.
Within 10 years nearly all the perhaps 100,000 genes that make up
the human genome are likely to be found. Within 15 years the
program is expected to culminate in a reference DNA sequence of
the entire genome.

Never has such a mass of data flowed into biology and medicine.
An understanding of how genetic variations account for much of
the richness and adventure of human diversity will be greatly
increased. More practically, there can be little doubt of
tremendous payoffs in terms of diagnoses and, ultimately,
specific therapies for many human diseases.

Moreover, new technologies and rapidly developing analytical
tools to characterize the human genome will have widespread
impact beyond human health. They will find application in
revealing the genetic inheritance of many organisms of potential
scientific and commercial interest and will provide an important
stimulus to broaden and deepen the impact of modern biology in
areas such as energy, environmental protection and waste
treatment, agriculture, and the materials sciences.

Of particular importance is the facile access to proteins that
rapidly follows discovery of their genes. As a result of genome
projects, we will soon be in a position to begin the systematic
large-scale characterization of proteins and their structure. The
interplay of molecular biology, structural studies,
high-performance computing, and advanced molecular graphics will
certainly lead to an understanding of macromolecular
structure-function relationships. The scientific and economic
implications of such a predictive understanding cannot be
overestimated. It is the key to full realization of the potential
of modern biology.

Intense X-ray light and neutrons produced by unique, large, and
expensive machines (synchrotrons and reactors) at DOE
laboratories are important national resources for the
determination of biological structure and, hence, for the
national effort in biotechnology. A central goal of OHER is to
provide access to these machines by making facilities and
technical support available to structural-biology users, a need
that has been projected to increase tenfold in the next several
years.

Finally, as Robert Sinsheimer elegantly pointed out in The FASEB
Journal (November 1991), the Human Genome Project is an epic
venture of discovery that will in time clarify many endlessly and
fruitlessly debated mysteries of human nature. With this project
we are launched upon a new stage of the age-old quest to
illuminate the record of the human past_the prehistory of our
species as recorded in the genetic script or blueprint for our
being. When complete, the project will have provided us with an
unprecedented resource_the complete text of our genetic
endowment. It will be seen as a turning point in human history.



David A. Smith, Director
Health Effects and Life Sciences Research Division
Office of Health and Environmental Research
Office of Energy Research
U.S. Department of Energy
Acknowledgements

The DOE Office of Health and Environmental Research gratefully
acknowledges the contributions made by genome research grantees
and contractors in submitting abstracts, photographs, captions,
and narratives. The Human Genome Management Information System at
Oak Ridge National Laboratory (managed by Martin Marietta Energy
Systems, Inc., for the U.S. Department of Energy under contract
DE-AC05-84OR21400) collected and organized the information,
prepared the manuscript, and implemented the design and
production of this publication.




Introduction

The U.S. Human Genome Project is the national coordinated 15-year
effort to characterize all the human genetic material_the
genome_by improving existing human genetic maps, constructing
physical maps of entire chromosomes, and ultimately determining
the complete sequence of the deoxyribonucleic acid (DNA) subunits
in the human genome. Parallel studies are being carried out on
selected model organisms to facilitate the interpretation of
human gene function. The ultimate goal of the U.S. project is to
discover all of the more than 100,000 human genes and render them
accessible for further biological study.

Current technology could probably be used to attain the
objectives of the Human Genome Project, but the cost and time
required would be unacceptable. For this reason, a major feature
of the first 10 years of the project is to optimize existing
methods and develop new technology to increase efficiency in DNA
mapping and sequencing by 1 or 2 orders of magnitude. The genome
will eventually be sequenced using continually evolving
technologies and revolutionary methods not in existence today.

Information obtained as part of the Human Genome Project will
dramatically change almost all biological and medical research
and dwarf the catalog of current genetic knowledge. In addition,
both the methods and the data developed as part of the project
are likely to benefit investigations of many other genomes,
including a large number of commercially important plants and
animals.

For more information on the science of genomics, see Appendix A,
"Primer on Molecular Genetics," p. 191. Terms are defined in the
Glossary, p. 229. An acronym list is on the inside back cover.


History of the DOE Human Genome Program

A brief history of the U.S. Department of Energy (DOE) Human
Genome Program will be useful in a discussion of the objectives
of the DOE program as well as those of the collaborative U.S.
Human Genome Project. The Office of Health and Environmental
Research (OHER) of DOE and its predecessor agencies_the Atomic
Energy Commission and the Energy Research and Development
Administration_have long sponsored research into genetics, both
in microbial systems and in mammals, including basic studies on
genome structure, replication, damage, and repair and the
consequences of genetic mutations.

In 1984, OHER and the International Commission on Protection
Against Environmental Mutagens and Carcinogens cosponsored a
conference in Alta, Utah, which highlighted the growing roles of
recombinant DNA technologies. Substantial portions of the
meeting's proceedings were incorporated into the Congressional
Office of Technology Assessment report, Technologies for
Detecting Heritable Mutations in Humans, in which the value of a
reference sequence of the human genome was recognized.

Acquisition of such a reference sequence was, however, far beyond
the capabilities of biomedical research resources and
infrastructure existing at that time. Although the small genomes
of several microbes had been mapped or partially sequenced, the
detailed mapping and eventual sequencing of 24 distinct human
chromosomes (22 autosomes and the sex chromosomes X and Y) that
together comprise an estimated 3 billion subunits was a task some
thousandsfold larger.

DOE OHER was already engaged in several multidisciplinary
projects contributing to the nation's biomedical capabilities,
including the GenBankr DNA sequence repository, which was
initiated and sustained by DOE computer and data-management
expertise. Several major user facilities supporting
microstructure research were developed and are maintained by DOE
(see box, p. 55). Unique chromosome-processing resources and
capabilities were in place at Los Alamos National Laboratory and
Lawrence Livermore National Laboratory. Among these were the
fluorescence-activated cell sorter (FACS) systems to purify human
chromosomes within the National Laboratory Gene Library Project
for the production of libraries of DNA clones. The availability
of these monochromosomal libraries opened an important path_a
practical means of subdividing the huge total genome into 24 much
more manageable components.

With these capabilities, OHER began in 1986 to consider the
feasibility of a dedicated human genome program. Leading
scientists were invited to the March 1986 international
conference at Santa Fe, New Mexico, to assess the desirability
and feasibility of implementing such a project. With virtual
unanimity, participants agreed that ordering and eventually
sequencing DNA clones representing the human genome were
desirable and feasible goals. With the receipt of this
enthusiastic response, OHER initiated several pilot projects.
Program guidance was further sought from the DOE Health Effects
Research Advisory Committee (HERAC, see Appendix C for a list of
current members).


The HERAC Recommendation. The April 1987 HERAC report recommended
that DOE and the nation commit to a large, multidisciplinary,
scientific, and technological undertaking to map and sequence the
human genome. DOE was particularly well suited to focus on
resource and technology development, the report noted; HERAC
further recommended a leadership role for DOE because of its
demonstrated expertise in managing complex and long-term
multidisciplinary projects involving both the development of new
technologies and the coordination of efforts in industries,
universities, and its own laboratories. Evolution of the nation's
Human Genome Project further benefited from a 1988 study by the
National Research Council (NRC) entitled Mapping and Sequencing
the Human Genome, which recommended that the United States
support this research effort and presented an outline for a
multiphase plan.


DOE-NIH Coordination

The National Institutes of Health (NIH) was a necessary
participant in the large-scale effort to map and sequence the
human genome because of its long history of support for
biomedical research and its vast community of scientists. This
was confirmed by the NRC report, which recommended a major role
for NIH. In 1987, under the leadership of Director James
Wyngaarden, NIH established the Office of Genome Research in the
Director's Office. In 1989 this office became the National Center
for Human Genome Research (NCHGR), directed by James D. Watson.
After Watson's resignation in April 1992, Michael Gottesman was
appointed NCHGR Acting Director.

In addition to extramural support for research projects in
physical mapping and the development of index linkage markers and
technology, NIH also provides support for genetic mapping based
on family studies and, following NRC recommendations, for studies
on several relevant model organisms. DOE-supported genome
research is focused almost exclusively on the human genome
through support of large-scale physical mapping, resource and
instrumentation technology development, and improvements in
computational and database capabilities and research
infrastructure. A significant portion of the DOE Human Genome
Program is allocated to the DOE national laboratories.

In several important areas, DOE and NIH cooperate to support
critical resources such as the Genome Data Base (GDB) at Johns
Hopkins University. Cofunded since 1991 as the central
international repository of human chromosome mapping data, GDB is
expected to receive supporting funds from other nations. DOE and
NIH also cooperate to support joint workshops; a number of
ethical, legal, and social issues projects; and the Human Genome
News newsletter.

Joint task groups under the DOE-NIH Joint Subcommittee on the
Human Genome meet periodically to define program needs and
develop recommendations for their parent DOE and NIH committees.
OHER and NCHGR cosponsor workshops and meetings of the task
groups on mapping; sequencing; informatics; the use of the mouse
as a mammalian model; and_in a departure from most scientific
programs_ethical, legal, and social issues related to data
produced in the project.

Many other highlights of the DOE OHER program follow in the
succeeding sections of this report, including reports from the
human genome centers; further details of program infrastructure,
management, and coordination; resource allocation; and abstracts
of individual research projects.




Scientific Five-Year Goals of the U.S. Human Genome Project from
the NIH-DOE Five Year Plan* [Implemented October 1, 1990 (FY
1991)]

1. Mapping and Sequencing the Human Genome

Genetic Mapping

     Complete a fully connected human genetic map with markers
     spaced an average of 2 to 5 cM apart. Identify each marker
     by a sequence tagged site (STS).

Physical Mapping

     Assemble STS maps of all human chromosomes with the goal of
     having markers spaced at approximately 100,000-bp intervals.

     Generate overlapping sets of cloned DNA or closely spaced
     unambiguously ordered markers with continuity over lengths
     of 2 Mb for large parts of the human genome.

DNA Sequencing

     Improve current and develop new methods for DNA sequencing
     that will allow large-scale sequencing of DNA at a cost of
     $0.50 per base pair.
     Determine the sequence of an aggregate of 10 Mb of human DNA
     in large continuous stretches in the course of technology
     development and validation.

2. Model Organisms

     Prepare a mouse genome genetic map based on DNA markers.
     Start physical mapping on one or two chromosomes.

     Sequence an aggregate of about 20 Mb of DNA from a variety
     of model organisms, focusing on stretches that are 1 Mb
     long, in the course of developing and validating new and
     improved DNA sequencing technology.

3. Informatics_Data Collection and Analysis

     Develop effective software and database designs to support
     large-scale mapping and sequencing projects.

     Create database tools that provide easy access to up-to-date
     physical mapping, genetic mapping, chromosome mapping, and
     sequencing information and allow ready comparison of the
     data in these several data sets.

     Develop algorithms and analytical tools that can be used in
     the interpretation of genomic information.

4. Ethical, Legal, and Social Considerations

     Develop programs directed toward understanding the ethical,
     legal, and social implications of Human Genome Project data.
     Identify and define the major issues and develop initial
     policy options to address them.

5. Research Training

     Support research training of pre- and postdoctoral fellows
     starting in FY 1990. Increase the number of trainees
     supported until a steady state of about 600 per year is
     reached by the fifth year.

     Examine the need for other types of research training in the
     next year (FY 1991).

6. Technology Development

     Support automated instrumentation and innovative and
     high-risk technological developments as well as improvements
     in current technology to meet the needs of the genome
     project as a whole.

7. Technology Transfer

     Enhance the already close working relationships with
     industry.

     Encourage and facilitate the transfer of technologies and of
     medically important information to the medical community.


*Understanding Our Genetic Inheritance; The U.S. Human Genome
Project: The First Five Years FY 1991-1995, DOE/ER-0452P, U.S.
Department of Health and Human Services and U.S. Department of
Energy, April 1990.





Highlights of Research Progress

Mapping

A major goal for DOE and NIH, as stated in the Five Year Plan (p.
5) for the Human Genome Project officially implemented in FY
1991, is to develop refined physical maps of chromosomes.
Increasingly detailed maps will provide biomedical scientists
with rapid access to important areas on chromosomes through their
specific markers and ordered sets of DNA clones.

Page numbers for research abstracts of investigators noted in
parentheses can be located in the "Index to Principal and
Coinvestigators Listed in Abstracts," p. 243.


Physical Map Construction

DOE sponsors both extensive physical mapping studies and
supportive resource and technology development. Physical mapping
of chromosomes 5, 11, 16, 17, 19, 21, 22, and X has been or is
being supported directly. Increasingly detailed maps facilitate
access to important chromosomal loci through their constituent
markers and ordered DNA clones.

The earliest concerted mapping efforts began on chromosome 16 at
the Los Alamos National Laboratory (LANL) Center for Human Genome
Studies and on chromosome 19 at the Lawrence Livermore National
Laboratory (LLNL) Human Genome Center. These efforts have
achieved excellent progress (see detailed narratives, pp. 46 and
36, respectively) through the development of effective
multidisciplinary teams and efficient methods for generating
clone "fingerprints." The fingerprints provide data for
recognizing clone pairs that overlap, facilitating the
construction of increasingly larger sets of overlapping clones,
called contigs. Approximately 90% of chromosomes 16 and 19 is now
represented by fingerprinted clones, and multiclone contigs span
at least 80% of their length. Initial contig assembly
methodologies are complemented by strategies designed to finish
the physical maps and align them with genetic maps. This
progress, together with the many contributions from other
research groups (presented in the Abstracts section of this
report), shows that resources and technologies required to
achieve the mapping goals stated in the Five Year Plan are
rapidly being realized.


National Laboratory Gene Library Project (NLGLP)

Among the resources most crucial to mapping progress are the
libraries of clones representing each of the human chromosomes.
Their availability reduces the total genome map ping effort to 24
smaller, more-manageable mapping projects. This
chromosome-specific clone library production from physically
purified chromosomes depends on the unique LANL and LLNL
chromosome-sorting facilities maintained through the DOE NLGLP.
These library resources are either distributed from the
laboratories or through the American Type Culture Collection. As
of December 1991 over 620 chromosome-specific libraries were
distributed as resources for entire chromosome mapping efforts
and for more-selective gene hunts. Current library production is
focused on the needs of the major chromosome mapping projects (L.
Deaven, LANL; P. de Jong, LLNL).


Recombinant Clone Types

Other biological resources are also being developed to further
chromosome mapping progress. These resources include several
useful genetic elements or recombinant DNAs and their cellular
hosts. The largest elements are the intact, single human
chromosomes maintained in somatic cell hybrids, such as single
human chromosome/hamster-host cell hybrids. They are valuable for
sorting out the human chromosomes for construction of
single-chromosome libraries. Insert sizes of recombinants range
from millions to a few hundred bases. Recombinant cosmid clones
with 40- to 50-kb human DNA inserts predominated in the early
contig-building efforts and continue to be a basic resource
(refer to Abstracts: Resource Development, p. 82).


Monochromosomal Yeast Artificial Chromosomes (YACs)

YACs with inserts of 200 kb and larger, whose initial development
was pioneered with NIH support, are now widely used in physical
mapping projects. The recently developed capability to produce
YACs from flow-sorted chromosomes is making available
mono-chromosomal YAC libraries to speed mapping projects (M.
McCormick, L. Deaven, and R. Moyzis, LANL). These libraries are
made up of YACs containing human DNA inserts. This contrasts with
libraries made from somatic cell hybrids, which are made up of
YACs that contain mostly nonhuman DNA inserts.


Clone Library Array and Analysis

When user laboratories maintain clone libraries in the same
arrayed-format addressing system, the information obtained from
these libraries is maximized because the accumulated data from
different laboratories can be readily combined. The tedious task
of arraying thousands of DNA clones has been greatly alleviated
through the development and implementation of automated or
robotic processing systems (T. Beugelsdijk and P. Medvick, LANL;
J. Jaklevic, Lawrence Berkeley Laboratory (LBL); and A. Olsen,
LLNL). These systems are being increasingly utilized in clone
analyses and in comparisons needed for overlap detection.


Multiplexed Clone Overlap Detection

Overlap detection of sequence homologies by DNA hybridization is
speeded by multiplexing strategies in which the processing of
pools of clones or their derivative probes replaces the more
tedious analysis of individual clones. Multiplexing was first
implemented by the chromosome 11 mapping group (G. Evans, Salk
Institute for Biological Studies). Several second-generation
multiplexing schemes are now being implemented to speed overlap
detection both within libraries and between members of different
types of libraries (J. F. Cheng, LBL; P. de Jong, LLNL).

Messenger RNA/cDNAs Used To Generate Sequence Tagged Sites (STSs)

STS marking of DNA clones provides a common language for uniting
the results obtained with different types of recombinant DNAs and
varied approaches to map generation. An STS is a short, unique
DNA sequence (generally 100 to 300 bp) that distinguishes a
chromosomal locus. The STS segment can be selectively amplified
within the entire genome by the polymerase chain reaction to
provide an identifying tag for any DNA clone containing the site.
DOE is emphasizing the use of STSs for expressed genes, as
represented by their derivative cDNAs. Mapping these STSs onto
contigs and to their chromosomal loci is thus rapidly placing
genes on the developing chromosome maps (refer to Abstracts:
Resource Development, p. 82).


Microdissection Libraries

Chromosome microdissection can facilitate region-specific mapping
efforts, such as the localized ordering of clones on the much
longer chromosomes, by identifying sets of clones derived from
the specific region. Region-specific probes can also serve in the
identification of locally expressed genes by selectively
displaying their counterparts within complex cDNA libraries
(F.-T. Kao, Eleanor Roosevelt Institute).


Libraries of Hybrid Somatic Cells with Partial Human Chromosomes

Aberrant chromosomes arising from rearrangement processes can be
moved into host rodent cells, providing for the maintenance of a
human subchromosomal segment. A large hybrid set has been
assembled for chromosome 16 (G. Sutherland, Adelaide Children's
Hospital, South Australia). These partial chromosomes together
define over 100 chromosomal segment "bins" to which clones,
contigs, and other DNA markers can be assigned by DNA
hybridization tests. This resource system is greatly speeding the
completion of the chromosome 16 map.


Fluorescence In Situ Hybridization (FISH)

The previous mapping of DNA clones by FISH onto metaphase
chromosomes has now been extended to the much less condensed
interphase and pronuclear DNAs. Mapping onto less-condensed
chromosomes increases spatial resolution and the capacity to
order closely spaced markers. As a component of evolving mapping
strategies, FISH is serving to locate and orient cosmid contigs
on intact chromosomes and measure distances between the cosmids
as well as to mapped cDNAs. (J. Gray, University of California;
J. Korenberg, Cedars-Sinai Medical Center; B. Trask, LLNL).


Fragile X Locus Cloned

The fragile X locus has been cloned and its mode of action is
being characterized (C. T. Caskey and D. L. Nelson, Baylor
College of Medicine; and collaborators). Fragile X syndrome may
be the most common form of inherited mental retardation. About 1
in 1500 males and 1 in 2500 females are affected by the syndrome,
which is caused by a high mutation frequency at the fragile X
locus.


Myotonic Dystrophy Locus Cloned

The gene responsible for myotonic dystrophy, an autosomal
dominant disease, has been identified and cloned. The structural
defect is characterized by a tandemly repeated segment of DNA
within or close to the coding region on 19q13.3. The extent of
the amplified region appears to be associated with the severity
of the disease (C. T. Caskey, Baylor College of Medicine; P. de
Jong and A. Carrano, LLNL; and collaborators).


Informatics

Multiple informatics capabilities will be crucial to the
successful application of data derived from the genome project.
Informatics expertise, software, and hardware are being developed
in the following areas: chromosome map assembly, databases, DNA
sequence analysis, and laboratory automation.


Map Assembly

Algorithms for automatically assembling physical maps from cloned
fingerprint data have been further improved (E. Branscomb, LLNL;
M. Cinkosky, V. Faber, J. Fickett, and D. Torney, LANL).

Software permitting fast parallel computations on multiple
computers was developed to speed computation-intensive mapping
analyses
(E. Branscomb, LLNL).

A computer communication and interrogation system is being
assembled to minimize redundancy during the production of STS
chromosomal markers from cDNAs. Participating laboratories will
rapidly query distant databases to determine the novelty of a
candidate mRNA/cDNA before further pursuing the STS-generation
process.


Databases

Graphical interfaces for mapping databases were constructed to
display several different types of aligned chromosomal data and
provide expandable views [R. Douthart, Pacific Northwest
Laboratory (PNL); J. Fickett, LANL; S. Lewis, Lawrence Berkeley
Laboratory (LBL); R. Overbeek, Argonne National Laboratory
(ANL)].

The electronic Laboratory Notebook database and similar databases
are being continuously expanded to include new data types as
mapping strategies evolve (J. Fickett, LANL).

The internationally available Genome Data Base (GDB), housed at
Johns Hopkins University and cofunded since September 1991 by DOE
and NIH, is the primary reference data-base for human chromosome
mapping data produced in the United States and abroad. The
organizational structure of GDB is shown on the opposite page (P.
Pearson, GDB).

In a collaboration between LLNL and GDB, computer system
interfaces have been devised for automatically transferring large
amounts of data from mapping centers to GDB for integration into
and updating of chromosome maps.

Enhancements of the GenBankr DNA sequence database located at
LANL continue. Primarily supported by NIH with contributions from
DOE, GenBank exchanges data daily with European and Japanese
databases. GenBank has expanded its electronic data-publishing
facilities and has reached agreements with a number of journals
to facilitate electronic publication of large volumes of DNA
sequence data (J. Cassatt, NIH).


Sequence Analysis

gm, developed at New Mexico State University, is the first DNA
sequence analysis algorithm capable of recognizing and ordering
the set of protein-coding regions (exons) from among the
noncoding regions (introns) comprising a gene, rather than
predicting isolated protein-coding sequences. gm has been
distributed to laboratories worldwide (C. Fields, now at NIH, and
C. Soderlund, now at LANL).

Gene Recognition and Analysis Internet Link (GRAIL), a novel
neural network-based algorithm for identifying exons within DNA
sequences, is online at Oak Ridge National Laboratory (ORNL) to
serve the biological community by automatically analyzing
sequences. From a number of examples, this artificial
intelligence system learns several distinct sequence
characteristics through which exons can be recognized. GRAIL
automatically accepts input sequences sent to ORNL over Internet
and returns the output analysis to the sender (R. Mural and E.
Uberbacher, ORNL).


Laboratory Automation

Advances continue in the linking of laboratory instruments
directly to data-acquisition computers and analysis software at
the LANL, LLNL, and LBL human genome centers.


Sequencing

The DOE Human Genome Program has supported both evolutionary
(incremental, gel-based) improvements to classical sequencing
methods and several revolutionary (completely novel, gel-less)
technologies. Steady advances have occurred in the evolutionary
area with the implementation of automated sample preparation,
multiplex sequencing, and strategies that minimize the need for
prior subcloning.


Gel Sequencing Approaches

Multiplex sequencing systems have matured enough for transfer to
the commercial sector (G. Church, Harvard Medical School; R.
Gesteland, University of Utah).

The readout of multiplexed gels and blots using stable isotopes
as nucleic acid labels has the potential to increase sequencing
speeds by at least a factor of 10 because resonance ionization
mass spectroscopy is capable of differentiating many isotopes (H.
Arlinghaus, Atom Sciences, Inc.; K. B. Jacobson, ORNL).

Chemiluminescent label systems are now substituting for the
less-desirable radioactive labels in many applications (I.
Bronstein, Tropix, Inc.).

Systems have been developed to retain chromosome continuity
information by bypassing the customary subcloning step in the
sequencing of recombinant DNAs (D. Berg, Washington University;
C. Berg and L. Strausbaugh, University of Connecticut; J. Dunn
and F. Studier, Brookhaven National Laboratory; R. Gesteland and
R. Weiss, University of Utah).

Fractionation speeds on capillary and very thin slab gels are
10-fold faster than on traditional thick gels (N. Dovichi,
University of Alberta, Canada; B. Karger, Northeastern
University; L. Smith, University of Wisconsin).

The fluorescence/luminescence detection of fractionated nucleic
acids has been significantly improved to allow detection of the
smaller amounts of DNA loaded on capillary and thin slab gels (N.
Dovichi, University of Alberta; R. Mathies, University of
California; E. Yeung, Ames Laboratory).

Over 300 kb have been sequenced from human and mouse T-cell
receptors, providing fundamental new insights into the molecular
biology of the immune response (L. Hood and T. Hunkapiller,
California Institute of Technology).


Gel-less Sequencing Technologies

The technology for interrogating or sequencing clones by
hybridization with short oligomers has passed a second
proof-of-concept test. Three unknown DNA fragments were fully and
accurately sequenced (R. Crkvenjakov and R. Drmanac, ANL).

In research and development for single-molecule sequencing by
processive nucleotide release, the capacity to detect single
nucleotides by laser-induced fluorescence has been demonstrated
(R. Keller and J. Jett, LANL).

Progress is being made in developing methods to sequence DNA
using lasers coupled to a mass spectrometer. The great advantage
of these approaches is that the mass spectrum can be acquired in
milliseconds (C. Chen, ORNL; J. Jaklevic, W. Benner, and J. Katz,
LBL; L. Smith and B. Chait, University of Wisconsin; R. Smith,
PNL; P. Williams and N. Woodbury, Arizona State University).


Activities Addressing Ethical, Legal, and Social Issues Related
to Human Genome Project Data

In FY 1991, DOE activities on ethical, legal, and social issues
(ELSI) included two conferences, three education projects, and
three research projects. The first conference, Justice and the
Human Genome, held in November 1991 at the University of Illinois
College of Medicine, considered discrimination that could result
from the use of genetic information about ethnic and other
groups. The second conference, held in March 1992 at the Texas
Medical Center Institute of Religion, focused on Genetics,
Religion, and Ethics.

The three education projects on the science and the societal
implications of data produced in the Human Genome Project, listed
with their preparers, include (1) a module to be developed and
distributed to all U.S. high school biology teachers (Biological
Sciences Curriculum Study); (2) an educational television series,
"Medicine at the Crossroads," which will address the role of
genetics in understanding and treating disease (WNET, New York,
cofunded with NIH and the National Science Foundation); and (3) a
program of hands-on workshops for public officials and other
nonscientists (Cold Spring Harbor Laboratory).

The three ongoing research projects, listed with the institutions
developing them, are (1) a study of ethical issues arising from
the rapid proliferation of genetic tests that can predict future
disease in otherwise healthy individuals [National Academy of
Sciences (NAS) Institute of Medicine, cofunded with NIH]; (2) a
legal study of confidentiality protection for genetic data
(Shriver Center); and (3) a study to consider problems in funding
young investigators in biological and biomedical sciences (NAS).

In its first 2 years, the DOE Human Genome Program funded a
variety of ELSI activities, noted above. To avoid being spread
too thinly, the ELSI component of the DOE Program now focuses on
confidentiality and privacy concerns raised by increased genetic
data about individuals. This sensitive, personal information,
which may predict disorders before symptoms occur or treatments
are available, can affect a person's self-image, employability,
status in the eyes of others, and ability to obtain health
insurance. Since genetic knowledge can also lead to better
understanding of disease causation and to more-accurate
assessments of environmental affronts, a balance must be achieved
between the health of the public and the privacy interests of the
individual.

The DOE Human Genome Program is funding six new projects covering
ELSI activities in research and education. One of the three
projects investigating genetic discrimination will compare two
states (Florida and Georgia), contrasting their genetic testing,
screening, and counseling programs and the impact on different
ethnic and socioeconomic communities. Another will examine the
impact of two genetic conditions (cystic fibrosis and sickle cell
disease) on African-Americans and Caucasians. A third will
identify particular social institutions that may engage in
discrimination and will consider whether the discrimination, if
present, is the result of ignorance or systematic policy. A
fourth project will explore in detail (a) the effect of genetic
knowledge on the right of privacy and (b) the uses of genetic
information in public health planning. A fifth project will
develop a program of educational workshops for secondary and high
school science teachers, focused on both the science and the
ethical, legal, and social issues arising from data generated by
human genome research. A six the project will involve a second
educational television series, "The Secret of Life" (WGBH,
Boston), which will address the current revolution in molecular
biology and genetics.

Other activities include conferences on Genes and Human Behavior:
A New Era? (October 1991); Computers, Freedom, and Privacy (March
1992); and Science, Technology, and Ethical Responsibility
(scheduled for June 1992).

While very challenging issues are raised by genome research,
solutions are not simple; defensible rights often exist on both
sides of any issue. Further research is needed, as well as
activities to promote public awareness and assist in policy
development. Also, with the increasing use of computers to
assemble, store, and organize data (including genetic data) into
large databases, the issues of security and access control become
more acute. To begin reorienting and better defining the scope of
ELSI activities in the DOE program, the DOE-NIH Joint ELSI
Working Group has established a collaborative effort on privacy
to identify an ELSI research agenda and develop a more detailed
approach to some of these concerns.


Technology Transfer and Industrial Collaboration

Technology transfer, considered one of the three most important
facets of the DOE mission (along with meeting the nation's
defense and energy needs), is enhancing U.S. investment in
research and technological competitiveness. By creating new
products, markets, and jobs, the rapid deployment of technology
from the research laboratory to the marketplace can play an
important role in vitalizing the U.S. economy. A vast potential
exists for commercial development of genome resources and
technology; applications to clinical medicine have already begun.

All participants in the Human Genome Program are encouraged to
engage in active collaborations with the private sector and
transfer their resources and technologies for commercial
development.

Each national laboratory has a technology transfer office. The
LLNL, LBL, and LANL human genome centers provide a variety of
opportunities for collaborations on joint projects or for
obtaining direct access to technology. They are also exploring
additional ways to increase cooperation with the private sector;
a number of interactive projects are now under way, and
additional interactions are in the preliminary stages. In some
instances, private industries are marketing technologies
developed at DOE-sponsored research laboratories and are
providing research funds or other resources to the centers; other
collaborative programs involve joint development of technologies
and their applications to achieve project goals.

One mechanism being used by the DOE national laboratories is the
Cooperative Research and Development Agreement (CRADA). The first
CRADA in the genome project, established by DOE in the spring of
1991, was between Life Technologies, Inc. (LTI) and the LANL
Center for Human Genome Studies for technologies developed in the
single-molecule sequencing project. In this project an
LTI-modified DNA polymerase will be used to label a single DNA
strand with four different fluorescent, base-specific tags. After
an exonuclease cuts the labeled nucleic acid base pairs from the
DNA, the labeled bases will be induced to fluoresce as they pass
sequentially through a focused laser beam. The bases can be
identified and counted by a sensitive photodetector (see figure
on p. 25 for more information). If successful, the technology
will allow sequencing of 50,000-bp DNA fragments at 1000 bp/s.
LTI will have the first opportunity to license products resulting
from the joint effort and would pay royal ties to LANL under such
a license.

Potential commercial advancements in the Human Genome Program
have also been recognized outside the genome community. Research
and Development magazine selected an achievement by Edward Yeung
and other Ames Laboratory scientists as one of the 100 most
significant developments of 1991. This R&D 100 Award was given
for the development of a user-friendly instrument that detects
with extremely high sensitivity the fluorescent molecule
concentration (based on laser-excited fluorescence), an
improvement that may lead to routine high-speed DNA sequencing by
capillary gel electrophoresis. A U.S. patent for portions of this
technology has been issued, and several commercial manufacturers
are considering the possibilities of marketing the instrument.

A technology pioneered by LLNL to identify chromosomal
abnormalities (e.g., aneuploidy, translocations, and deletions)
has been licensed to Imagenetics, Inc., a medical diagnostics
firm that will manufacture the technology and provide funding for
future research and development. This technology involves the use
of specially developed fluorescent dyes called Whole Chromosome
PaintsÖ to detect diseases such as cancers and leukemia. Whole
Chromosome Paints are being marketed by LTI.

Some other technology transfers from DOE-sponsored genome
research, both at the national laboratories and extramurally, are
highlighted below. In progress or awaiting finalization are many
more developments and agreements, some of which cannot be
disclosed at this time because of their proprietary nature.

Resources. Collaborative agreements have aided in the further
development of several new technologies used in genome research,
as well as in their commercial applications. New methods are
being evaluated for use in isolating mRNA, chromosomes, and
restriction fragments; in amplifying hybridization signals; and
in extending DNA molecules. In addition, bacterial host strains
have been developed that give greater stability to cosmid
constructs containing human DNAs. Improvements are being made in
DNA detection methods by the development of new probes, stains,
and fluorescent dyes.

As a result of the recent cloning of the fragile X gene, several
companies are negotiating for licenses to develop assays for
diagnosing fragile X syndrome, probably the most frequently
inherited form of mental retardation.

Hardware. Automation and enhancement of data collection and
analysis has been the goal of many collaborations with the
commercial sector. Equipment is being designed to automate (1)
the production of high-density arrays on agarose or filters and
(2) clone fingerprinting by gel electrophoresis (as well as the
data collection and analysis software). Advanced applications for
robotic systems are also being developed.

The resolution of DNA fragments is being enhanced by improvements
in pulsed-field gel electrophoresis. Resonance ionization
spectroscopy is being modified to enable rapid detection of
stable isotope labels on DNA following gel electrophoresis. A
commercial gel scanner is being developed for reading DNA gels.

Software. To aid physical map construction, programs are being
designed for efficient clone analysis. Several other
image-analysis programs are being developed, including
data-capture software for images from video screens in
combination with a DNA molecule imaging system.

Sequencing. Multiplex sequencing technologies are being used to
sequence pathogenic microbes.





Human Genome Center Research Narratives

Lawrence Berkeley Laboratory

Since its inception in 1987, the Lawrence Berkeley Laboratory
(LBL) Human Genome Center has focused on developing the necessary
research and analytical technology to speed genome mapping and
decrease the cost of sequencing. Over the last year, LBL has
strengthened its ties with the University of California,
Berkeley, particularly in the biological sciences. This
collaboration fosters interdisciplinary activities in biology,
instrumentation, and informatics.


Biology

The biology component at LBL is concentrating on developing and
improving mapping and sequencing strategies for human chromosome
21. To achieve these goals, investigators in each biology project
draw on the expertise of the center's instrumentation and
computing groups.

Two major biology projects are under way, and a third is in
development. Physical mapping at LBL is focused on a 10-Mb region
of human chromosome 21, and over 90 unique chromosome 21-specific
yeast artificial chromosomes (YACs) have been located by
fluorescence in situ hybridization (FISH). A new method has been
developed that permits rapid isolation of chromosome-specific
YACs, using probes isolated from flow-sorted chromosome libraries
from Lawrence Livermore National Laboratory. In addition, cDNAs
specific to a given YAC are being isolated by an automatable
procedure based on magnetic beads.

The second major biology effort involves testing new approaches
to physical mapping and genomic sequencing. These projects
exploit current methods, such as FISH and appropriate pooling
strategies, for efficient isolation of overlapping clones. In
addition, new work has begun on subcloning and ordering libraries
of clones for mapping and on the use of gamma delta transposons
as the primer site for sequencing studies. Increased efficiency
in constructing physical maps results from a clone-limited
strategy for generating maps based on sequence tagged sites
(STSs). This nonrandom selection strategy reduces the number of
STS assays required and produces contigs that cover a larger
fraction of the genome.

The third biology project is aimed at developing automated
methods for generating genetic maps. A simple filter assay will
be used to detect heterozygosity at mapped loci in yeast, mice,
and human DNA samples.


Instrumentation
The instrumentation program within the LBL Human Genome Center
has two major areas of effort: (1) biology and instrumentation
development and support and (2) new instrumentation development
based on emerging technologies. Supporting activities include the
design and fabrication of gel boxes, automation of protocols on
existing robotic frameworks, and the installation and networking
of a variety of image-acquisition systems. In addition, advanced
robotic [high-speed colony picking, robotic-based polymerase
chain reaction, and DNA synthesis] and laboratory systems
integration is under development.

Efforts to produce new, adaptable technologies for the genome
program include optimizing large-molecule detection systems;
designing versatile optical fluorescence systems for multiplex
labeling; and developing microfabricated arrays for application
to large-scale clone libraries, sequencing by hybridization, and
other procedures. The use of computer-controlled robotic systems
provides a mechanism for automatically capturing the vast amount
of data generated by laboratory operations. This requires a close
coordination between hardware and software development in
laboratory system design that goes far beyond automation of a few
discrete protocols.




Informatics

A major part of the computing and instrumentation effort is
driven by biology projects. The center's computing group focuses
on specific applications in four major areas: raw data
acquisition and analysis, information tracking and management,
data interpretation and comparison analysis, and development of
software tools. Visual data for mapping (including in situ
pictures, autoradiograms, ethidium gels, and chemiluminescent
staining) are handled by BioPix, a set of programs that assemble
and integrate data from image capture to analysis. A similar
system is being developed for sequence data. The Chromosome
Information System (CIS) allows biologists to search, edit, and
compare various maps, markers, and related reference information
and to interact with other programs to exchange data. The
laboratory data analysis system uses existing software packages
and provides system management and support throughout the center.
New, in-house analysis packages are being devised for sequence
alignment and assembly. Software development tools permit rapid
design and modification of database management systems, thus
facilitating increased productivity, vendor independence, and
conceptual clarity.


Achievements

*    Over 90 independent YACs averaging 100 kb were regionally
     assigned to human chromosome 21 by FISH. These YACs include
     genetic markers to help integrate maps.

*    Two hundred unique probes were isolated for chromosome 21
     and are being used to identify YACs from genomic libraries.

*    A rapid cDNA clone-screening method uses immobilized YAC
     clones to screen cDNA libraries, which are then localized on
     specific chromosomes. An alternative screening method uses
     individual YACs or cosmids attached to magnetic beads to
     isolate specific cDNAs, a method that can be readily
     automated to speed identification of coding sequences for
     physical mapping.

*    Marker-selected libraries, highly enriched for clones
     containing (CA)n repeats, were constructed from primary
     genomic libraries. These enriched libraries increase the
     efficiency of screening almost 50-fold.

*    A probe-mapping procedure determines the distance between
     the probe and the chromosome or YAC end. This method, which
     uses X rays to break large DNA pieces randomly, can be used
     to map cDNAs and to estimate the length of entire genes.

*    A double-ended, clone-limited strategy for physical mapping
     of chromosomes was devised. This strategy maps chromosomes
     on the order of 100 Mb and should result in larger contigs
     with a minimum of assays.

*    CIS, developed by the genome center computing group, was
     used to produce consensus maps at workshops on human
     chromosomes 3 and 21 and is being expanded for use with a
     number of plant species in the Plant Genome Program of the
     U.S. Department of Agriculture.

*    High-level database design tools have been developed to
     permit molecular biologists to define data objects in a way
     that captures biological concepts. The software
     automatically generates low-level commands for a commercial
     database management system, facilitating the evolutionary
     development of modular system components. These tools are
     also being used by researchers to design the Superconducting
     Super Collider database and the Integrated Genome Database.

*    A variety of mechanical, electrical, and chemical means have
     been used to manipulate DNA molecules; these methods include
     stretching molecules physically by externally applied
     electrical fields and guiding the molecules through grooves
     in a glass surface; digesting and separating single
     molecules; and picking up, transporting, and releasing DNA
     with scanning tunneling microscope (STM) tips.

*    Investigation of the feasibility of using STM for
     visualizing the individual bases of single-stranded DNA has
     shown that while purines and pyrimidines can be
     distinguished from each other, two bases in the same class
     cannot be differentiated by this method.

*    A fast, filter-based assay was developed to identify single
     base-pair polymorphisms, eliminating the need for gel
     assays.

*    Higher throughput was achieved through the construction of a
     dedicated high-speed colony-picking workstation. The pick
     rate is 10 to 20 times faster than the initial picking
     system and both faster and more accurate than a highly
     qualified human. The new picker arrayed an entire library of
     over 10,000 clones in 1 day.

*    Robots have been modified for use with a number of chemistry
     protocols, including cosmid and YAC library replication,
     various pooling schemes, and high-density filter array
     production. Using the robot to replicate libraries has made
     copies available to researchers in the private sector and in
     other national laboratories.

Future Plans

*    Construction of a 10-Mb contig of human chromosome 21 based
     on overlapping YACs. The sequence will be determined by the
     most efficient strategy available.

*    Sequencing of a P1 clone. Subclone assembly will use a
     nonrandom strategy, and primer sequences will originate in
     the transposon gamma delta.

*    Construction of chromosome genetic maps of human chromosomes
     16 and 19 in collaboration with other DOE genome centers. A
     simple gel-based heterozygosity assay is being developed to
     support this research.

*    Development of a computational biology program within the
     computing group to design and implement new algorithms for
     sequence assembly. Preliminary data will come from
     collaborations with other genome centers.

*    Design and implementation of a software tool suite for
     managing information and for optimizing the unique strategy
     of particular research groups. As large-scale sequencing
     projects develop, new acquisition and analysis software will
     be integrated into CIS.

*    Implementation of QUEST, a database tool that will provide a
     single entry point to the conceptual data model. QUEST will
     then implement automatically any changes in the user
     interface, the database query procedures, and the database
     schema definition.

*    Optimization of improved detectors and the associated mass
     spectrometry system for large biological molecules.

*    Automation of handling and analysis of dot-blot
     hybridization experiments and the implementation of a
     high-speed colony-picking apparatus.

For more information on the LBL Human Genome Center, contact
Jasper Rine, Director, or Sylvia Spengler, Deputy Director, at
510/486-4943.


Lawrence Livermore National Laboratory

The Human Genome Center at Lawrence Livermore National Laboratory
(LLNL) is a multidisciplinary team effort that brings together
chemists, biologists, molecular biologists, physicists,
mathematicians, computer scientists, and engineers in an
interactive research environment. Many of these individuals have
previously collaborated on research projects in molecular
biology, cytogenetics, mutagenesis, and instrumentation, as well
as in the National Laboratory Gene Library Project (NLGLP). These
projects have contributed substantially to the identification and
characterization of human DNA repair genes, specifically the
three on chromosome 19 that are a focus of interest at LLNL.

The short- and long-term goals of the LLNL effort are to (1)
develop biological and physical resources useful for genome
research, (2) model and evaluate DNA mapping and sequencing
strategies, (3) couple these resources and strategies in an
optimal way to construct ordered clone maps and DNA sequences of
human chromosomes, and (4) use the map and sequence information
to study genome organization and variation. To achieve these
goals, the Human Genome Center is organized into three broad
research and support areas, each consisting of multiple projects
led by a principal investigator. Extensive interaction occurs
within and among all projects that have as their common goal the
construction of ordered clone maps of the human genome. The
program structure of the center includes a core facility and
projects that focus on physical mapping and enabling
technologies.


Research and Support Areas

Coordination and collaboration take place with other research
groups throughout the world that are involved in the genome
initiative or other mutual scientific interests. The role of LLNL
in the Human Genome Project is seen as encompassing several
areas, including technology development, map construction, map
interpretation, and integration with ongoing and new programs in
structural biology and mutagenesis. The following three
components are highly interactive; individual staff members often
have responsibilities in more than one component.

Core facilities. The administrative group is concerned with
budget oversight, external and internal meeting coordination,
preparation of center reports, training coordination, property
and space management, safety oversight, and secretarial support.
The scientific core provides general support to the physical
mapping effort, including cell culture and DNA extraction;
library, probe, and clone management; oligonucleotide synthesis;
fluorescence-based restriction mapping; and DNA sequencing. The
core also facilitates material distribution to collaborators in
the external community.

Mapping activities. Five projects represent the coordinated
effort to obtain an overlapping set of clones for human
chromosome 19 and to further characterize genomic organization:

*    Assembly, closure, and characterization of a chromosome 19
     contig map. The goal of this project is to construct an
     overlapping set of cosmid clones using a variety of
     techniques. An automated fluorescence-based
     restriction-fragment fingerprinting strategy is used to
     establish a foundation map of cosmid contigs. The contig
     closure effort will focus on using yeast artificial
     chromosomes (YACs) and cosmids with two hybridization-based
     techniques; one is based on fragments generated from Alu
     sequence primers or sequence tagged sites (STSs) by the
     polymerase chain reaction (PCR) and the second on RNA
     transcripts generated from the ends of cloned inserts.

*    Interdigitation of the physical and genetic maps of human
     chromosome 19. The goals of this effort are to locate known
     genetic markers on the expanding contig map, to coordinate
     the isolation of chromosome 19-specific STSs, and to
     localize them on the cosmid map.

*    DNA sequence mapping by fluorescence in situ hybridization
     (FISH). This project exploits the power of FISH on metaphase
     chromosomes, interphase cells, and pronuclear DNA. FISH will
     be used to determine the location of genes of interest and
     the relative order and orientation of the cosmid contigs.

*    cDNA mapping. The goal of this project is to isolate,
     sequence, and map cDNAs-expressed in a variety of human
     tissues_that will become the STSs on which future studies of
     genetic organization and gene function will be based.

*    New mapping strategies. New methods useful for library
     construction, contig closure, and overlap detection will be
     developed and validated. Focus is on improving Alu-PCR-based
     technology and pooling schemes to achieve closure of the
     chromosome 19 map with cosmids and YACs.


Enabling technologies. The following groups provide
computational, resource, and instrumentation support for research
activities:

     ∙Computational support for the Human Genome Center. This
     group is responsible for mathematical modeling of mapping
     and sequencing strategies and the development and
     application of data analysis algorithms and software. They
     are also responsible for the construction and maintenance of
     interactive relational databases that enable internal and
     external data access, including development of graphical
     visualization tools.

*    NLGLP. This project, a joint effort with Los Alamos National
     Laboratory, draws upon LLNL experience in flow
     instrumentation and chromosome sorting to construct human
     chromosome-specific libraries in lambda and cosmid vectors
     for use in physical mapping and other studies.

*    Instrumentation for cytogenetics and gene mapping. This
     group is responsible for developing instrumentation to
     facilitate flow systems analysis and chromosome sorting and
     to support FISH.


Accomplishments

The LLNL Human Genome Center has made excellent progress in the
construction of an ordered set of cosmids for chromosome 19, the
development and application of new biochemical and mathematical
approaches for constructing ordered clone maps, the automation of
fingerprinting chemistries, and high-resolution imaging of DNA.
Major accomplishments are highlighted below.

*    Considerable progress has been made toward the closure of
     the chromosome 19 physical map. More than 10,000 cosmids
     have been analyzed by an automated fluorescence-based
     fingerprinting approach and assembled into over 870 contigs
     that span about 80% of the chromosome. FISH has been used to
     locate over 400 cosmids and 117 contigs on the cytological
     map, and more than 70 known genetic markers have been
     located on cosmid contigs. Closure of the gaps between
     contigs is under way using YACs and cosmids.

*    Cosmid contigs analyzed in the carcinoembryonic antigen
     (CEA) gene family region of chromosome 19 were found to be
     tightly linked over relatively short stretches of DNA. This
     gene family of about 22 members appears to span a contiguous
     region of about 1 Mb. With probes made from the ends of
     these contigs, hybridization techniques were applied to join
     contigs established by fingerprinting into larger contigs.
     In addition, almost 2 Mb surrounding the myotonic dystrophy
     locus were linked with cosmids and YACs.
*    More than 20 clones containing DNA sequences corresponding
     to a number of important genes and regions that map to chromosome
     19 were isolated from two separate YAC libraries. Among these
     clones were the region encoding the LDL receptor and ApoE gene,
     two important components of the regulation of cholesterol and
     triglyceride metabolism in humans. Similarly, a region was
     isolated that encodes a family of serine proteases called
     Kallikreins, whose role is the specific proteolytic activation of
     peptide hormones and growth factors. Clones of these regions are
     being used for the structural analysis and mapping of these
     genes.

*    A structural defect found in the cloned gene linked to the
     autosomal dominant disease myotonic dystrophy has been
     identified through an international collaboration. This
     chromosome 19 defect, which is characterized by a tandemly
     repeated segment of DNA within or close to the coding region
     on q13.3, is similar to that seen in the fragile X syndrome.
     The extent of the amplified region appears to be associated
     with the severity of the disease.

*    The gene for DNA ligase 1 was mapped to the long arm of
     chromosome 19. A defect in this gene may be associated with
     increased cancer risk. This is the fourth gene involved in
     DNA metabolism that has been mapped to this region of
     chromosome 19.

*    Significant progress was accomplished in defining the
     organization of the cytochrome P450 genes mapping to
     chromosome 19. Multiple members of each of the three
     subfamilies were identified. The cosmids containing these
     genes will be useful resources for studies of the function
     and physiological importance of the genes.

*    Three levels of resolution of FISH have been developed and
     applied to localize and orient cosmids. Localizing cosmids
     to metaphase chromosomes provides a resolution of about 1 to
     3 Mb. Localization to somatic interphase cells gives a
     resolution of from 50 kb to 1 Mb and hybridization to sperm
     pronuclei a 20-kb to 1-Mb resolution. With FISH, a linear
     relationship was demonstrated between physical distance and
     genomic distance of 20 kb up to at least 800 kb in pronuclei
     derived from human spermatozoa. With a single probe, the
     presence of multiple copies of the closely related genes of
     the CEA family has been detected in human sperm pronuclei.
     Single and multicolor hybridizations are routinely
     performed.

*    A reproducible method of mapping YACs by FISH has been
     developed. This procedure involves isolating YACs with
     pulsed-field gels, digesting with the restriction enzyme Mbo
     I, ligating to oligonucleotide linker adapters, and
     amplifying with PCR. The products are then mapped onto human
     metaphase chromosomes by standard FISH methods.

*    The technique of Alu-PCR has been further exploited. To
     isolate region-specific DNA probes from human-rodent hybrid
     cell lines, previously developed PCR procedures were
     expanded. Human sequences are preferentially amplified using
     PCR primers specific for repeats of the human Alu repeat
     family. Several new primers have been developed that amplify
     human DNA sequences very efficiently, further facilitating
     probe isolation from human genome regions present in the
     available hybrids. Many different human sequences amplify
     from the hybrids; individual probe sequences are obtained by
     subsequent cloning in plasmid vectors in Escherichia coli.
     To expedite this, ligation-independent cloning has been
     developed to increase efficiency of cloning and eliminate
     the common background of clones that do not contain
     recombinant DNA molecules. In addition, an efficient
     procedure has been developed to clone the PCR products
     common to two cell lines. This method _coincidence
     cloning_permits a further enrichment for sequences derived
     from defined regions of the genome.

*    Clone-pooling schemes have been developed to facilitate
     screening of both cosmid and YAC libraries. Each clone is
     present in a number of different pools, reducing the number
     of DNA samples that must be deposited on a high-density
     filter for hybridization-based screening and the number of
     tubes needed for PCR-based screening. Since each clone is
     defined by a unique combination of pools, the screening of
     pools by probe hybridization permits identification of the
     recombinants shared by a number of pools. This approach was
     used very successfully to screen a 10,000-clone cosmid
     library. The idea also was used to consolidate a
     60,000-clone YAC library into about 1800 sample pools.
     Results demonstrated that hybridization-positive YAC pools
     can, indeed, be distinguished from hybridization-negative
     YAC pools, thus allowing the efficient identification of YAC
     clones.

*    Human YACs were isolated from a library constructed using a
     monochromosomal 19 hybrid cell line. The YACs vary in size
     between 120 and 350 kb. One of the analyzed YACs carries
     sequences from the telomere region of chromosome 19, and
     another maps to the centromere region of chromosome 19 by
     FISH.

*    A second-generation suite of robust, reliable computer
     programs was completed for signal preparation and analysis
     of chromosome 19 restriction fragment fingerprints. These
     programs implement methods for random noise suppression,
     background subtraction, and color decorrelation. A new
     program (TIMEWARP) was also completed to map peak locations
     in a gel to a common coordinate system by dynamic
     programming and shape-preserving spline interpolation.

*    The Sybase database has been enhanced to contain all the
     laboratory notebook and experimental data important to
     physical map construction. This includes clone repository
     information, restriction fragment fingerprinting, and data
     on probe hybridization and FISH. The database is coupled to
     the graphical browser so the end user can retrieve many of
     the experimental results in graphical form.

*    The graphical database browser was enhanced to run Human
     Genome Project data remotely over Internet. The browser's
     ability to link to multiple databases at external
     collaborator sites has been demonstrated.

*    In a collaborative effort, automatic transnetwork methods
     for transferring physical mapping results to the central
     Genome Data Base (GDB) at Johns Hopkins were built, tested,
     and implemented by GDB and LLNL. This work was in support of
     DOE concerns that all laboratories should effect mechanisms
     to ensure that data are made available to the appropriate
     public databases after a suitable time period. Prototype
     methods were implemented, tested, and publicly demonstrated
     for logically linking our database with the major sequence
     and mapping databases (GenBankr and GDB). Direct
     transnetwork queries that logically integrate these data
     sets are now feasible.

*    As part of NLGLP, high-speed flow sorting was used to purify
     individual human chromosomes for cloning. Large-insert phage
     and cosmid libraries have been made for chromosomes 9, 12,
     18, 19, 21, 22, and Y. Several libraries have been
     distributed to users and evaluation sites. In addition, the
     high-speed sorter has been rebuilt with new fluidics to
     optimize sterility and with new electronics to increase the
     purity of the sorted material.

*    Construction of a new high-speed chromosome sorter was
     completed. This instrument has new digital acquisition
     electronics, a new fluidic system, and a more stable sample
     stream. The instrument analyzes chromosomes at the rate of
     up to 20,000/s and can reliably produce 250 to 1000 ng of
     sorted chromosome DNA equivalents per day.

*    Using scanning tunneling microscopy (STM), individual images
     of the bases adenine and thymine were obtained at atomic
     resolution, indicating that a scanning-probe microscopy
     technique can discriminate between purines and pyrimidines.

*    Several technologies have been transferred to industry. They
     include software for analysis and graphical display of
     physical map data, sequence information for the
     commercialization of Alu-PCR primers, and vectors for the
     construction of cosmid libraries. In addition, collaborative
     research programs with industry have continued in the areas
     of fluorescence-based restriction fragment analysis,
     development of pulsed-field gel systems, development and
     testing of automated and high-throughput plasmid/cosmid DNA
     extraction, and development and testing of a robot for
     high-density colony replication on filters.


Future Plans

The LLNL genome center's first priority is to complete, to the
extent possible, an ordered clone map of chromosome 19; this
physical map will likely be a composite linear array of cosmid,
lambda, and YAC clones. It will be correlated with the genetic
map to assist the scientific community in localizing and
isolating all genes from chromosome 19. State-of-the-art
technology will be used to sequence selected high-interest
regions of the chromosome. Once the technology has been validated
for map construction of a large portion of chromosome 19, efforts
will be directed to chromosome 2.

When Human Genome Project emphasis shifts from mapping to
sequencing, exploration will turn to rapid automated DNA
sequencing methods that can use large fragments such as cosmids
or YACs as templates. STM and X-ray imaging technologies under
development at LLNL are expected to contribute to advancements in
sequencing.

Automation is an essential element of physical mapping. New
processes and instruments will be explored to reduce the need for
human intervention in highly repetitive tasks. A number of
instruments for clone manipulation and biochemical processes will
be considered for automation.

An effort to map and sequence the cDNAs expressed in a variety of
human tissues has recently been initiated. These cDNAs will be
used to generate STSs and will serve as the foundation for future
studies of gene organization and gene function.

Assisting the scientific community in completing ordered clone
maps is critical and will remain a high priority. LLNL intends to
serve as a resource laboratory for clones and for map information
on chromosomes of interest. Ultimately, map and sequence
information will be used to study the global architecture of the
chromosome and also to evaluate human somatic and genetic
variation, both spontaneous and induced.

For more information on the LLNL Human Genome Center, contact
Anthony Carrano, Director, at 510/422-5698 or Leilani Corell,
Administrator, at 510/423-3841.


Los Alamos National Laboratory

The Center for Human Genome Studies at Los Alamos National
Laboratory (LANL) provides direction, coordination, and technical
oversight for the LANL portion of the DOE Human Genome Program.
The center draws scientific talent from six technical divisions
at LANL. Molecular biologists, chemists, physicists,
mathematicians, computer scientists, and engineers are
contributing to progress in physical mapping, technology
development, and informatics. Although a specific goal is the
assembly of a complete physical map for human chromosome 16, much
of the work is broadly supportive of the worldwide Human Genome
Project. Collaborative research and development programs have
also been initiated with private-sector and other institutions
involved in human genome research. The major technical
subdivisions of the center are physical mapping, technology
development, and informatics. Activities are also under way at
the center to explore ethical, legal, and social issues arising
from genome research data and to transfer technology developed
within the center's projects.


Physical Mapping

Physical mapping includes the development of conceptual advances
in mapping strategy and the construction of a physical map of
chromosome 16. The physical map will be composed of phage,
cosmid, and YAC contigs ordered by repetitive sequence
fingerprinting. These ordered contigs will be integrated with the
genetic linkage map, the cytogenetic map, and known gene
sequences on chromosome 16. The final map, along with its
eventual translation into a sequence tagged site (STS) map, will
provide the means for rapid access to any region of the
chromosome for further analysis. In addition, the ordered clone
sets will be available for eventual sequencing.


Technology Development

Technology development efforts include the application of
robotics to the handling and storage of DNA fragments, the
development and application o f methods for the construction of
DNA libraries from flow-sorted chromosomes, and the development
of new methods for rapid, inexpensive, large-scale sequencing.
All these projects are or will be supportive of the physical
mapping of chromosome 16, and they also contribute to the larger
genome program. For example, the construction and distribution of
various kinds of libraries from sorted chromosomes is playing a
significant role at many of the genome research centers.


Informatics

Informatics efforts involving the collection and analysis of
genome-related data will play an increasingly important role in
the genome project. LANL has a long history of expertise in this
research area and will continue to lead in providing these
essential resources.


Ethical, Legal, and Social Issues (ELSI) Activities

The center also sponsors active participation in ELSI studies
related to data produced by human genome research and is
compiling a comprehensive literature bibliography in
collaboration with Georgetown University. LANL scientists
participated in a series of discussions on ELSI issues sponsored
by the University of California Humanities Research Institute.


Technology Transfer

LANL will continue to put a high priority on collaborations with
private industry to use the skills and resources of the private
sector and to ensure effective technology transfer to the U.S.
commercial sector. The first Cooperative Research and Development
Agreement (CRADA) involving human genome research activity was
signed in 1991 by LANL and Life Technologies, Inc. (LTI).


Recent Progress and Future Directions

Construction of a physical map of chromosome 16. The
chromosome-mapping strategy at LANL involves the rapid generation
of cosmid contigs representing around 60% of the target
chromosome, followed by directed gap closure with yeast
artificial chromosomes (YACs). The first phase of this goal, the
rapid generation of nucleation contigs on chromosome 16, has been
completed [Stallings et al., Proc. Natl. Acad. Sci. USA 87:
6218-22 (1990)]. An approach for identifying overlapping cosmid
clones by exploiting the high density of repetitive sequences in
human DNA was used to generate 553 contigs following the
fingerprinting of over 4500 individual cosmid clones. These
contigs represent more than 80% of the euchromatic arms of
chromosome 16 and were constructed with about one-fourth as many
cosmid fingerprints as random strategies requiring 50% minimum
overlap detection.

Nucleating at specific regions allows (a) the rapid generation of
large (>100 kb ) contigs in the early stages of contig mapping
and (b) the production of a contig map with useful landmarks
[i.e., (GT)n repeats] for rapid integration of the genetic and
physical maps. All 4500 fingerprinted cosmids in contigs and
singlets have been rearrayed on high-density filters. Such
filters already provide investigators with access to more than
90% of chromosome 16, with a 60% probability that any region is
already present in a contig. These high-density
chromosome-specific cosmid filter arrays have also proved useful
for YAC fingerprinting with repetitive sequence polymerase chain
reaction (PCR) techniques. In collaboration with the laboratories
of David Ward (Yale University) and David Callen (Adelaide
Children's Hospital, Australia), 130 of these arrayed cosmids
have been regionally localized via in situ hybridization or
somatic cell hybrid panels. The average gap (containing only
singlets), approximately 65 kb in length, can be easily closed
with YACs. A single walk from each end of current contigs should,
statistically, reduce the number of contigs to approximately 50,
one of the 5-year goals of the Human Genome Project (i.e., 1- to
2-Mb contigs; >95% coverage). To facilitate closure, LANL
investigators are constructing from monochromosomal hybrids and
flow-sorted material both a total genomic YAC library (from cell
line GM130, using the vectors pJS97 and pJS98; currently onefold
representation) and chromosome 16 YAC clones. One hundred STS
markers are being generated to key contigs. Extensive analyses of
the DNA sequences obtained from contig ends are in progress using
multiple approaches to identify potential coding regions. These
approaches include nucleotide and translated amino acid sequence
homology searches against GenBank, using BLAST and FASTA, and the
new adaptive network program, GRAIL, developed and made available
by the Oak Ridge National Laboratory. Current progress with YAC
closure indicates that the complete physical map of chromosome 16
will be achieved in the next few years.


Low-abundance repetitive DNA sequences identified on chromosome
16. Chromosome 16-specific, low-abundance repetitive DNA
sequences (designated CH16LARs) have been identified during
construction of the cosmid contig map of this chromosome.
CH16LARs were initially identified by in situ hybridization of
cosmid and YAC clones to normal human chromosomes (in
collaboration with David Ward). The cosmid clones all came from
contig 55. The hybridization signals were unusually intense and
occurred on four regions of human chromosome 16: bands p13, p12,
p11, and q22. Contig 55 contains more clones than any other
contig (78 clones or 2% of all clones fingerprinted thus far).
Ordering clones within contig 55 is not possible because the
presence of these low-abundance repetitive DNA sequences has
generated false overlaps. The regions containing CH16LARs may
cover as much as 5% of the euchromatic arms of chromosome 16 (~5
Mb of DNA). One CH16LAR sequence (CH16LAR1) was cloned and
sequenced, and a minisatellite type of repetitive sequence was
identified. The region containing CH16LARs is of biological
interest since the pericentric inversion breakpoints commonly
found in myelomonocytic leukemia fall within these regions
[Mitelman, Hereditas 104: 113 (1986)]. Alternative strategies for
mapping and ordering clones from this region are being
implemented.


Construction and distribution of DNA libraries from flow-sorted
chromosomes: National Laboratory Gene Library Project (NLGLP).
NLGLP is a cooperative project between LANL and Lawrence
Livermore National Laboratory. Investigators at LANL have cloned
a set of complete digest libraries into the EcoR I insertion site
of Charon 21A; they are available from the American Type Culture
Collection, Rockville, Maryland. Sets of partial digest libraries
in the cosmid vector sCos1 and in the phage vector Charon 40 are
being constructed for human chromosomes 4, 5, 6, 8, 10, 11, 13,
14, 15, 16, 17, 20, and X. Individual human chromosomes are first
sorted from rodent-human hybrid cell lines until about 1 µg of
DNA has been accumulated. The sorted chromosomes are then
examined for purity by in situ hybridization, and the DNA is
extracted and partially digested with the restriction enzyme Sau
3AI, dephosphorylated, and cloned into vectors. Partial digest
libraries have been constructed for chromosomes 4, 5, 6, 8, 11,
13, 16, 17, and X. Purity estimates from sorted chromosomes,
flow-karyotype analysis, and plaque or colony hybridization
indicate that most of these libraries are 90 to 95% pure.
Additional cosmid library constructions and arrays of libraries
having five- to tenfold genomic coverage into microtiter plates
are in progress. Libraries have been constructed in M13 or
bluescript vectors to generate STS markers for selecting
chromosome-specific inserts from a genomic YAC library. LANL has
also cloned sorted DNA into YAC vectors and expects to construct
a series of YAC libraries representing individual chromosomes
(see below).

A YAC library for human chromosome 21. YACs have been constructed
using DNA isolated from aliquots of flow-sorted human chromosome
21. Chromosomes were prepared from the somatic cell hybrid
WAV-17, which contains chromosome 21 as the only human
chromosome. DNA isolated from sorted chromosomes was restricted
with either Cla I or Eag I or both Not I and Nhe I, ligated to
YAC vectors pJS97 and pHS98, and transformed into Saccharomyces
cerevisiae strain YPH 250. The transformation efficiency of YACs
ranged from 600 to 2500 cfu/µg of sorted DNA. About 1200 human
YACs with an average size of 200 kb have been identified. The
locations of 20 random YACs on chromosome 21 were confirmed by
hybridization to somatic cell hybrid mapping panels. Three YACs
that hybridize to D21S55 have been identified and are being used
to initiate construction of a physical map of the Down's syndrome
region of chromosome 21. Sixty YAC clones from the chromosome 21
library were localized on chromosome 21 by in situ hybridization.
The results indicate that the library contains inserts that are
well distributed along the length of the chromosome and that the
frequency of chimeric inserts is low (below 3%). A collaboration
between the genome centers at LANL and Lawrence Berkeley
Laboratory (LBL) will use the library for comprehensive physical
mapping of chromosome 21 . The ability to construct
chromosome-specific YAC libraries from sorted chromosomes will
facilitate isolation of disease genes and construction of
long-range physical maps of complex genomes. LBL is working on
chromosome 21 in cooperation with LANL.


Chromosome-specific STS libraries. Specific STSs have been
systematically generated using flow-sorted chromosomes. DNA from
about 200,000 chromosomes was digested with either one or two
restriction enzymes (usually BamH I and Hind III) and cloned
directly into bacteriophage M13mp18. One-pass sequencing was
conducted, either manually or with a Dupont Genesis 2000
automated sequencer. DNA sequences were analyzed for the presence
of sequence similarity to common human repetitive sequences, and
appropriate PCR oligomers were synthesized. An acceptable STS-PCR
assay yielded the appropriately sized product from both the
hybrid cell line DNA containing only the human chromosome of
interest and the pools of 384 anonymous YAC clones, spiked with 5
ng/ml total human DNA. To date, over 340 kb of anonymous DNA
sequence from human chromosomes 5 and 7 have been analyzed. Two
hundred STS markers for chromosome 7 have been generated in
collaboration with Maynard Olson's laboratory at Washington
University [Green et al., Genomics (in press)], and the first 100
STS markers for chromosome 5 are currently being generated in
collaboration with John Wasmuth's laboratory at the University of
California, Irvine; 50 STSs for chromosome 5 have been regionally
localized. The overall efficiency of PCR reactions yielding
appropriate products, with the anonymous genomic sequences from
flow-sorted chromosomes, has been approximately 75%. GRAIL
analyses indicate that approximately 15% of both the chromosome
16 STSs and the randomly selected STSs for chromosomes 5 and 7
contain putative coding regions.


Informatics. The Laboratory Notebook database, designed to manage
all information necessary for map assembly, has been expanded to
include sequences, STS mapping information, and grid
hybridization data, as well as clone fingerprints and completed
maps. The forms-based interface is being expanded to provide easy
access to the new tables. Graphical interfaces and innovative
algorithms to aid map assembly have been prototyped and are being
refined. Integrated, multilevel maps are increasing in
importance. A strong emphasis for the coming year will be to
implement the Software for Integrated Genome Map Assembly (SIGMA)
system, which was designed to aid in display, assembly,
evaluation, and editing of integrated maps.

DNA sequencing based upon single-molecule detection in flow
cytometry. This project addresses the problem of rapidly
sequencing bases in large fragments of DNA. A DNA fragment of
about 40 kb will be labeled with base-identifying tags and
suspended in the flow stream of a flow cytometer capable of
single-molecule detection. The tagged bases will be sequentially
cleaved from the single fragment and identified as the liberated
tag passes through the laser beam. A sequencing rate of 100 to
1000 bases/s on DNA strands of around 40 kb is projected [Genet.
Anal. 8: 1 (1991)]. Accomplishments of this project are as
follows:

*    Signed CRADA with LTI for joint research on DNA sequencing.
     LTI will offer expertise in nucleic acid chemistry and
     enzymology, and LANL will specialize in detection technology
     and DNA handling. LTI will commercialize the technique [for
     more information, refer to the figure on p. 25 and to Human
     Genome News, 3(1): 5 (May 1991)].

*    Detected several different kinds of single fluorescing
     molecules with ~85% efficiency and low error rates [Chem.
     Phys. Lett. 174: 553 (1990)].

*    Observed photon bursts simultaneously from rhodamine-6G and
     Texas Red, using both a doubled Nd/YAG and a synchronously
     pumped dye laser for excitation and dual-wavelength
     detection.

*    Synthesized DNA fragments up to 500 nucleotides long that
     contain one fluorescent nucleotide and three normal
     nucleotides. DNA synthesis was observed with rhodamine-dCTP,
     rhodamine-dATP, rhodamine-dUTP, fluorescein-dATP, and
     fluorescein-dUTP. This work was a collaboration with LTI.

*    Digested the fluoresceinated DNAs described above by six
     different exonucleases: native T4 polymerase, native T7
     polymerase, Klenow fragment of Escherichia coli pol I, exo
     III, E. coli pol III holoenzyme, and snake venom
     phosphodiesterase. LTI also participated in these
     investigations.


Robotic workcell for DNA filter array construction. A gantry
robot-based workcell has been assembled to array small spots of
DNA in an interleaved format. Grid densities on these membrane
filters can be varied from 576 to 9216 spots per 22 cm2. The
robot picks a microtiter plate from a dispenser, scans a barcode
label, removes the plate cover, and inserts a 96-pin gridding
tool into the plate wells. The tool is then positioned at the
appropriate place on the membrane, and the solutions on the pins
are transferred as spots. The gridding tool is washed and
sterilized, the lid replaced on the microtiter plate, and the
plate placed into a receiving stacker. The entire sequence is
repeated with new plates until the desired array has been
constructed.

For more information on the LANL Center for Human Genome Studies,
contact Robert K. Moyzis, Director, or Larry Deaven, Deputy
Director, at 505/667-3912.





Program Management Infrastructure

DOE OHER Mission

Genetics and radiation biology have been a long-term concern of
the DOE Office of Health and Environmental Research (OHER) and
DOE forerunners_the Atomic Energy Commission (AEC) and the Energy
Research and Development Administration (ERDA). In the United
States, the first federal support for genetics research was
through AEC. In the early days of nuclear energy development, the
focus was on radiation effects and later broadened under ERDA and
DOE to include the health implications of all energy technologies
and their by-products (see "Enabling Legislation" in box below).
Today, an extensive program of OHER-sponsored research on genomic
structure, maintenance, damage, and repair continues at the
national laboratories and universities. Some major components of
OHER genetics research are (1) molecular cloning and
characterization of DNA repair genes, (2) improvement of
methodologies and resources for quantitating and characterizing
mutations, and (3) the focused resource and technology
development needed to map and sequence the human genome_the Human
Genome Program.


     Enabling Legislation
     The Atomic Energy Act of 1946 (P.L. 79-585) provided the
     initial charter for a comprehensive program of research and
     development related to the utilization of fissionable and
     radioactive materials for medical, biological, and health
     purposes.

     The Atomic Energy Act of 1954 (P.L. 83-703) further
     authorized AEC "to conduct research on the biologic effects
     of ionizing radiation."

     The Energy Reorganization Act of 1974 (P.L. 93-438) provided
     that responsibilities of ERDA shall include "engaging in and
     supporting environmental, biomedical, physical and safety
     research related to the development of energy resources and
     utilization technologies."

     The Federal Nonnuclear Energy Research and Development Act
     of 1974 (P.L. 93-577) authorized ERDA to conduct a
     comprehensive nonnuclear energy research, development, and
     demonstration program to include the environmental and
     social consequences of the various technologies.

     The DOE Organization Act of 1977 (P.L. 95-91) instructed the
     department "to assure incorporation of national
     environmental protection goals in the formulation and
     implementation of energy programs; and to advance the goal
     of restoring, protecting, and enhancing environmental
     quality, and assuring public health and safety," and to
     conduct "a comprehensive program of research and development
     on the environmental effects of energy technology and
     programs."


Human exposure to environmental factors and the body's response
to such factors are a major concern. Unavoidable genome-damaging
agents in the environment include natural radiation sources, such
as the components of sunlight, cosmic rays from space, and radon
from the earth. Both inorganic and organic chemicals, some
natural to the environment and others generated by human commerce
and energy-related processes, put people at risk. Normal
biological functions also contribute to the risk of genetic
damage when the body's own cells produce potentially damaging
molecules in the course of metabolic processes such as defensive
actions against microbes, detoxification of harmful environmental
substances, and cell proliferation. Even DNA is not completely
stable chemically; its normal methylcytosine constituent has a
low but measurable rate of spontaneous mutagenic change.
Systems that reverse many types of DNA damage have evolved to
include a wide range of repair mechanisms within cells of all
species. Humans show great diversity in this capacity, with
repair-gene deficiencies showing up as sensitivity to DNA damage
from low-level radiation and in diseases such as cancer. Some
human genes that contribute to DNA repair processes have been
characterized, and others await detection and molecular cloning.
A goal of the OHER program is to improve the capabilities for
diagnosing individual susceptibility to genome damage.

The genome program is providing fundamental information about the
linear structure of chromosomes and genes, but understanding gene
function requires other types of knowledge. Elucidating the
three-dimensional (3-D) structure of proteins is crucial in
explicating their functions. To advance these studies, several
unique facilities for 3-D microstructure research, developed and
maintained at DOE laboratories (see box on DOE facilities), are
increasingly in demand by molecular biologists.

To carry out its national research and development obligations,
OHER conducts the following activities:

*    Sponsors research and development projects at universities,
     in the private sector, and at DOE national laboratories;

*    Uses the unique capabilities of multidisciplinary DOE
     national laboratories for the nation's benefit;

*    With advice from the scientific community and other sectors
     of government, considers novel, beneficial initiatives; and

*    Provides expertise on various governmental working groups.

David J. Galas has directed OHER, an office of the DOE Office of
Energy Research, since April 1990. He also serves under the White
House Office of Science and Technology Policy as Cochair of the
Committee on Life Sciences and Health and as Chairman of its
Subcommittee on Biotechnology Research. John C. Wooley became
OHER Deputy Associate Director in June 1992.

The Human Genome Program, conceived as an Initiative within OHER,
is administered primarily through the Health Effects and Life
Science Research Division, directed by David A. Smith. The
Medical Applications and Biophysical Research Division, directed
by Robert W. Wood, monitors the instrumentation sector of the
Human Genome Program and, more broadly, sponsors research and
development of resources and instrumentation having biomedical
and biotechnological applications.

Major DOE Facilities and Resources Relevant to Molecular Biology
Research

Center for X-Ray Optics                             LBL
GenBankr Data Sequence Repository                   LANL
High Flux Beam Reactor                              BNL
Los Alamos Neutron Scattering Center                LANL
National Flow Cytometry Resource                    LANL
National Laboratory Gene Library Project            LANL, LLNL
Protein Structure Data Bank                         BNL
National Synchrotron Light Source                   BNL
Scanning Transmission Electron Microscope Resource  BNL
Stanford Synchrotron Radiation Laboratory           Stanford
GRAIL, Online Sequence Interpretation Service       ORNL


Program Management Task Group

The Human Genome Program Management Task Group (see box for list
of members) reports to the OHER Director and works to coordinate
the following within OHER:

*    peer review of research proposals, using both prospective
     and retrospective evaluations and

*    administration of awards, collaboration with all concerned
     agencies and organizations, organization of periodic
     workshops, and responses to the needs of the developing
     program.

DOE Human Genome Program Management Task Group in 1992

David A. Smith, Chair    Molecular biologist
Ann M. Barber            Computational biologist
Benjamin J. Barnhart     Geneticist
Daniel W. Drell          Biologist
Gerald Goldstein         Physical scientist
Murray Schulman          Radiation biologist
Jay Snoddy*              Molecular biologist
Marvin Stodolsky         Molecular biologist
John C. Wooley           Biophysicist

*On detail from Argonne National Laboratory.


Field Coordination

Human Genome Coordinating Committee (HGCC)

Another component of the OHER management structure, HGCC was
formed in October 1988 to represent DOE genome program
researchers along with observers from other government and
private agencies (see box for list of HGCC members). Members of
the Human Genome Program Management Task Group are ex-officio
members of HGCC, and they participate in the regularly scheduled
HGCC meetings. HGCC responsibilities include the following:

*    assisting OHER with overall coordination of DOE-funded
     genome research;

*    facilitating the development and dissemination of novel
     genome technologies;

*    ensuring proper management and sharing of data and samples;

*    participating with other national and international efforts;
     and

*    recommending establishment of ad hoc task groups to analyze
     specific areas, such as ethical, legal, and social issues;
     informatics requirements; mapping and sequencing
     technologies; use of the mouse as a model organism; cost of
     resource distribution; and use of chromosome flow-sorting
     facilities.

Human Genome Coordinating Committee Members in 1992

Elbert W. Branscomb, Computational Biologist, Human Genome
Center, Lawrence Livermore National Laboratory

Charles R. Cantor, Principal Scientist, DOE Human Genome Program,
Lawrence Berkeley Laboratory

Anthony V. Carrano, Director, Human Genome Center and Leader,
Biomedical Sciences Division, Lawrence Livermore National
Laboratory

C. Thomas Caskey, Director, Institute for Molecular Genetics,
Baylor College of Medicine

David J. Galas, Office of Health and Environmental Research, DOE

Raymond F. Gesteland, Professor and Cochair, Department of Human
Genetics, University of Utah; Investigator, Howard Hughes Medical
Institute Laboratory for Genetic Studies at the Eccles Institute,
University of Utah

Leroy E. Hood, Director, Center for Integrated Protein and
Nucleic Acid Chemistry and Biological Computation; Director,
Cancer Center, California Institute of Technology

Robert K. Moyzis, Director, Center for Human Genome Studies, Los
Alamos National Laboratory

Jasper Rine, Director, Human Genome Center, Lawrence Berkeley
Laboratory

Robert J. Robbins, Director, Welch Medical Library for Applied
Research in Academic Information, Johns Hopkins University

David A. Smith, Office of Health and Environmental Research, DOE

Lloyd M. Smith, Assistant Professor, Analytical Division,
Department of Chemistry, University of Wisconsin, Madison

John C. Wooley, Office of Health and Environmental Research, DOE
______________

HGCC Executive Officer: Sylvia J. Spengler, Deputy Director Human
Genome Center, Lawrence Berkeley Laboratory


A Principal Scientist is a member of HGCC, reports to the Human
Genome Program Task Group regarding the responsibility of keeping
the program at the leading edge of genome research, and conveys
recommendations on broad scientific policies to HGCC. Currently
serving as a Principal Scientist is Charles R. Cantor, Lawrence
Berkeley Laboratory.


Human Genome Management Information System (HGMIS)

As an aid to the DOE Human Genome Program Task Group,
communication and information services are provided by HGMIS at
Oak Ridge National Laboratory. In this role HGMIS facilitates
international communication among management and research
personnel and informs other interested persons about genome
research. HGMIS publications, such as the bimonthly newsletter
Human Genome News and technical and program reports, are
available to anyone interested in the genome project. Human
Genome News is jointly supported by OHER and the NIH National
Center for Human Genome Research (NCHGR).

Subscribers to the newsletter number over 13,000 and include
genome and basic researchers at national laboratories,
universities, and other research institutions; professors and
teachers; industry representatives; legal personnel; ethicists;
students; genetic counselors; physicians; the press; and other
interested individuals. In the first quarter of 1992, over 5000
Genome Data Base users were added to the mailing list.
Subscribers outside the United States include more than 3000
individuals and institutions in 48 countries.


Human Genome Distinguished Postdoctoral Fellowships

In 1990 OHER established the Human Genome Distinguished
Postdoctoral Research Program to support research on projects
related to the DOE Human Genome Program. The postdoctoral program
developed from a 1988 recommendation of the DOE Energy Research
Advisory Board to "increase support through expansion of the
targeted (science and engineering) graduate and postgraduate
research fellowship programs with emphasis given to
energy-related areas of greatest projected human resource
shortages." Recipients of the first fellowships, awarded in FY
1991, are listed below.

1991 DOE Human Genome Distinguished Postdoctoral Fellows*

Xiaohua Huang (Stanford University, Biophysical Chemistry)
Host: University of California, Berkeley

Ben Koop (Wayne State University, Molecular Biology and Genetics)
Host: California Institute of Technology

Carol Soderlund (New Mexico State University, Computer Science)
Host: Los Alamos National Laboratory

Harold Swerdlow (University of Utah, Bioengineering)
Host: University of Utah

*Contact: Linda Holmes: 615/576-3192, Fax: [phone].

Fellowship appointments are tenable at DOE and university
laboratories having substantial DOE-sponsored research projects
supportive of the Human Genome Program. Fellows will participate
in advanced genetics-related research, interact with outstanding
professionals, and become familiar with major issues while making
personal contributions to the program's goal of mapping and
sequencing the human genome. This interaction, involving the
exchange of ideas, skills, and technologies, will benefit the
fellow, the host laboratory, and the DOE program.

These fellowships complement the Alexander Hollaender
Distinguished Postdoctoral Fellowships initiated by OHER. The
Hollaender Fellowships, established in memory of the 1983
recipient of the prestigious DOE Enrico Fermi Award, provide
support in all areas of OHER-sponsored research. Both
postdoctoral programs are administered by Oak Ridge Associated
Universities, which is a university consortium and DOE
contractor.


Resource Allocation

Reports by the Health and Environmental Research Advisory
Committee (HERAC) and the National Research Council (NRC)
recommended that national funding for the Human Genome Project
increase to a sustaining yearly level of $200 million. DOE
program expenditures were $5.5 million in FY 1987, $10.7 million
in FY 1988, $17.5 million in FY 1989, $25.9 million in FY 1990,
$46 million in FY 1991, and $59 million in FY 1992. The proposed
presidential budget for the DOE Human Genome Program in FY 1993
is $64.7 million (graph). DOE-sponsored research is conducted in
a variety of institutions (upper table). The lower table
categorizes research expenditures for FY 1992.

Types of Institutions Conducting DOE-Sponsored Genome Research

 8   National laboratories
 3   Other federal organizations
41   Academic institutions
10   Private-sector institutions
12   Nonacademic, commercial organizations

Human Genome Program Funds Distribution in FY 1992 (in $K)
(Commitments as of May 1, 1992)

----------------------------------------------------------------------------
| Organization  Mapping     Instrumenta  Informa  ELSI     Totals Percent  |
| Type          &           tion         tics                     of       |
|               Sequencing  Development                           568001   |
|--------------------------------------------------------------------------|
| DOE Labs      23671       7559         5122     236      36588  64.4     |
|                                                                          |
| Academic      5462        3341         4528     736      14067  24.8     |
|                                                                          |
| Institutions  2173        0            602      847      3622   6.4      |
| (nonprofit)                                                              |
|                                                                          |
| NIH Labs      680         0            0        0        680    1.2      |
|                                                                          |
| Companies     1550        0            314      392      2256   3.9      |
| and SBIR2                                                                |
|                                                                          |
| All           33536       10900        10566    2211     57213           |
| Organizations                                                            |
|                                                                          |
| [Percent      [59.0]      [19.2]       [18.6]   [3.9]    [100.7]^3       |
| of 56800]                                                                |
----------------------------------------------------------------------------



1  Total allocation of $59 million less capital equipment funds of $2.2
   million.
2  Small Business Innovation Research grants.
3  Excess occurs because funding for genome SBIR projects is received from
   the DOE-wide SBIR program, to which OHER contributes.




Interagency Coordination

Joint DOE-NIH Activities

The NIH Human Genome Program, led by NIH NCHGR, has emphasized
the study of disease genes in the construction of complete
genetic and physical maps of the genomes of humans and selected
model organisms. NIH is also developing new technologies and
information systems to manage mapping and sequencing data.

In the fall of 1988 DOE and NIH began coordinating their human
genome research programs under the Memorandum of Understanding,
an outgrowth of the HERAC and NRC reports, "to foster interagency
cooperation that will enhance the human genome research
capabilities of both agencies." More information on
NCHGR-sponsored projects and infrastructure may be obtained by
contacting the NCHGR Office of Communications at 301/402-0911.

Joint DOE-NIH Subcommittee on the Human Genome in 1992

Cochairs:

Paul Berg (PACHG)        Stanford University School of Medicine
Sheldon Wolff (HERAC)    University of California, San Francisco
Charles R. Cantor        Lawrence Berkeley Laboratory (HGCC)
Anthony V. Carrano       Lawrence Livermore National Laboratory (HGCC)
Joseph L. Goldstein      University of Texas Southwestern Medical Center
Leroy E. Hood            California Institute of Technology
Leonard S. Lerman        Massachusetts Institute of Technology (HERAC)
Victor A. McKusick       Johns Hopkins Hospital
Robert K. Moyzis         Los Alamos National Laboratory (HGCC)
Maynard V. Olson         Washington University School of Medicine (PACHG)
MaryLou Pardue           Massachusetts Institute of Technology (HERAC)
Mark L. Pearson          E. I. du Pont de Nemours & Company (PACHG)
Diane C. Smith           Xerox Corporation (PACHG)
Robert T. Tjian          University of California, Berkeley
Nancy S. Wexler          Columbia University (PACHG)
John C. Wooley           Office of Health and Environmental Research, DOE


Ex Officio Members:

David J. Galas           Office of Health and Environmental Research, DOE
Mark S. Guyer            National Center for Human Genome Research, NIH
Elke Jordan              National Center for Human Genome Research, NIH
David A. Smith           Office of Health and Environmental Research, DOE
Michael Gottesman        National Center for Human Genome Research, NIH


A national plan, primarily authored by NIH and DOE, for a
coordinated multiyear research project was presented to Congress
in early 1990. Understanding Our Genetic Inheritance, The U.S.
Human Genome Project: The First Five Years (1991-1995) detailed a
comprehensive spending plan and optimal strategies for mapping
and sequencing the human genome. Referred to as the Five Year
Plan, it calls for open biannual meetings of the DOE-NIH Joint
Subcommittee on the Human Genome. The joint subcommittee invites
reports from experts, including those on national and
international genome efforts; medical genetics; and related
ethical, legal, and social issues as they pertain to data
produced in the project. The subcommittee is made up of members
from the NIH Program Advisory Committee on the Human Genome
(PACHG) and from the DOE HERAC or the HGCC members appointed by
HERAC. The subcommittee reports to its parent committees_PACHG
and HERAC.

Many workshops and meetings have since been cosponsored by the
two agencies (see Appendix B). In addition, the Joint
Subcommittee on the Human Genome has established five joint
working groups that meet regularly to address specific areas of
genome research and make recommendations to the joint
subcommittee. The objectives of these five joint working groups,
listed below, include establishing research priorities;
identifying research, training, and technical needs; and
coordinating U.S. research activities with those of other
countries. Members of the working groups represent various
disciplines. (Membership lists of the working groups are included
in Appendix D.)

Joint Mapping Working Group. The mapping working group encourages
development and use of methodologies to integrate genetic linkage
and physical maps, meet project mapping goals, and identify
informatics needs associated with map generation and completion.

Joint Informatics Task Force (JITF). An ad hoc committee, JITF
prepared a comprehensive report on genome information needs and
data analysis tools. The report was presented to the DOE-NIH
Joint Subcommittee on the Human Genome in January 1992.

Joint Sequencing Working Group. The sequencing working group
investigates and makes recommendations on research and technology
development priorities to enable the sequencing of 3 billion
nucleotides of human DNA within 15 years.

Joint Working Group on Ethical, Legal, and Social Issues (ELSI).
ELSI identifies and addresses the social concerns that may arise
as genome technology is developed and genetic data becomes
available; stimulates bioethics research; promotes education of
professional and lay groups; and collaborates with international
groups such as the Human Genome Organization (HUGO), United
Nations Educational, Scientific, and Cultural Organization
(UNESCO), and the European Community (see next section).

Joint Working Group on the Mouse. The mouse working group was
established to develop a strategy for efficiently using the mouse
to accomplish mapping project goals as outlined in the Five Year
Plan. This strategy will take advantage of the extensive genetic
map data amassed on the mouse. Because of numerous similarities
between mouse and human genomes, these studies are considered
essential to understanding human biology and to interpreting more
complex data obtained in studies of humans.


Other U.S. Genome Research

U.S. Department of Agriculture (USDA). USDA has implemented a
Plant Genome Research Program to foster and coordinate research
on single and multigenic traits related to agricultural,
forestry, and environmental concerns. The goal of this 5-year
program is to improve plant varieties by locating important genes
and markers on chromosomes, determining gene structure, and
transferring genes to improve the performance of economically
important crops such as corn, wheat, soybeans, and pine. Use of
these "molecular breeding" techniques will increase U.S.
competitiveness in the world marketplace.

National Science Foundation (NSF). NSF coordinates an interagency
research effort to map and sequence the small genome of
Arabidopsis thaliana, a simple weed that provides an ideal model
for studying plant biochemistry, genetics, and physiology.
Knowledge of the function of every Arabidopsis gene will be
applicable to the understanding and manipulation of higher plants
and to genome research in general. These studies are also
supported by DOE, NIH, and USDA as part of their own genome
initiatives, and the four agencies coordinate their Arabidopsis
activities. NSF also has instrumentation, computational, and
informatics programs that support genomics research, in addition
to individual awards in genetics and molecular biology.

Howard Hughes Medical Institute (HHMI). HHMI, a private medical
research organization, contributes to the genome effort through
its support of biomedical research primarily at university
molecular biology and genetics laboratories. In addition, HHMI
has cosponsored several genomics conferences and, between 1985
and September 1991, supported the collection and dissemination of
genome mapping data through a network of databases.




International Coordination

Genomic research is being carried out in countries throughout the
world. The two international organizations described on the next
two pages are working to coordinate and facilitate national
efforts. HUGO includes a number of DOE and NIH genome
investigators and administrators. HUGO and UNESCO have been
informed of dedicated genome programs in the following nations
and international agencies: Commonwealth of Independent States
(formerly U.S.S.R.), Denmark, European Community, France,
Germany, Hungary, Italy, Japan, Netherlands, United Kingdom, and
United States.


HUGO: Worldwide Genome Research Coordination

HUGO, formed by scientists to coordinate worldwide genome mapping
and sequencing, now has regional offices in the United States
(Bethesda, Maryland) and Europe (London) and a satellite office
in Moscow. A Pacific office is under development in Osaka, Japan.

HUGO offices were funded initially by several charitable
organizations. In 1990 HHMI awarded HUGO a 4-year, $1 million
grant to support the HUGO Americas office; in that same year The
Wellcome Trust provided a 3-year grant, with the first year's
funds amounting to over $400,000, to assist with activities in
the European office. The Imperial Cancer Research Fund (U.K.)
provides support for the HUGO president's office, and the Osaka
office has received private support as well. To support future
activities, HUGO directors intend to raise funds from various
countries that have active genome research programs.

HUGO members are elected; there are over 400 members from 32
countries. The international officers in 1992: Sir Walter Bodmer
(United Kingdom), President; Charles R. Cantor (United States),
Vice-President; Andrei Mirzabekov (Russia), Vice-President;
Kenichi Matsubara (Japan), Vice-President; Bronwen Loder (United
Kingdom), Secretary; and Robert Sparkes (United States),
Treasurer. Each office operates with its own trustees.

The objectives of HUGO include

*    fostering collaboration to avoid unnecessary competition or
     duplication of effort and to coordinate human genome
     research with model organism studies;

*    coordinating exchanges of relevant data and materials;

*    educating researchers and the public on the scientific,
     ethical, social, legal, and commercial implications of the
     research; and

*    acting as a clearinghouse for genome-related information,
     such as relevant conferences, worldwide genome programs and
     researchers, and database and material availability. A
     training program may be initiated to encourage the spread of
     new and promising technologies.

HUGO has established expert international ad hoc advisory
committees on mapping workshops and databases, informatics,
ethics, mouse mapping, and intellectual property and ownership.

Single-chromosome workshops are crucial to the success of the
Human Genome Project. Working with the funding agencies, HUGO is
playing a central role in the coordinated development of such
meetings and has assisted in planning workshops for chromosomes
2, 3, 13, 16, 19, and X in 1992. HUGO expects to work with the
scientific community to select workshop chairs and to assist in
fundraising and organizing and running these and future meetings.
Chromosome workshops and other meetings are listed in Appendix B.


UNESCO: Promoting the Interests of Developing Countries

A UNESCO Human Genome Program was approved for 1990-91 at the
25th session of the UNESCO General Conference. Attendees
concluded that full knowledge of the human genome is vitally
important and that UNESCO could be influential in stimulating
governments and agencies to support coordinated programs. UNESCO
expects to play a key role in promoting the interests of
developing countries. The Scientific Coordinating Committee
(SCC), composed of 13 scientists, plans and implements the
program, which was budgeted at $350,000 for the first year; SCC
members include representatives selected from geographic regions
and from international genome organizations such as HUGO. Members
of SCC and of the UNESCO Secretariat agreed that UNESCO will
concentrate its activities on access to and use of data obtained
from human genome mapping and sequencing research, as well as on
related ethical and social issues.

UNESCO emphasizes the use of training programs as one of the best
means of obtaining cooperation and diminishing the gap between
developed and developing countries. The Third World Academy of
Sciences (TWAS) joined UNESCO in sponsoring a training program
that provided 19 fellowships in 1991 to awardees from Algeria,
Argentina, Cameroon, Chile, China, Costa Rica, Cyprus,
Czechoslovakia, Egypt, Guinea, India, Indonesia, Myanmar, the
Republic of Korea, Peru, Spain, Ukraine, Russia, and Yugoslavia.
The 1- to 3-month fellowships enable scientists from developing
countries to carry out research in well-established scientific
centers and to learn new research techniques. UNESCO and TWAS are
also jointly compiling a directory to identify third-world genome
researchers and their needs.

To avoid overlap with other genome projects, UNESCO focuses on
communication among countries about major trends and regional
efforts, one of which, the Latin American Human Genome Program,
was established during a UNESCO-supported symposium in Chile in
1990. The first annual UNESCO South-North Human Genome Conference
was held in 1992 in Caxambu, Brazil, to increase interaction
between scientists from developed countries and those of the
third world. The second conference is planned for Thailand in
1993, and the third will probably take place in China in 1994.