Full Text HG-97-002
 
LOW-COST, HIGH-ACCURACY DNA SEQUENCING TECHNOLOGIES
 
NIH GUIDE, Volume 26, Number 16, May 16, 1997
 
RFA:  HG-97-002
 
P.T.  34

Keywords: 
  Human Genome 
  Nucleic Acid Sequencing 

 
National Human Genome Research Institute
 
Letter of Intent Receipt Date:  August 1, 1997
Application Receipt Date:  October 16, 1997
 
PURPOSE
 
The purpose of this Request for Applications (RFA) is to stimulate
research on next-generation technologies that have the potential to
reduce the cost of high-accuracy genomic DNA sequencing by at least
an order of magnitude.
 
HEALTHY PEOPLE 2000
 
The Public Health Service (PHS) is committed to achieving the health
promotion and disease prevention objectives of "Healthy People 2000,"
a PHS-led national activity for setting priority areas.  This RFA,
Low-Cost, High-Accuracy DNA Sequencing Technologies, is related to
several priority areas including cancer, heart disease and stroke,
diabetes and chronic disability conditions, and maternal and infant
health.  Potential applicants may obtain a copy of "Healthy People
2000" (Full Report:  Stock No. 017-001-00474-0 or Summary Report:
Stock No. 017-001-00473-1) through the Superintendent of Documents,
Government Printing Office, Washington, DC 20402-9325 (telephone 202-
512-1800).
 
ELIGIBILITY REQUIREMENTS
 
Applications may be submitted by domestic for-profit and non-profit
organizations, public and private, such as universities, colleges,
hospitals, laboratories, companies, units of State and local
governments, and eligible agencies of the Federal government.
Racial/ethnic minority individuals, women, and persons with
disabilities are encouraged to apply as Principal Investigators.
Applications from foreign institutions will not be accepted. However,
subcontracts to foreign institutions are allowable, with sufficient
justification.
 
MECHANISM OF SUPPORT
 
This RFA will use the National Institutes of Health (NIH) research
project grant (R01), First Independent Research Support and
Transition (FIRST) (R29) award, exploratory/developmental grant
(R21), and program project (P01) mechanisms.  The total project
period for an R01 or P01 application submitted in response to this
RFA may not exceed three years.  R29 grants are subject to the usual
conditions for the FIRST awards.  Exploratory/developmental (R21)
grants will be limited to $100,000 direct cost per year for a maximum
of 3 years (one year longer than NHGRI~s standard R21 grant).  The
R21 grant mechanism is used to support highly creative approaches for
which substantial preliminary data are not yet available.  Specific
information about the R21 grant mechanism can be found in the NHGRI
Program Announcement PA-97-045, "Pilot Projects or Feasibility
Studies for Genomic Mapping, Sequencing and Analysis" (available from
http://www.nhgri.nih.gov/Grant_info/Funding/Research/pilotpa.html).
The R21 grants are not renewable, but future project continuation is
possible through other grant mechanisms such as the R01 or P01.
Responsibility for the planning, direction, and execution of the
proposed project will be solely that of the applicant.  Awards will
be administered under PHS grants policy as stated in the Public
Health Service Grants Policy Statement.  The anticipated award date
is July 1, 1998.  It is anticipated that another RFA related to DNA
sequencing technology will be issued by NHGRI next year.
 
FUNDS AVAILABLE
 
It is anticipated that approximately $5 million (total costs) will be
available for this initiative in Fiscal Year 1998.  NHGRI anticipates
that projects at very different stages of development will be
submitted in response to this RFA.  Therefore, the size of awards may
vary substantially; accordingly the number of grants funded may be as
few as five or as many as 20, depending on the quality and scope of
the applications received.  Awards pursuant to this RFA are
contingent upon the availability of funds for this purpose.  The
amount of funding for this solicitation may be increased if a large
number of highly meritorious applications is received and if funds
are available.  Only applications found to be of high scientific
merit will be considered for funding and all of the funds will not be
spent if there are not enough highly meritorious applications.  Any
applicant planning to submit an application for more than $500,000
direct cost in any one year MUST contact the NHGRI staff listed under
INQUIRIES in order for the application to be accepted by NIH.
 
RESEARCH OBJECTIVES
 
Background
 
NHGRI is currently engaged, along with several other federal,
private, and international organizations, in a fifteen year research
program called the Human Genome Project (HGP).  The goals are to
characterize the genomes of human and selected model organisms, to
develop technologies to analyze the human genome, to examine the
ethical, legal, and social implications of human genetics research,
and to train scientists who will be able to utilize the tools and
resources developed through the HGP to pursue biological studies that
will improve human health.
 
Significant progress toward completing these goals has been made in
the past seven years, with several having already been achieved.  The
genetic mapping goals for both the human and the mouse have been met.
Progress toward the human and mouse physical mapping goals is steady,
with sufficient support in place to allow the achievement of these
goals ahead of schedule.  There has also been good progress toward
meeting the sequencing goals.  The genomic sequence of both E. coli
and S. cerevisiae have been determined, the sequence of C. elegans is
expected to be finished by 1998, and the complete sequence of D.
melanogaster is expected to be finished shortly after the end of this
century.
 
As a result of recent improvements in sequencing technology and
strategies, confidence is high that current technology, enhanced by
foreseeable improvements, will be sufficient to complete a reference
human genomic DNA sequence by the target date, 2005.  To this end,
pilot projects for large-scale production of human genomic DNA
sequence were initiated in 1996.  However, even with anticipated
improvements, DNA sequencing is likely to remain too expensive to
meet the scientific demand for sequence information.  For example,
additional sequencing will be needed to understand the sequence
variation between individuals that is associated with individual
differences in inherited susceptibility to disease.  Such studies may
require obtaining the sequence of much of the genomic DNA from large
numbers (tens to possibly thousands) of individuals.  Similarly, the
utility of the initial complete genomic sequence of a few organisms
for understanding their biology will increase the incentive to
collect genomic sequence information for many other organisms to
study their biology and evolutionary and symbiotic relationships. DNA
sequencing of that magnitude can only be contemplated when sequencing
techniques have been made considerably more cost-effective and robust
than they are today, or will be in the foreseeable future.  The
purpose of this RFA is to stimulate the development of the
technologies needed to achieve these goals.
 
Objectives and Scope
 
Technologies for de novo sequencing and re-sequencing are needed.  It
should be noted that the conceptual distinction between these DNA
sequencing technologies is not fundamental, but is instead a function
of the limitations of the technologies as currently implemented.  As
novel methods are introduced and sequencing technologies mature,
throughput and accuracy will increase and cost will decrease, and the
distinction may not persist.  However, at least for the present, the
capabilities of these approaches and their potential near-term
applications are sufficiently different to justify distinguishing
between them for the purpose of this RFA.
 
De novo sequencing involves determining DNA sequence without any
prior knowledge of that sequence.  The initial reference human
sequence will be determined by de novo sequencing, as were the
sequences of yeast, H. influenzae, M. genitalium, M. jannaschii, and
E. coli.  Technology for de novo sequencing will continue to be
needed to determine the complete sequence of the genomes of numerous
other organisms including pathogens, agriculturally important
organisms, and those that have utility as model organisms and sources
of pharmaceutical products.
 
Technology is also needed for re-sequencing or rapidly comparing
sequences to identify differences.  Re-sequencing takes advantage of
sequence information obtained from one sample, to design a more
efficient approach to determining the sequence of another, similar
sample.  Today~s re-sequencing technologies are effective for samples
that are extremely similar (e.g., for identifying single-base
differences in a particular gene isolated from two individuals).
With additional development, however, the data quality and throughput
of re-sequencing technology may be improved, and expanded to allow
determination of sequence in cases such as insertions or deletions
relative to a reference sequence.  Re-sequencing technology may be
the most cost-effective way, for example, to collect the large
amounts of sequence data from large numbers of individuals that is
needed to understand the sequence variations associated with
individual differences in inherited susceptibility to disease.
 
This RFA seeks to stimulate research on next-generation technologies
(including those for de novo sequencing, re-sequencing, or both) that
have the potential to reduce the cost of high-accuracy genomic DNA
sequencing by at least an order of magnitude.  State-of-the-art
technology can currently generate de novo sequence data containing
less than 1 error per 10,000 base pairs at a total cost (including
machines, personnel, supplies, and overhead) of approximately $0.50
per base pair.  The goal of research under this RFA will be to drive
the total cost of obtaining accurate (<1 error in 10,000 bp) de novo
sequence to well below $0.05 per base pair; re-sequencing should cost
considerably less.
 
Applications responsive to this RFA will include those designed to:
 
o  conduct research on novel scientific or engineering principles
which have promise for being applicable to the development of cost-
effective DNA sequencing technologies;
 
o  study the application to DNA sequencing of principles that are
well established in other fields of science or engineering, and that
have strong potential for application to DNA sequencing, but for
which such application may not have been demonstrated; and
 
o  further develop technologies for which proof of principle for DNA
sequencing may already have been demonstrated, but for which
substantial additional work is required to achieve high throughput
and low cost for genomic sequencing (examples include mass
spectrometry, sequencing by hybridization, and micromachined and
micro-electro-mechanical systems [MEMS]).
 
This list is not intended to be all-inclusive, but instead to provide
examples of responsive projects.  Potential applicants who have
questions about the responsiveness of specific ideas are encouraged
to contact NHGRI staff listed under INQUIRIES before submitting an
application.
 
Applicants should directly address the advantages of the proposed
approach over existing approaches, and justify their assertion that
successful development of the technology will result in a ten-fold
decrease in the cost of sequencing.  Applicants proposing to develop
technologies for which proof of principle for DNA sequencing has not
yet been demonstrated should describe clearly the manner in which the
proposed technology might be applied to sequencing.  For such
projects, it will be difficult to predict with confidence the cost of
sequencing using the technology.  It is therefore particularly
important to present a clear conceptual overview of the entire system
in which the technology would be used and if possible to estimate the
cost of developing, producing, and using such a system.
 
Current DNA sequencing approaches require some combination of steps,
including the isolation of DNA from biological samples, biochemical
amplification of the DNA within the sample, incorporation of
fluorescent label into the sample, determination of the nucleotide
sequence of each sample, ~assembly~ of data from numerous overlapping
and redundant determinations into a continuous dataset, and analysis
of the sequence data.  As new technologies are developed, some or all
of these steps may still be required.  Research on all of these
steps, and particularly on the integration of steps into a continuous
process, will be supported under this RFA.  For projects whose aim is
to develop integrated systems, applicants should address the
throughput of the various system components, and how the entire
system will support the achievement of the cost and quality goals of
this RFA.
 
The RFA will also accept applications to develop computational tools
needed in support of systems or in conjunction with components
eligible for funding under this RFA.  Support for development of
computational tools may be included as part of the technology
development application.  An application to develop computational
tools that is submitted independently of a proposal to develop
hardware systems should describe how the results of the independent
research will be integrated with existing or planned technology.
 
The following types of research will NOT be supported under this RFA:
projects to improve slab gels, microchannels, and capillary array
electrophoresis, in systems in which the well-to-read distance is
measured in tens of centimeters.  This type of research is currently
receiving support from NHGRI as a result of recent RFAs.  However,
NHGRI continues to encourage this type of technology development for
DNA sequencing; applications for such studies should be submitted
under the Program Announcement PA-97-044  ~Technologies for Genomic
Mapping, Sequencing, and Analysis~ (available from
http://www.nhgri.nih.gov/Grant_info/Funding/Research/techpa.html).
 
INCLUSION OF WOMEN AND MINORITIES IN RESEARCH INVOLVING HUMAN
SUBJECTS
 
It is the policy of the NIH that women and members of minority groups
and their sub-populations must be included in all NIH supported
biomedical and behavioral research projects involving human subjects,
unless a clear and compelling rationale and justification is provided
that inclusion is inappropriate with respect to the health of the
subjects or the purpose of the research.  This policy results from
the NIH Revitalization ACT of 1993 (Section 492B of Public Law 103-
43).
 
All investigators proposing research involving human subjects should
read the "NIH Guidelines for Inclusion of Women and Minorities as
Subjects in Clinical Research," which have been published in the
Federal Register of March 28, 1994 (FR 59 14508-14513) and in the NIH
Guide for Grants and Contracts, Volume 23, Number 11, March 18, 1994.
 
SPECIAL REQUIREMENTS
 
Statement of milestones:  It has been the experience of NGHRI that
technology development projects that establish a clear statement of
their milestones, and benchmarks by which attainment of those
milestones can be measured, make more rapid progress toward achieving
their short- and long-range goals.  Therefore, applicants should
present a clear timetable for the achievement of specific milestones,
and should define the benchmarks by which progress toward those
milestones will be measured. Both the milestones and benchmarks
should be stated as quantitatively as possible.
 
Dissemination of the results of technology development research:
Proposals should address the issue of access by groups other than the
developers to any instruments or software developed through this
program.
 
Post-award management:  During the course of the grant period,
technologies will improve and the rate of progress and focus of work
supported by the grants may change.  It is expected that the
principal investigators will make any necessary adjustments in
scientific direction to accommodate the changing environment.  During
the award period, the principal investigators may be invited to meet
with NIH program staff in Bethesda, MD, or at the grantee site, to
review scientific progress.  Other scientists external to and
knowledgeable about these studies may also be invited to participate.
Applicants should include travel funds for the P.I. to meet annually
with NIH staff in the Washington D.C. area, should such meetings be
advisable.
 
Special human subjects issues:  Recently, it has become evident that
special human subjects issues are raised by the large-scale
sequencing of human genomic DNA because large amounts of DNA sequence
information from single individuals may be generated.  Similar issues
can be anticipated in projects in which sequence variations are
identified in individuals.  The NHGRI and the DOE have recently
issued a document, "Guidance on Human Subjects Issues in Large-Scale
DNA Sequencing" to address these issues.  This document can be found
on the NHGRI web site at
(http://www.NHGRI.nih.gov/Grant_info/Funding/Statements/large_scale.h
tml).  Any application submitted in response to this RFA that
includes a plan to sequence at least 1 megabase of human DNA during
the period of the grant, or to determine a large number of human
sequence polymorphisms, in the context of testing the technology
under development, should address these special human subjects
issues.
 
LETTER OF INTENT
 
Prospective applicants are asked to submit, by August 1, 1997, a
letter of intent that includes a descriptive title of the proposed
research, the name, address, and telephone number of the Principal
Investigator, and the identities of other key personnel and
participating institutions, and the number and title of the RFA in
response to which the application may be submitted.  Although a
letter of intent is not required, is not binding, and does not enter
into the review of a subsequent application, it can help establish an
early dialogue with NHGRI staff, and the information that it contains
allows NHGRI staff to estimate the potential review workload and to
avoid conflict of interest in the review.
 
The letter of intent is to be sent to:
 
Jeffery A. Schloss Ph.D.
Division of Extramural Research
National Human Genome Research Institute
Building 38A, Room 614
Bethesda, MD  20892-6050
Telephone:  (301) 496-7531
FAX:  (301) 480-2770
Email:  Jeff_Schloss@nih.gov
 
APPLICATION PROCEDURES
 
The research grant application form PHS 398 (rev. 5/95) is to be used
in applying for these grants.  These forms are available at most
institutional offices of sponsored research; from the Division of
Extramural Outreach and Information Resources, National Institutes of
Health, 6701 Rockledge Drive, MSC 7910, Bethesda, MD 20892-7910,
telephone 301/435-0714, e-mail:  ASKNIH@odrockm1.od.nih.gov; and from
the program administrator listed under INQUIRIES.
 
The RFA label available in the application form must be affixed to
the bottom of the face page of the application.  Failure to use this
label could result in delayed processing of the application such that
it may not reach the review committee in time for review.  In
addition, the RFA title and number must be typed on line 2 of the
face page of the application form and the YES box must be marked.
 
Submit a signed, typewritten original of the application, including
the Checklist, and three signed photocopies, in one package to:
 
DIVISION OF RESEARCH GRANTS
NATIONAL INSTITUTES OF HEALTH
6701 ROCKLEDGE DRIVE, ROOM 1040
BETHESDA, MD  20892-7710
BETHESDA, MD  20817 (for express/courier service)
 
At the time of submission, two additional copies of the application,
including appendices, must also be sent to:
 
Rudy Pozzatti, Ph.D.
Office of Scientific Review
National Human Genome Research Institute
Building 38A, Room 613
Bethesda, MD  20892-6050
 
Applications must be received by October 16, 1997.  If an application
is received after that date, it will be returned to the applicant
without review. The Division of Research Grants (DRG) will not accept
any application in response to this RFA that is essentially the same
as one currently pending initial review, unless the applicant
withdraws the pending application.  The DRG will not accept any
application that is essentially the same as one already reviewed.
This does not preclude the submission of substantial revisions of
applications already reviewed, but such applications must include an
introduction addressing the previous critique.  The applicants should
also ensure that their revised applications respond to the review
criteria by which applications received in response to this RFA will
be evaluated.
 
REVIEW CONSIDERATIONS
 
Upon receipt, applications will be reviewed for completeness by DRG
and for responsiveness to the RFA by NHGRI program staff.  Incomplete
applications will be returned to the applicant without further
consideration.  If the application is not responsive to the RFA, NIH
staff will contact the applicant to determine whether to return the
application to the applicant or submit it for review in competition
with unsolicited applications at the next review cycle.
 
Those applications that are complete and responsive will be evaluated
for scientific and technical merit in accordance with the criteria
stated below by an appropriate peer review group convened by the
NHGRI.  As part of the initial merit review, all applications will
receive a written critique and may undergo a process in which only
those applications deemed to have the highest scientific merit will
be discussed and assigned a priority score.  All applications will
receive a second level of review by the National Advisory Council for
Human Genome Research.
 
Review criteria will include:
 
o  scientific and technical merit of the proposed research;
 
o  potential of the proposed technology to achieve the cost and
quality goals of this RFA;
 
o  appropriateness and adequacy of the experimental approach and
methodology proposed to carry out the research;
 
o  adequacy with which critical technical issues have been
identified, and solutions proposed;
 
o  appropriateness of the timeline and milestones established by the
investigator to ensure continued progress toward the specific aims,
and adequacy of the specific benchmarks proposed for measuring
progress toward the milestones;
 
o  adequacy of plans to integrate the proposed technology with other
components of a process required to accomplish DNA sequencing;
 
o  qualifications and research experience of the principal
investigator and staff in the area of the proposed research;
 
o  availability of the resources necessary to perform the research;
 
o  adequacy of plans for dissemination of technical advances and
software tools developed under grant support;
 
o  appropriateness of the proposed budget and duration in relation to
the proposed research; and
 
o  adequacy of plans to protect human subjects and to include women
and minorities, if applicable.
 
For R21 applications, preliminary data are not required.  However,
the applicant does have the responsibility for developing a sound
research plan and for presenting any other information that can be
considered as evidence of feasibility.
 
AWARD CRITERIA
 
Factors that will be used to make award decisions are:
 
o  quality of the proposed project as determined by peer review;
 
o  balance among the projects received in response to the RFA in
addressing different experimental approaches and their
complementarity to other ongoing efforts, and value of the proposed
research for achieving the goals of the National Human Genome
Research Institute;
 
o  adequacy of plans to manage and share data, resources and
technology in a timely manner; and
 
o  availability of funds.
 
INQUIRIES
 
Inquiries concerning this RFA are encouraged.  The opportunity to
clarify any issues or questions from potential applicants is welcome.
 
Direct inquiries regarding programmatic issues to:
 
Jeffery A. Schloss, Ph.D.
Division of Extramural Research
National Human Genome Research Institute
Building 38A, Room 614
Bethesda, MD  20892-6050
Telephone:  (301) 496-7531
FAX:  (301) 480-2770
Email:  Jeff_Schloss@nih.gov
 
Direct inquiries regarding fiscal matters to:
 
Ms. Jean Cahill
Grants Management Office
National Human Genome Research Institute
Building 38A, Room 613
Bethesda, MD  20892-6050
Telephone:  (301) 402-0733
FAX:  (301) 402-1951
Email:  Jean_Cahill@nih.gov
 
AUTHORITY AND REGULATIONS
 
This program is described in the Catalog of Federal Domestic
Assistance No. 93.172.  Awards are made under authorization of the
Public Health Service Act, Title IV, Part A (Public Law 78-410, as
amended by Public Law 99-158, 42 USC 241 and 285) and administered
under PHS grants policies and Federal Regulations 42 CFR 52 and 45
CFR Part 74.  This program is not subject to the intergovernmental
review requirements of Executive Order 12372 or Health Systems Agency
review.
 
The PHS strongly encourages all grant recipients to provide a smoke-
free workplace and promote the non-use of all tobacco products.  In
addition, Public Law 103-227, the Pro-Children Act of 1994, prohibits
smoking in certain facilities (or in some cases, any portion of a
facility) in which regular or routine education, library, day care,
health care or early childhood development services are provided to
children.  This is consistent with the PHS mission to protect and
advance the physical and mental health of the American people.
 
.

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