NETWORK FOR LARGE-SCALE SEQUENCING OF THE MOUSE GENOME

Release Date:  December 23, 1998

RFA:  HG-99-001

P.T.

National Human Genome Research Institute

Letter of Intent Receipt Date: March 1, 1999
Application Receipt Date: April 29, 1999

PURPOSE

The purpose of this RFA is to establish a Mouse Genome Sequencing Network that
will support the mapping and sequencing of the mouse genome.  The goals of the
Network are to generate the necessary mapping resources and begin production of
a working draft of the DNA sequence of the mouse genome.  Applications for both
pilot sequencing projects in new groups and the expansion of the capacity of
existing sequencing centers are encouraged. The long-term goal of the Mouse
Genome Sequencing Network is to complete a high quality DNA sequence of the mouse
genome in cooperation with the international mouse research community.

HEALTHY PEOPLE 2000

The National Institutes of Health (NIH) is committed to achieving the health
promotion and disease prevention objectives of "Healthy People 2000," a NIH-led
national activity for setting priority areas. This RFA, Network for Large Scale
Sequencing of the Mouse Genome, 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" at  http://odphp.osophs.dhhs.gov/pubs/hp2000/.

REQUIREMENTS

Applications may be submitted by domestic non-profit and for-profit
organizations, private and public, such as universities, colleges, private
companies, hospitals, laboratories, units of state or local governments, and
eligible agencies of the Federal government. Applications from minority
individuals and women are encouraged. Applications from foreign institutions will
not be accepted; however subcontracts to foreign institutions will be considered.
For this RFA, NIH intramural investigators are eligible to become components of
the Mouse Genome Sequencing Network.  Applications from intramural groups will
be peer reviewed in competition with extramural investigators and, if successful,
will receive funding from an appropriate source.  Existing sequencing groups that
are requesting funding for expansion of sequencing capacity for mouse production
sequencing must have deposited 2 Mb of finished DNA sequence in a public database
by the application date.

MECHANISM OF SUPPORT

The administrative and funding mechanism to be used to support this program will
be the Cooperative Agreement (U01), an "assistance" mechanism, which is
distinguished from a regular research grant in that substantial scientific and/or
programmatic involvement by NHGRI staff with the awardee is anticipated. The
cooperative agreement is used when participation by NIH staff is warranted to
support and/or stimulate the recipient's activity by involvement in and otherwise
working jointly with the award recipient in a partner role; NIH staff will not
assume direction, prime responsibility, or a dominant role in the activity.
Details of the responsibilities, relationships, and governance of the studies
funded under cooperative agreement(s) are discussed later in this document under
the section "Terms and Conditions of Award".  Each component, with the exception
of NIH intramural projects, of the Mouse Genome Sequencing Network will be
awarded as a separate U01.

The length of project period that may be requested is discussed for each type of
project described under Research Objectives and Scope (see below).  The sizes of
the awards will vary depending upon the research objectives of each. The
anticipated award date is September 30, 1999.

It is NHGRI's intention to continue the Mouse Genome Sequencing Network through
the completion of the mouse genomic DNA sequence.  This RFA solicits applications
to initiate the Mouse Genome Sequencing Network.  During the third year of
support of the applications funded under this RFA, it is anticipated that a
renewal solicitation will be issued to complete the sequence.

FUNDS AVAILABLE

This is a trans-NIH initiative managed by the NHGRI on behalf of the NIH.  The
estimated funds available for the first year of support for awards under this RFA
will be $21 million (total costs) to support all of the objectives listed below.
It is expected that from one to four efforts will be funded for characterization
of mouse BAC libraries, generation of a mapping resource and construction of a
map of sequenced clones.  For the sequence production component of the Network,
it is anticipated that three to five new sequence production projects and up to
four existing centers will be funded.  One to three intramural projects may be
funded.  Applicants may request funding for any one or combination of the
objectives listed below.

This level of support is dependent on the receipt of a sufficient number of
applications of high scientific merit. Beyond the first year, the funding level
for the overall Mouse Genome Sequencing Network will be dependent upon the
availability of funds.  The funding level of each of the projects and sequencing
centers will be subject to an annual evaluation by the Scientific Advisory Panel
of the Mouse Genome Sequencing Network (see below for details). The usual NIH
policies governing grants administration and management will apply.

RESEARCH OBJECTIVES AND SCOPE

Background

The NHGRI is currently engaged, along with several other federal, private, and
international organizations, in a research program called the Human Genome
Project (HGP).  The goals of the HGP, as set out in a series of five-year plans
(see http://WWW.NHGRI.NIH.GOV/HGP/HGP_goals/ ), are to characterize the genomes
of human and selected model organisms through complete mapping and sequencing,
to develop technologies for genomic analysis, 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.

The HGP started in 1990.  Significant progress toward completing these goals has
been made in the past eight years and several goals have already been achieved.
The genetic mapping goals for both the human and the mouse have been met.  The
human and mouse physical mapping goals are nearly complete. The goal of
determining 80Mb of genomic DNA sequence by 1998 has been exceeded (for example,
over 200 Mb of human DNA sequence have been determined, as have 5 Mb of mouse
genomic DNA in regions syntenic to those that have been sequenced in the human). 
The DNA sequence of the E. coli and S. cerevisiae genomes has been completely
determined (as have those of several other microorganisms), and the sequence of
the C. elegans genome has just been published.

In the fall of 1998, the NHGRI and DOE published a new five-year plan (Science,
Vol. 282, p 682, October 23, 1998), http://www.nhgri.nih.gov/98plan/. The plan
calls for an accelerated timetable for the sequencing of the human genome with
completion of a "working draft" by 2001 and the final sequence by 2003. A
timetable for sequencing the mouse genome is also included.  The purpose of this
RFA is to fund research to establish the infrastructure and resources needed to
meet or exceed the goals for the mouse genome laid out in the new five-year plan.

The detailed characterization of the mouse genome is of widespread interest
across the NIH.  In order to help define and establish priorities for the genomic
analysis of the mouse, the NIH Director convened a meeting of a distinguished
group of scientists in March 1998; a follow-up meeting was held in October 1998.
Summaries of the two meetings can be found at
http://www.nih.gov/welcome/director/reports/mgenome.htm and  
http://www.nih.gov/welcome/director/reports/mgenom3.htm.  (Links to all the
reports concerning the mouse genome initiative can be found on the page
http://www.nih.gov/welcome/director/keymeet.htm, under the heading Special
Reports).  It was assumed at the first meeting that sequencing the mouse genome
would be based on prior construction of sequence-ready physical maps.  However,
at the second meeting, a "sequence first, map second" strategy was discussed and
recommended. The second meeting also recommended that a working draft quality
sequence based on mapped BACs be developed useful intermediate to the finished
sequence and should be taken on as an objective on an accelerated timetable.

At the October meeting, a strategy for efficiently generating a working draft
sequence was recommended.  This starts with the sequencing of clones chosen
randomly from a library of fingerprinted and end-sequenced BACs. These clones
would not have to be mapped at the time of selection for sequencing, but
subsequently would be mapped.  Close integration of all groups involved in such
a whole genome, BAC-based sequencing effort would be required.  The necessary
coordination could be achieved by a central server that would collect mapping and
sequencing information from all groups and allow database searches against
completed projects, on-going projects, and BAC end sequences to avoid extensive
overlaps as each sequencer chooses the next BAC for sequencing.  The National
Center for Biotechnology Information (NCBI) is committed to designing the central
server required for this effort. This sequencing approach would initially lead
to sequence coverage in small contigs and single BACs.  At an appropriate time,
a more directed strategy for clone selection would be implemented to enlarge the
contigs and close the gaps between them.  The attendees at the October meeting
also agreed that the strain that should be used for the initial sequencing is
C57BL6/J.  A BAC library for this strain has been constructed and is available
through commercial distributors.

This "sequence first, map later" approach recommended at the October 5, 1998
meeting was thought to have several benefits.  It would allow mouse sequencing
to scale up rapidly, and would eliminate the need for every group participating
in the effort to have a large-scale mapping capability.  Groups with only limited
experience with sequencing or in building maps, but who are interested in
becoming "start up" centers for mouse genomic sequencing, would be able to
concentrate their learning curves on sequencing alone, thereby increasing their
chances for success.  Although these advantages are sufficient to warrant focus
on this strategy at present, an important lesson of the genome project to date
is that the methods and strategies can emerge quickly.  Therefore, which ever
strategy an applicant proposes, (map first, sequence later or sequence first, map
later or yet another strategy) must remain flexible and willing to adapt to
changes in the field as strategies evolve rapidly.  Additionally, applicants must
be willing to coordinate efforts with the international community that is
participating in sequencing the mouse genome.

NHGRI has successfully initiated new large-scale sequencing efforts through a
pilot project program for human genome sequencing. This program was established
to test different strategies and technologies for scaling up the production of
high quality finished genomic DNA sequence efficiently and cost effectively. 
During the three-year program, significant progress has been made in many aspects
of sequencing, including technology implementation, management, cost reduction,
and capacity increase.  Many of the lessons learned over the past three years
will be used to scale up production to the levels necessary to complete the
sequencing of the human genome by 2003.  To date, the pilot project program has
produced more than 124 Mb of finished human DNA sequence.  The pilot mouse genome
sequencing program being solicited through this RFA will be patterned after the
human sequencing program in many ways.  It is expected that the experience that
has been gained to date in the sequencing of the human genome can be applied to
enable new groups to participate in the sequencing of the mouse genome and allow
the sequencing of the mouse genome to scale up more rapidly.

Research Scope

The initial goals of the Mouse Genome Sequencing Network will be to establish
mouse genomic mapping resources, to establish pilot sequencing projects and to
expand the capacity of existing large-scale sequencing groups to generate a
working draft sequence of 90% of the mouse genome sequence by 2003.  This RFA
calls for projects (from both the extramural and the NIH intramural research
community) with the following objectives:

A.  BAC library characterization: For the strategy of sequencing chosen BACs to
be successful, a considerable amount of information about the BAC clones is
necessary in order to guide and coordinate the effort.  Applications are sought
to fingerprint and end sequence the currently available C57BL/6J BAC library. 
If other BAC libraries are found to be necessary for successful completion of the
mouse genomic sequence, they will have to be characterized similarly. Proposals
are not limited to fingerprinting and BAC end sequencing and applicants are
encouraged to propose other, better ways of characterizing BAC libraries. 
However, the application must propose an efficient strategy for characterizing
an entire library in a way that will contribute to the success of a genome-wide,
working draft sequence strategy.  A plan to make the data rapidly available to
the research community must be included in the proposal.  Library
characterization should be completed in one to two years.

B.  Generation of a mapping resource, such as a set of radiation hybrids for
constructing a radiation hybrid map, and of a map containing anchor markers and
all of the sequenced clones.  Although the sequencing strategy being discussed
for the mouse genome does not require a map to guide the initial clone selection,
efficient completion of the sequence will depend on the availability of a map on
which sequenced clones have been localized.  Therefore, a suitable mapping
resource is needed to generate a map that can support the sequencing effort
beyond the initial random phase.  This map should contain enough existing mapped
markers to ensure that it can be easily cross-referenced to existing maps of the
mouse genome.  Proposals should also include enough effort to efficiently map all
clones sequenced during the term of the grant.  This is estimated to be 10,000
clones in the first three years.  As the mapping effort must be tightly linked
to the genomic sequencing projects, applicants must describe plans for
coordination and cooperation with the national and international sequencing
efforts, as well as with the centralized database.  The mapping resource should
be completed as soon as possible, ideally within one year.  Mapping will continue
until the mouse sequence is completed.

C.  Establishment of sequencing efforts by groups that wish to participate in the
sequencing of the mouse genome, whether or not they are presently engaged in
large-scale sequencing activities.  Applicants for production sequencing, in both
new and existing centers, must address the items listed in "Application Guidance
for Production Sequencing" under Application Procedures.  Applications to
complete this portion of the RFA may request three years of funding.

Two types of sequencing projects will be included in the Mouse Genome Sequencing
Network:

1.  New pilot projects for sequencing the mouse genome.  The initiation of the
mouse genomic sequencing effort provides an opportunity for NHGRI to establish
new groups interested in participating in large-scale sequencing. Applicants who
wish to participate in this way must propose concrete plans that address all
issues related to the rapid scale up of sequencing activities in a new center,
including the following:

o   Sequencing Experience: Although it is not expected that those applying for
new sequence production centers will have much experience with large-scale
production sequencing, any such experience should be described.  A list of
questions on this topic, to be answered as part of the progress report, is
attached.
o  Strategic Plan: All applications for pilot sequencing projects must present
a strategic plan, including a time line, that describes how and when the proposed
effort will scale up to the point at which it can make a substantial contribution
to the mouse genome sequencing effort.
o  Cost:  The unit cost of working draft sequence (measured as the cost per lane
of sequencing) in a pilot project may initially be quite high as compared to
established sequencing efforts (estimated to be between $5 and $7.50 per lane). 
However, from NHGRI's experience with the human genome pilot sequencing program,
it can be expected that these costs should rapidly decline as the pilot project
scales.  Thus, by the end of the second year, it is expected that the per lane
sequencing cost for a new pilot project would have decreased significantly and
be comparable to other sequencing centers by the end of the third year.  This
rapid decline in cost will be necessary if a group is to be competitive for
further scale up at the end of the initial three years.  NHGRI is seeking
ambitious but realistic plans to lower costs and scale up to initiate the project
as quickly as possible. A list of questions on this topic, to be answered as part
of the progress report, is attached.
o  Sequence Quality: Sequence quality is an important issue in the Human Genome
Project.  It is not expected that applicants for new pilot projects will have
much, if any, sequence data available to be checked for quality.  However, it is
anticipated that by the end of the first year of funding sufficient data
(sequence of at least two large-insert clones) will have been generated to allow
quality assessment. See section below, entitled "Sequence Quality" under NHGRI
Policies Concerning Pilot Project and Large-scale Sequencing for more information
about NHGRI plans to assess sequence quality.
o  New Technological Developments: Successful applications will need a clear-cut
scientific and budgetary strategy for maintaining a state-of-the-art sequencing
capability. Applicants must address the ways in which the proposed project will
allow incorporation/integration of any new technological developments in DNA
sequencing that arise during the term of the grant.

2.  Additional capacity for mouse genomics in experienced groups.  In order to
rapidly initiate the sequencing of the mouse genome, this RFA invites experienced
sequencing groups to apply for funds to expand their capacity to initiate or
expand mouse genomic sequencing. Experienced groups are defined as those that
have produced at least 2 Mb of finished DNA sequence which has been deposited in
a public data base.

In order to evaluate requests from existing centers, reviewers will need reliable
information about the current sequencing effort. A list of questions on this
topic, to be answered as part of the progress report, is attached.  If, at the
time of submission of the application, the quality of a center's sequence data
has not been checked in the past six months, then it will be analyzed in a
quality control exercise similar to that previously conducted for human sequence. 
The analysis will take place between the date of submission of the grant
application and the review. Information about previous quality control exercises
can be found at 
http://www.nhgri.nih.gov/Grant_info/Funding/Statements/RFA/quality_standard.html
NHGRI estimates that with the funds available for this RFA, new and existing
sequencing centers should be able to generate at least a 5-fold coverage of a
significant fraction of the mouse genome during the first three years of the
Sequencing Network and the entire mouse genome by 2003. However, applicants may
propose generating sequence of a different depth of coverage depending upon the
center's ability to scale its capacity and decrease its costs.  A principal
investigator may submit an application for one or more of the objectives A, B,
and C1 or C2 listed above.

NHGRI POLICIES CONCERNING PILOT PROJECT AND LARGE-SCALE SEQUENCING

Over the past two years, as the human sequencing program began to produce
significant quantities of human genomic DNA sequence, a number of issues arose
that required the development of new policies by NHGRI. These policies will be
extended to both extramural and NIH intramural investigators funded as part of
the Mouse Genome Sequencing Network. Thus, where appropriate, applicants must
present plans to adhere to the policies.

Intellectual Property.  In NHGRI's opinion, in the absence of specific biological
information, genomic DNA sequence information should not be patented but released
into the public domain where it will be freely available for use by the entire
research community.  NHGRI will monitor its grantees' activities with respect to
patenting genomic sequence. (see web site:
http://www.nhgri.nih.gov/Grant_info/Funding/Statements/RFA/intellectual_property.html).

Data Release.  Applicants should fully describe their plans for the release of
mapping data and of finished and unfinished sequence data.

Finished mapping and sequence data: The U.S. HGP has adopted a policy of
encouraging rapid release of mapping and sequence data into public databases.
This policy extends to all genomic sequence funded with NHGRI funds. (see
http://www.nhgri.nih.gov/Grant_info/Funding/Statements/RFA/data_release.html).

Unfinished sequence data: Participants in the international human DNA sequencing
effort have recommended that early stage sequence data, from any organism should
be rapidly released (Genome Research, Vol. 8, Issue 5, 413-413, May 1998). 
Accordingly, NHGRI has determined that its grantees should release DNA sequence
assemblies of 2,000 base pair units or larger from all organisms being sequenced
with its support within 24 hours of assembly (see
http://www.nhgri.nih.gov/Grant_info/Funding/Statements/).

Sequence Quality.  NHGRI has adopted a quality standard for finished DNA sequence
of 99.99% accuracy, with no gaps either within or between clones.  It is more
difficult to define a comparable quality standard for working draft sequence. 
The shotgun sequence reads that make up the working draft should be of high
enough quality that they will be used in finishing the sequence of the region and
not be discarded, i.e., be "interconvertible" with those that make up finished
sequence. In that way, the working draft sequence called for in this RFA will
contribute directly to high quality finished mouse sequence that meets the
quality standard.  Applicants must address how they will assess the quality of
their sequence reads to ensure that they meet the standard of
intereconvertibility.  If a better quality standard is developed for working
draft sequence, data from groups funded as part of the Mouse Genome Sequencing
Network will have to meet the standard.  At regular intervals, a quality control
center, funded by NHGRI through a separate mechanism, will check the quality of
sequence generated by the Mouse Genome Sequencing Network.  The quality control
center will participate as part of the Steering Committee of the Sequencing
Network.

SPECIAL REQUIREMENTS FOR COOPERATIVE AGREEMENTS

I. Definitions

ARBITRATION PANEL: A panel that is formed to review scientific or programmatic
disagreement (within the scope of the award) that may arise between award
recipients and NHGRI. It will be composed of three members: a designee of the
Steering Committee chosen without the NHGRI staff voting, one NHGRI designee, and
a third designee with expertise in the relevant area who is chosen by the other
two (in the case of an individual disagreement, the first member may be chosen
by the individual awardee). The Arbitration Panel will help resolve both
scientific and programmatic issues that develop during the course of work that
restrict progress.

AWARDEE: The institution to which the cooperative agreement is awarded.

COOPERATIVE AGREEMENT: An assistance mechanism in which there is anticipated
substantial NHGRI programmatic involvement with the recipient organization during
the performance of the planned activity.

MOUSE GENOME SEQUENCING NETWORK: A group of scientists, each funded by a separate
cooperative agreement, working together to complete the DNA sequence of the mouse
genome.  The Mouse Genome Sequencing Network will be made up of extramural, and
possibly NIH intramural, researchers.  In order to participate in the Mouse
Genome Sequencing Network, a P.I., whether funded through a cooperative agreement
or another mechanism, must agree to abide by the decisions of the Steering
Committee and the NHGRI policies that apply to genomic resources and large-scale
sequencing.

NHGRI PROGRAM DIRECTOR(S): A scientist(s) of the NHGRI extramural staff who
provides normal stewardship for the award and who, in addition, has substantial
scientific/programming involvement during conduct of this activity, as defined
in the terms and conditions of award. This involvement includes coordinating
NHGRI's participation in the Mouse Genome Sequencing Network, functioning as a
peer with the Principal Investigators, facilitating the partnership relationship
between NHGRI and the Mouse Genome  Sequencing Network, helping to maintain the
overall scientific balance in the program commensurate with new research and
emerging research opportunities, and ensuring that the Mouse Genome  Sequencing
Network program is consistent with the NHGRI missions and goals and with the
activities of other mouse sequencing groups.

PRINCIPAL INVESTIGATOR (P.I.): The person who assembles the project, is
responsible for submitting the application in response to this RFA, and is
responsible for the performance of the project. The Principal Investigator will
coordinate project activities scientifically and administratively.  The Principal
Investigator may be a researcher from the extramural or NIH intramural research
community.

STEERING COMMITTEE (SC): A committee that is the main governing board of the
Mouse Genome Sequencing Network. Membership includes the NHGRI Program
Director(s), the P.I. of each awarded cooperative agreement and intramural
project (including the projects to characterize the mouse libraries and the new
and existing sequence production centers) and the quality control center, and
three research scientists with relevant expertise, but who are not affiliated
with any of the projects participating in the Mouse Genome Sequencing Network.
Each group and advisor will have one vote.

SCIENTIFIC ADVISORY PANEL (AP): A panel that evaluates the progress of the Mouse
Genome Sequencing Network and provides recommendations to the Director, NHGRI
about continued support of the components of the Mouse Genome  Sequencing
Network. The Advisory Panel will be composed of four to six senior scientists
with relevant expertise and who are not P.I.s of a cooperative agreement involved
in the Mouse Genome Sequencing Network. It will be appointed by the NHGRI
Director.  The AP will meet at least annually and a report will be prepared to
the NIH Institute and Center Directors on the progress of the sequencing network.

II. Terms and Conditions of Award

The following terms and conditions will be incorporated into the award statement
and will be provided to the Principal Investigator, as well as the appropriate
institutional official, at the time of award. Intramural participants in the
Mouse Genome Sequencing Network will be held to similar conditions for their
funding.  The following special terms of award are in addition to, and not in
lieu of, otherwise applicable OMB administrative guidelines, HHS grant
administration regulations at 45 CFR Parts 74 and 92 [Part 92 is applicable when
State and local Governments are eligible to apply], and other HHS, NIH, and NIH
grant administration policies:

1.  The administrative and funding instrument used for this program will be the
Cooperative Agreement (U01) grants and intramural project(s).  The cooperative
agreement is an "assistance" mechanism (rather than an "acquisition" mechanism),
in which substantial NIH scientific and/or programmatic involvement with the
awardee is anticipated during the performance of the activity. Under the
Cooperative Agreement, the NIH purpose is to support and/or stimulate the
recipient's activity by involvement in and otherwise working jointly with the
award recipient in a partner role, but it is not to assume direction, prime
responsibility, or a dominant role in the activity. Consistent with this concept,
the dominant role and prime responsibility for the activity resides with the
awardee(s) for the project as a whole, although specific tasks and activities in
carrying out the study will be shared among the awardee(s) and the NHGRI Program
Director(s).

2.  P.I. Rights and Responsibilities

The P.I. (extramural or NIH intramural) will have the primary responsibility for
defining the details for the project within the guidelines of the RFA and for
performing the scientific activity. The P.I. will agree to accept close
coordination, cooperation, and participation of NHGRI staff in those aspects of
scientific and technical management of the project as described under "NHGRI
Program Staff Responsibilities".

The P.I. of a sequence production center will:

o  Determine experimental approaches, design protocols, set project milestones
and conduct experiments
o  Ensure that the genomic sequence produced meets a quality standard and cost
agreed upon at the time of award
o  Ensure that data are released according to NHGRI policies and that results are
published and submitted to a public database
o  Submit data for quality assessment in any manner specified by the Steering
Committee and the Advisory Committee.
o  Submit periodic progress reports in a standard format, as agreed upon by the
Steering Committee and the Advisory Committee
o  Adhere to the NHGRI policies regarding intellectual property, data release and
other policies that might be established during the course of this activity
o  Accept and implement the common guidelines and procedures approved by the
Steering Committee
o  Accept and participate in the cooperative nature of the group
o  Attend Steering Committee meetings
o  Coordinate and collaborate with other U.S. and international groups sequencing
the mouse genome

The P.I. (extramural or NIH intramural) of a project to characterize mapping
resources will:

o  Determine experimental approaches, design protocols, set project milestones
and conduct experiments
o  Ensure the production of resources that will be used in mapping and sequencing
the mouse genome
o  Ensure that data are released according to NHGRI policies and that results are
published and submitted to a public database
o  Submit periodic progress reports in a standard format, as agreed upon by the
Steering Committee and the Advisory Committee
o  Adhere to the NHGRI policies regarding intellectual property, data release and
other policies as might be established during the course of this activity
o  Accept and participate in the cooperative nature of the group
o  Accept and implement the common guidelines and procedures approved by the
Steering Committee
o  Attend Steering Committee meetings
o  Coordinate and collaborate with other U.S. and international groups generating
resources for sequencing the mouse genome

3. NHGRI Program Staff Responsibilities:

The NHGRI Program Director(s) will have substantial scientific/programmatic
involvement during the conduct of this activity through technical assistance,
advice and coordination such as participating in the design of Mouse Genome
Sequencing Network activities, advising in the selection of sources or resources,
coordinating or participating in collection and/or analysis of data, advising in
management and technical performance, or participating in the preparation of
publications. However, the role of NHGRI will be to facilitate and not to direct
the activities. It is anticipated that decisions in all activities will be
reached by consensus of the Mouse Genome Sequencing Network and that NHGRI staff
will be given the opportunity to offer input to this process. One to three NHGRI
Program Director(s) shall participate as a member of the Steering Committee. 
NHGRI staff will have total of one vote.

The Program Director(s) will:

o  Participate (with the other Steering Committee members) in the group process
of setting research priorities, deciding optimal research approaches and protocol
designs, and contributing to the adjustment of research protocols or approaches
as warranted. The Program Director(s) will assist and facilitate the group
process and not direct it.
o  Serve as liaison, helping to coordinate activities among the awardees; act as
a liaison to the NHGRI and the other Institutes and Centers of the NIH, and as
an information resource about extramural genome research activities. The Program
Director(s) will coordinate the efforts of the Sequencing Network with other U.S.
efforts and the international mouse sequencing community.
o  Attend the Steering Committee meetings as a voting member and assist in
developing operating guidelines, quality control procedures, and consistent
policies for dealing with recurrent situations that require coordinated action.
The Program Director(s) must be informed of all major interactions of members of
the Steering Committee. The NHGRI Program Director(s) will be responsible for
scheduling the time and preparing concise (3 to 4 pages) minutes or a summary of
the Steering Committee meetings, which will be delivered to members of the group
within 30 days after each meeting.  The Program Director(s) will report progress
to the other NIH Institutes and Centers two to three times per year.
o  Lend his/her relevant expertise and overall knowledge of the NHGRI- and NIH-
sponsored research to facilitate the selection of scientists not affiliated with
the awardee institutions who are to serve on the Advisory Committee and the
Steering Committee.
o  Serve as liaison between the Steering Committee and the Advisory Committee,
attending Advisory Committee meetings in a non-voting liaison member role.
o  Serve on subcommittees of the Steering Committee and the Advisory Panel, as
appropriate.
o  Provide advice in the management and technical performance of the
investigation.
o  Provide members of the Steering Committee access to the Quality Control
Center, which will also be a member of the Steering Committee.
o  Serves as scientific liaison between the awardees and other program staff at
NHGRI.
o  Assist in promoting the availability of the mouse genome sequence and related
resources to the scientific community at large.
o  Retain the option to recommend the withholding or reduction of support from
any project (extramural or NIH intramural) within the Mouse Genome Sequencing
Network that substantially fails to achieve its sequencing goals at the quality
and cost agreed to at the time of award, fails to remain state of the art in its
production sequencing capabilities, or fails to comply with the Terms and
Conditions of the award.
o  Participate in data analyses, interpretations, and where warranted, co-
authorship of the publication of results of studies conducted through the Mouse
Genome Sequencing Network.

4. Collaborative Responsibilities

The Steering Committee will serve as the main governing board of the Mouse Genome
Sequencing Network and will overlap substantially with the Human Genome
Sequencing Network Steering Committee. The Steering Committee membership will
include the NHGRI Program Director(s), the P.I. from each awarded cooperative
agreement (including those of the projects to characterize and generate mapping
resources, sequence production centers and the quality control center),
intramural projects and three research scientists with relevant expertise, but
who are not affiliated with any of the cooperative agreements or intramural
project(s). The rest of the Steering Committee will appoint the latter three
members by majority vote. One of these three members will be nominated to serve
as the Chair of the Steering Committee and will be appointed by the Program
Director(s). Additional members may be added by action of the Steering Committee.
Some of the outside scientists serving on the Mouse Genome Sequencing Steering
Committee may also serve on the Human Genome Sequencing Steering Committee. 
Other government staff may attend the Steering Committee meetings, if their
expertise is required for specific discussions. The National Center for
Biotechnology will maintain the central server to coordinate this project and
will attend the Steering Committee meetings. It will not be a member of the
committee or have a vote.

The Steering Committee will be responsible for discussing progress within the
Mouse Genome Sequencing Network, and for advising NHGRI as to how the Mouse
Genome Sequencing Network can complete the working draft mouse DNA sequence
within the stated goals of time and accuracy, and within budget. The Steering
Committee will work with the quality control center to develop uniform procedures
for data quality assessment. Members of the Steering Committee will be required
to accept and implement the common guidelines and procedures approved by the
Steering Committee.

The meetings of the Mouse and Human Genome Sequencing Steering Committees will
partially overlap and NHGRI staff will work with the steering committees to
select some overlapping outside scientists for the respective committees. Within
one month after award of the cooperative agreements and intramural projects, the
NHGRI Program Director(s) and the P.I.s will meet (perhaps by telephone
conference) to select the three outside committee members and to nominate a chair
from among those three.  The Program Director(s) will appoint the Chair and
schedule the first meeting of the Steering Committee once the Chair has been
selected. The Chair of the Steering Committee will be responsible for
coordinating the Committee's activities, preparing meeting agendas, and chairing
meetings. A meeting schedule will be developed at the first meeting.  At least
two meetings will be held each year, either in Bethesda or at one of the sites.
One of the meetings will partially overlap with the annual meeting of the
Advisory Committee.  The purpose of joint meeting will be to allow direct
interaction between members of the Mouse and Human Genome Sequencing Networks and
the Advisory Committee, prior to the latter's annual evaluation of the Mouse
Genome Sequencing Network's progress. Subcommittees will be established by the
Steering Committee, as it deems appropriate.

5. Scientific Advisory Panel

The Scientific Advisory Panel will be responsible for reviewing and evaluating
the progress of the Mouse Genome Sequencing Network toward producing a working
draft sequence of the mouse DNA sequence by 2003. The Advisory Panel will be
composed of four to six senior scientists with relevant expertise and may
partially overlap with the Advisory Panel for the Human Genome Network. The
Director, NHGRI, will select the members and Chair. The membership of the
Advisory Panel may be enlarged permanently, or on an ad hoc basis, as needed.

The Advisory Panel will meet at least once a year. The first part of this meeting
will be a joint meeting with the Steering Committee to allow the Advisory Panel
members to interact directly with the members of the Mouse Genome Sequencing
Network. Annually, the Advisory Panel will make recommendations regarding
progress of the Mouse Genome Sequencing Network and present advice about changes,
if any, which may be necessary in the Mouse Genome Sequencing Network program to
the Director, NHGRI. At the end of the second year of funding, the Advisory Panel
will perform a rigorous evaluation of the progress of the Mouse Genome Sequencing
Network (both extramural and NIH intramural projects) to determine if funds need
to be redistributed among the projects to enable those that have been most
successful to scale up in the third year in anticipation of further scale up
after renewal the following year.

6. Arbitration Process

Any disagreement that may arise on scientific/programmatic matters (within the
scope of the award), between award recipients or NIH intramural projects and the
NHGRI may be brought to arbitration.  An Arbitration Panel, composed of three
members - one Mouse Genome  Sequencing Network Steering Committee designee, one
NHGRI designee (with the NHGRI extramural member not voting), or the individual
U01 awardee or NIH intramural project in the event of an individual disagreement
and a third designee with expertise in the relevant area and chosen by the other
two designees, will be convened.  This special arbitration procedure in no way
affects the awardee's right to appeal an adverse action that is otherwise
appealable in accordance with NIH regulations 42 CFR Part 50, Subpart D and HHS
regulation at 45 CFR Part 16.

7. Yearly Milestones

All Awardees (extramural and NIH intramural) participating in the Mouse Genome
Sequencing Network will be asked to define yearly milestones at the time of the
award and to update these milestones annually at the anniversary date. In accord
with the procedures described above, NHGRI may withhold or reduce funds for
projects that substantially fail to meet their milestones or to maintain the
state of the art.

LETTER OF INTENT

Prospective applicants from both the extramural and the NIH intramural research
communities are asked to submit, by March 1, 1999, a letter of intent that
includes a descriptive title of the overall proposed research, the name, address
and telephone number of the Principal Investigator, the number and title of this
RFA, and a list of the key investigators and their institution(s) and projects.

The letter of intent is to be sent to:

Dr. Jane L. Peterson
Program Director, Large Scale Sequencing
National Human Genome Research Institute
38 Library Drive, Room 614, MSC 6050
Bethesda, MD 20892-6050

PUBLIC BRIEFING ON THE RESEARCH NETWORK FOR LARGE-SCALE SEQUENCING OF THE MOUSE
GENOME

Prospective applicants are invited to attend a briefing on this Sequencing
Network program on February 1, 1999 in the Natcher Building, Conference Room A
from 1-3 pm.  NHGRI staff will explain the purpose of the program, provide
detailed instructions about the application process and answer questions. 
Applicant institutions are urged to send a representative to this briefing.  For
further information about the meeting or accommodations in the area, please
contact the program staff listed in this RFA.

APPLICATION PROCEDURES

The research grant application form PHS 398 (rev. 4/98) is to be used in applying
for these grants. Application kits 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 301/710-0267, Email: GrantsInfo@nih.gov; and
from the program administrator listed under INQUIRIES.  Application kits are also
available on the web at:   http://www.nih.gov/grants/forms.htm

NIH intramural applicants see section "Additional Instructions for NIH Intramural
Project Applicants" below.

The RFA label available in the NIH 398 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 Panel 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:

CENTER FOR SCIENTIFIC REVIEW
NATIONAL INSTITUTES OF HEALTH
6701 ROCKLEDGE DRIVE, SUITE 1040 - MSC 7710
BETHESDA, MD 20892-7710
BETHESDA, MD 20817 (for express/courier service)

At the time of submission, two additional copies of the application must also be
sent to:

Dr. Ken Nakamura
Office of Scientific Review
National Human Genome Research Institute
38 Library Drive, Room 609, MSC 6050
Bethesda, MD  20982-6050
Telephone: (301) 402-0838

Applications must be received by April 29, 1999.  If an application is received
after that date, it will be returned to the applicant without review. The Center
for Scientific Review (CSR) 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 CSR 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.

APPLICATION GUIDANCE FOR PRODUCTION SEQUENCING

Applicants must consider and address the following in preparing applications for
sequence production projects called for in this RFA:

Sequence Production Plan. The applicant must present a plan and propose
milestones for achieving the proposed level of scale up. This plan must
thoroughly discuss the applicant's choice of sequence coverage for the working
draft, why it is the best choice for the funds requested and how it will lead
eventually to finished mouse sequence. The sequencing plan must cover all phases
of working draft sequence production, starting with subcloning of a BAC clone
through assembly and deposition of the sequence data in the unfinished division
of GenBank. It will be important to discuss bottlenecks or other problems that
may be anticipated as the project increases in scale and how they will be
addressed

Sequence Cost. The calculated cost of sequencing (both prior and projected
sequencing costs) must take into account all of the expenses associated with
working draft sequence production, beginning with construction of a subclone
library, through assembly of the working draft sequence to the depth proposed.
The total cost of sequencing must also include any production-related technology
development (see below) that has been or will be supported by the project.
However, the applicant must also provide a breakdown of costs so that the
reviewers can evaluate the contribution of different cost elements, such as
production-related technology development, to the reported total cost.

Sequence Quality: Applicants who have generated at least 2 Mb of finished
sequence must agree to submit their data for quality assessment during both the
pre-award period (in order to allow the peer reviewers to evaluate this important
factor), if it has not been evaluated by a NHGRI Quality Assessment exercise in
the last six months, and during the course of the project period.  The assessment
will be conducted using the methods employed in the previous NHGRI quality
assessment exercises
(http://www.nhgri.nih.gov/Grant_info/Funding/Statements/RFA/quality_standard.html), 
in which all NHGRI grantees funded for large-scale sequencing cooperated
in assessment of each other's data. This evaluation will be conducted after the
application is submitted, but prior to the review meeting. The finished sequence
to be evaluated will be chosen by NHGRI staff from a list of finished clones
submitted by the P.I. in the progress report. During the course of the project
period, the assessment will be done by an NHGRI-funded quality control center.
Each sequence production center must also implement an internal quality control
program that evaluates sequence accuracy and contiguity of the assembled working
draft sequence. If a program is already in use in the applicant's project,
evidence of its usefulness must be presented in the Progress Report.

Production-related technology implementation. One of the goals of the NHGRI
sequencing program is the continual improvement of the efficiency of production
sequencing and decrease in its cost. This will facilitate completion of the mouse
genome sequence in the shortest possible time and at the lowest possible cost.
Applicants must present a plan to address this issue and discuss how their
proposed project will implement new technologies and strategies as they become
available. Any cost incurred in technology implementation must be included in the
total cost of the sequence.

Management Plan. The management of a sequencing center requires a significant
commitment by the P.I. of the project.  A P.I. for a new pilot project is
expected to devote at least 30% effort to the project. A P.I. of an existing
large-scale sequencing center, who is already be devoting more than 30% effort
to the existing center, must commit an additional 10% to the mouse sequencing. 
If the P.I. of an existing project is not already committed to 30% effort on that
project, the commitment on this project should be greater than 10%.  The
applicant must propose a management plan for the project that takes into account
the changes that will occur as the project scales up.

Additional Instructions for NIH Intramural Projects

NIH intramural project applicants must use the NIH 398 application form using the
following instructions.

o  On the Face Page, fill out only items 1., 2., 3.  (leave 3c. blank), 4., 5,
6, 7, and 8.  The remainder of the items should be left blank, and the
application must not be signed by either the PI or an NIH Institute official. 
The RFA label must be affixed to the bottom of the Face Page, as described above
in section 2.
o  Do not submit Checklist", "Personnel Report", or "Personal Data" pages.
o  PI must provide information about current support in his laboratory,
specifically the yearly funding level of the laboratory, a brief description of
the research with an indication of whether there is overlap with the current
application.
o  The P.I. must obtain the approval of his/her NIH Institute Scientific Director
for applying, for collaboration, for participating as a component of the Mouse
Genome Sequencing Network under the terms and conditions of the RFA, and for
complying with the policies of the Steering Committee.  A copy of that letter of
approval must be provided as part of a cover letter, addressed to the NHGRI
Office of Scientific Review.
o The composite budget page and the individual budget pages for each part a
complete budget and budget justification for funds covering the years requested
in the format requested in the Form 398.
o  Submit one unsigned, typewritten original of the application, and twenty
photocopies of the application and six photocopies of the appendices to:

Scientific Review Administrator
Office of Scientific Review
National Human Genome Research Institute
38 Library Drive, Room 609, MSC 6050
Bethesda, MD  20982-6050

Do not send the application or any copies to the Center for Scientific Review.
NIH intramural project applications must be received by April 29, 1999.  If
an application is received after that date, it will be returned to the applicant
without review.

REVIEW CONSIDERATIONS

A. General Considerations

Upon receipt, applications will be reviewed for completeness by CSR and for
responsiveness by the NHGRI. Incomplete applications will be returned to the
applicant without further consideration. If NHGRI staff find that the application
is not responsive to the RFA, it will be returned without further consideration.

Applications that are complete and responsive to the RFA will be evaluated for
scientific and technical merit by an appropriate peer review group convened by
the NHGRI in accordance with the review criteria stated below.  As part of the
initial merit review, a process will be used by the initial review group in which
applications receive a written critique and undergo a process in which only those
applications deemed to have the highest scientific merit, generally the top half
of the applications under review, will be discussed, assigned a priority score,
and receive a second level review by the National Advisory Council for Human
Genome Research.

All applications will be judged on the basis of the scientific and technical
merit of the proposed projects and the documented ability of the investigators
to meet the RESEARCH OBJECTIVES of the RFA.

B. Review Criteria

The application must be directed toward attaining the programmatic goals as
stated under RESEARCH OBJECTIVES. The following criteria will be used by peer
review groups to evaluate these applications:

For projects to characterize mapping resources:

o  Scientific merit of the proposed research plan to provide well characterized
mapping resources that will be useful in sequencing the mouse genome
o  Likelihood that the data and resources generated will contribute significantly
to making the mouse genomic sequencing more efficient and cost effective
o  Cost and efficiency of the plans proposed
o  Prior demonstrated success and quality of the proposed plan for developing and
characterizing mapping resources
o  Track record of the P.I. and other key personnel
o  Past compliance with NHGRI data release policies, and plans for data and
materials release.
o  Plans to coordinate efforts with other U.S. and international large-scale
sequencing groups and mapping efforts
o  Availability of the facilities, resources, expertise and technology necessary
to perform the research, and the level of institutional commitment.
o  Appropriateness of the proposed budget and time-line in relation to the
proposed research.

For sequence production centers:

o  Pilot Sequence Projects (new centers)
o  Likelihood that the sequencing strategy, data management and overall
management plans proposed will support a successful scale up of the center so
that it is likely to make a significant contribution to the completion of the
working draft and complete sequence of the mouse genome.
o  Quality of the plans to integrate any new strategies and technology
developments into the sequencing effort
o  Sequence quality:
a)  Merit of sequence quality assessment plans, including  monitoring and
minimizing sequencing errors, and other QA/QC plans
b)  Results from NHGRI sequence quality assessment exercises
o  Track record of the P.I. and other key personnel
o  Past compliance with NHGRI policies, where appropriate, and plans for data
release
o  Plans to coordinate efforts with other U.S. and international large-scale
sequencing groups and mapping efforts
o  Availability of the facilities, resources, expertise and technology necessary
to perform the research, and the level of institutional commitment
o  Appropriateness of the proposed budget and time-line in relation to the
proposed research.

Existing large-scale sequencing centers:

o  Likelihood that the project  will produce a significant fraction of the mouse
working draft sequence:
o  Prior experience and quality of the proposed plan for:
a) Producing high quality sequence data
b) Increasing sequence throughput
c) Decreasing sequencing costs, including efficiency improvements due to
implementation of new technologies or strategies.
o  Prior experience and quality of the proposed plan for identifying and solving
critical integration problems, including adequacy of the informatics activities.
o  Sequence quality:
a)  Merit of sequence quality assessment plans, including monitoring and
minimizing sequencing errors, and other QA/QC plans
b)  Results from NHGRI sequence quality assessment exercises
o  Track Record of the P.I. and other key personnel
o  Quality of the center's existing management, including workflow, plans for
further scale-up to accommodate mouse genomic sequencing, divisions of
labor/responsibility among components, coordination between components,
appropriate staffing, training, etc.
o  Past compliance with NHGRI data release policies, and plans for data release.
o  Plans to coordinate efforts with other U.S. and international large-scale
sequencing groups and mapping efforts
o  Availability of the facilities, resources, expertise and technology necessary
to perform the research, and the level of institutional commitment.
o  Appropriateness of the proposed budget and time-line in relation to the
proposed research.

AWARD CRITERIA

Awards will be made on the basis of scientific and technical merit as determined
by peer review, including the significance of the projected contribution toward
meeting the NHGRI program goal of contributing to the completion of the mouse
genome working draft DNA sequence by the year 2003, program needs and balance,
data release and intellectual property, and the availability of funds.

INQUIRIES

Written and telephone inquiries concerning this RFA are encouraged. The
opportunity to clarify issues or questions about the RFA from potential
applicants is welcome.

Direct inquiries regarding programmatic issues to:

Dr. Jane L. Peterson (for sequencing)
Dr. Bettie Graham  (for mapping resources)
Division of Extramural Research
National Human Genome Research Institute
38 Library Drive, Room 614, MSC 6050
Bethesda, MD  20892-6050
Telephone:  (301) 496-7531
FAX:  (301) 480-2770
Email:  Jane_Peterson@nih.gov
Email:  Bettie_Graham@nih.gov

Direct inquiries regarding fiscal matters to:

Ms. Jean Cahill
Grants Administration Branch
National Human Genome Research Institute
38 Library Drive, Room 613, MSC 6050
Bethesda, MD  20892-6050
Telephone:  (301) 402-0733
FAX:  (301) 402-1951
Email:  Jean_Cahill@nih.gov

Schedule
Letter of Intent Receipt Date:  March 1, 1999
Application Receipt Date:       April 29, 1999
Scientific Review Date:         June 1999
Advisory Council Date:          September 1999
Anticipated Award Date:         September 1999

AUTHORITY AND REGULATIONS

This program is described in the catalog of Federal Domestic Assistance No.
93.172.  Awards are made under the authority 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 NIH grants policies and Federal Regulations 42
CFR Part 52 and 45 CFR Parts 74 and 92. This program is not subject to the
intergovernmental review requirements of Executive Order 122372 or Health Systems
Agency review.

The NIH strongly encourages all grant and contract 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 NIH mission to
protect and advance the physical and mental health of the American people.

PROGRESS REPORT: list of issues/questions to be addressed in the Progress Report
for new pilot sequencing projects (have completed less than 2 Mb of sequence that
has been placed in a public database)

Instructions:
The following series of questions is from the last several reviews NHGRI has
conducted for large-scale sequencing. They are designed to provide reviewers with
answers to questions that are central to the review of your grant. The questions
also provide a format to assist the reviewers in locating the answer to these
pertinent questions.  Therefore, it is preferable that the answers to the
questions appear immediately after the questions, if they do not, the location
of the answer must be provided in that space.  In order for your application to
be considered by the review committee, these questions MUST be answered.

For the purposes of this RFA, completed data is defined as any sequence data
deposited in a publicly available database.

Section A. Text

Please answer the following questions. The total length for this section should
not exceed 10-15 pages (5000-7500 words).
We encourage brief, concise answers. Please focus these answers on your
experience, rather than future plans, unless specifically asked for.
1.  How does your experience support the promise of your group to successfully
scale? To what level (in lanes/year) do you propose to scale your sequencing
effort in the next grant year?  Discussion must include, but is not limited to:
o  Prior experience in sequencing (including sequence production for types of
sequence other than genomic sequence) and increasing throughput. What is the
amount of sequence (of any type; e.g., cDNA, STSs, ESTs) produced and deposited
in a public database in the last three-year period by your project? Based on an
average of the last three months of sequencing, what is the total current
capacity of your group (include lanes per month, percentage of successful lanes,
number of base pairs per lane at of least phred 20--or equivalent--quality)?
Please include capacity from sequencing DNA of other organisms and capacity due
to funding from all sources. If your rate of sequencing increased over the last
year, please describe how.  Have the rates of different parts of the sequencing
process changed, and how have these changes contributed to your overall progress?

o  Prior experience in attaining milestones. What example(s) can you provide that
demonstrate that you have proposed milestones for a research project and then met
them on schedule?  Examples need not be in sequence production, but, if possible,
include resource production of some type.  What internal metrics have you used
to evaluate progress in the past and what internal metrics (for example,
reads/month, failed lanes, base pairs per lane in GenBank, etc.) do you believe
will be the most useful to you in managing your project's sequencing performance?

o  If appropriate, prior demonstrated experience in decreasing costs.  If you
have no experience in resource production and cost reduction, describe your plans
to control and/or decrease costs during the pilot project period.  On what
evidence do you base your cost estimates?  Total costs include all equipment and
indirect costs, as well as direct costs. How do you plan to monitor costs
internally?  Note below you will be asked to report costs in a specific format. 
It may be useful to incorporate that format into your planning.
o  If appropriate, prior experience in solving the critical integration problems
that arise as a program increases in scale. If you have no experience in resource
production, describe your plans to achieve process integration in your sequencing
project.  Particular attention should be given to how the informatics activities
facilitate data management, within the components as well as post-sequencing.
Examples would be useful.

2. Describe your plans for incorporating new strategies and technologies into
your sequencing project, and how this will affect productivity. Are there unique
technologies and strategies that you plan to test? Do you have any experience in
testing technology in sequencing or other fields?  If so, discuss the advantages
they have provided. Please describe collaborative efforts that may have
contributed to your success.

3. Discuss how your group plans to check the quality of the sequence it produces.
(Note: if you are participating in the quality assessment exercise you will be
given an opportunity to address its results.  If your data has been checked by
a quality assessment exercise in the past six months, the results from that
exercise will be provided to the reviewers by NHGRI.)

4. Have you had a management plan in the past, and if so, how do you expect it
to change to meet the needs of this project?  If not, what management plan do you
envision for the three year period of this project? Discuss, for example:
workflow strategy, division of responsibility between various components,
production/materials quality, training, hiring, turnover, or other management
issues.

5. State your data release policy.

6. This is an extra space for you to provide any additional comments that may be
useful.

Section B. Graphical and Tabular Material

Please provide the following material.

1. If you are currently producing DNA sequence of any type, please provide a
graph showing sequence output per month for at least the last 12 months. Please
distinguish between different types of sequence, e.g.,  finished or unfinished
genomic, EST stequence, STS sequence, etc.  (This should be a noncumulative
monthly total.)

2. If you are currently producing DNA sequence of any type, please provide a
graph indicating the numbers of lanes run per week for the past year and the
number of failed lanes for the same time period.

3. If you are currently producing any type of DNA sequence, please provide a
table of :

a. database entries, giving, where appropriate, laboratory name, accession
number, total size, unique size, number of gaps, number of ambiguities, estimated
number of errors (if available for unedited clones), and number of edits (for
finished clones). Please provide detailed legends

b. clones in progress, giving, where appropriate, laboratory name, GenBank
accession number, size, number of gaps, and status (e.g., libraries constructed)

4. It is important for the reviewers of your application to evaluate your budget
request in terms of how much of the funds are needed for each activity. The
format given below will provide them with information to understand the cost of
your shotgun sequencing and give you an opportunity to explain how you plan to
decrease it. Therefore, please provide budget information in the format given
below for the previous year (if you currently have a funded sequencing effort)
and for all (up to three) years of your request.

The categories are defined as:

FTEs are the number (not costs) of full time equivalents (100% effort) in
personnel needed for each activity.
Labor costs are those costs, including benefits, attributed to personnel involved
in shotgun  sequencing activities, but excluding personnel in
management/administration, informatics and process development.
Supplies costs are those attributed to the supplies needed for the shotgun
sequencing activities, excluding management/administration, informatics and
process development.
Management/Administration costs are costs of personnel (including benefits) and
other expenses related to managing and administering the shotgun sequencing
component of the project (for example, supplies needed for administration would
be included here).
Informatics costs are the costs of personnel (including benefits), supplies and
equipment used in all aspects of data management.  Informatics activities are
those involving higher level activities such as research and development,
annotation, etc.
Information Management includes routine computerized information management
activities such as routine data tracking, systems administration, etc.
Process Development costs are those that are incurred in the short term in
improving the process or the technology being used for shotgun sequencing. These
costs include personnel (including benefits), supplies, etc.
Allocated costs are those that contribute to more than one of the production
activities. They are not to be distributed among the production activities in the
table, but considered separately.  Non-computer equipment is to be depreciated
over five years. The 'large' and 'small' categories reflect the institutionally-
defined threshold for size of equipment purchases to be subject to indirect
costs.  For currently funded efforts, equipment purchased for the last two grant
years (1997-1998) should be included in the depreciation figures.
Computer equipment is to be depreciated at three years or less; the depreciation
time should be indicated.
Indirect costs are those costs paid to the grantee institution as part of the
indirect cost agreement.
The total should be the total cost of each activity.

Cost Table

PRODUCTION
ACTIVITY                  #FTE'S     DIRECT   INDIRECT     TOTAL     %

Subclone Construction
--labor
--supplies

Template Preparation
--labor
--supplies

Sequencing Reaction
--labor
--supplies

Gel Electrophoresis
--labor
--supplies

ALLOCATED COSTS
Other
--labor
--supplies
--travel
--service contracts
--off-site training

Management and Admin.
--labor
--supplies

Informatics
--labor
--supplies

Information Management
--labor
--supplies

Process Development
--labor
--supplies

Equipment (non-computer)
--small
--large

Equipment (computer)

10. This is an extra space to provide any other graphical material you feel would
be helpful.

PROGRESS REPORT:  list of issues/questions to be addressed in the Progress Report
for existing sequencing groups (have already completed at least 2 Mb sequence
that has been placed in a public database)

Instructions:

The following series of questions is based on experience from the last several
reviews NHGRI has conducted for large-scale sequencing. The questions are
designed to provide reviewers with information that is central to the review of
your grant.  Because the questions are organized in a format that will assist the
reviewers in locating the answers, it is preferable that your answers appear
immediately after the questions; if they do not, the location of the answer must
be provided in that space.  In order for your application to be considered by the
review committee, these questions MUST be answered.

For the purposes of this RFA, completed data is defined as any sequence data
deposited in a publicly available database.  Thus, "completed" data includes
genomic sequence finished to Bermuda standards, unfinished, ESTs, STSs, etc.

Section A. Text

Please answer the following questions. The total length for this section should
not exceed 10-15 pages (5000-7500 words).  We encourage brief, concise answers.
Please focus these answers on your progress, rather than future plans, unless
specifically asked for.

1. To what level (in lanes/yr) do you propose to scale your shotgun capacity to
accommodate mouse genome sequencing in the first grant year? How does your past
effort support the ability of your group to successfully scale to this level?
Discussion must include, but is not limited to:
o  Prior experience in sequencing (including sequence production for other types
of sequence, in addition to genomic sequence) and in increasing throughput.  What
is the amount of sequence (of any type; e.g., cDNA, STSs, ESTs, etc.) produced
and deposited in a public database in the last three-year period by your project? 
Based on an average of the last three months of shotgun production, what is the
total current capacity (in lanes) of your center (include lanes per month,
percentage of successful lanes, number of basepairs per lane at of least phred
20--or equivalent--quality)?  Please include capacity from sequencing DNA of
other organisms and capacity due to funding from all sources.  How has your rate
of shotgun production increased over the last year?  How have the rates of
different parts of the process changed, and how have these changes contributed
to your overall progress?
o  Prior demonstrated success in attaining milestones.  What internal metrics
(for example, lanes/month, failed lanes, basepairs per lane in GenBank, etc.) do
you consider to be the most useful to you in managing your center's performance?
o  Prior demonstrated success in decreasing costs; costs should be given as cost
per lane. Total costs include all equipment and indirect costs, as well as direct
costs. How does your center monitor costs internally? Note that you must also
give your costs broken down into the categories given in the table below (Section
B, question 9), for the past year and projected for the future years of the
application.
o  Prior demonstrated success in solving the critical integration issues that
arise as a program increases in scale. Particular attention should be given to
how informatics activities facilitate data management, within the components as
well as post-sequencing.

2.  Describe your success in incorporating new strategies and technologies into
your sequencing process, and how this has affected productivity.  Are there
unique technologies and strategies that have been tested by your center?  If so,
discuss the advantages they have provided. Please describe collaborative efforts
with other centers that may have contributed to your success.

3. Discuss how your center checks the quality of the sequence it produces. For
this section, please make reference to graphical materials in section B below as
needed. (Note: if you are participating in the quality assessment exercise you
will be given an opportunity to address its results.  If your data has been
checked by a quality assessment exercise in the past six months, please include
the results from that exercise in this answer.  Note that the NHGRI staff will
provide reviewers with the report and your responses written at the time the
exercise was completed.)

4. How and why has your management plan evolved as your sequencing effort has
scaled up? Discuss, for example: workflow strategy, division of responsibility
between various components, production/materials quality control (distinct from
what was in part 3 above), training, hiring, turnover, or other management
issues.

5. State your data release policy.

6. This is an extra space for you to provide any additional comments that may be
useful.

Section B. Graphical and Tabular Material

Please provide the following material.

1. Please provide a graph indicating the numbers of lanes run per week for the
past year and the number of failed lanes for the same time period.

2. Please provide a histogram showing the cycle time (in months) of clones that
have been taken to the working draft stage, and one for those remaining in the
pipeline, indicating how long they have been in the pipeline. Cycle time is
defined as starting when a large insert clone is subcloned in preparation for the
sequencing pipeline, and ending when the assembled clone sequence is deposited
in a public database.

3. Please provide a graph showing shotgun sequence output per month for at least
the last 12 months.  (This should be a noncumulative monthly total.)

4. Please provide a table of completed large-insert clones (both clones that have
been finished to "Bermuda' standards and those that have been taken to a working
draft standard) over 30 kb, giving laboratory name, GenBank accession number,
total size, unique size, number of gaps, number of ambiguities (N's,Y's or R's;
these may be noted separately in the table cell), estimated number of errors (if
available for unedited clones), and number of edits (for finished clones).  If
this list includes more than 50 clones, the list may be submitted electronically
on a disc or by e-mail.

5. Please provide a table of unfinished clones in progress, giving laboratory
name, GenBank accession number, size, number of gaps, and status (e.g., libraries
constructed). If this list includes more than 50 clones, the list may be
submitted electronically on a disc or by e-mail.

6. It is important for the reviewers of your application to evaluate your budget
request in terms of how much of the funds are needed for each activity. The
format given below will provide them with information to understand the cost of
your strategy and give you an opportunity to explain how you plan to decrease the
costs of sequencing. Therefore, please provide budget information in the format
given below for the previous year (if you currently have a funded sequencing
effort) and for all (up to five) years of your request. (Note that for year
before those requested in the current proposal, the row labeled 'sequencing--
working draft' should have 0 for each entry.)

The categories are defined as:

Subclone library construction: Begins at the point at which a large-insert clone
is selected for sequencing, i.e. from the point at which the isolate containing
the large-insert clone is taken from a glycerol stock or a colony on a plate. 
Ends at the point at which agar plates with the subclone library (as colonies or
plaques) are available and ready to pick.
Template Preparation: Begins with the plated sub-clone libraries.  Ends with
samples ready to pipette into the sequencing reactions.
Sequencing Reaction: Begins with "dipping the pipette into" the template DNA. 
Ends at the point at which the sample is ready to be loaded onto the sequencing
gel (but does not include any pre-loading treatments, e.g. heating, addition of
loading dye).
Gel Electrophoresis: Begins with the pre-loading processing.  Ends with the
collection of the data.
FTEs are the number (not costs) of full time equivalents (100% effort) in
personnel needed for each activity.
Labor costs are those costs, including benefits, attributed to personnel involved
in shotgun  sequencing activities, but excluding personnel in
management/administration, informatics and process development.
Supplies costs are those attributed to the supplies needed for the shotgun
sequencing activities, excluding management/administration, informatics and
process development.
Management/Administration costs are costs of personnel (including benefits) and
other expenses related to managing and administering the shotgun sequencing
component of the project (for example, supplies needed for administration would
be included here).
Informatics costs are the costs of personnel (including benefits), supplies and
equipment used in all aspects of data management.  Informatics activities are
those involving higher level activities such as research and development,
annotation, etc.
Information Management includes routine computerized information management
activities such as routine data tracking, systems administration, etc.
Process Development costs are those that are incurred in the short term in
improving the process or the technology being used for shotgun sequencing. These
costs include personnel (including benefits), supplies, etc.
Allocated costs are those that contribute to more than one of the production
activities. They are not to be distributed among the production activities in the
table, but considered separately.  Non-computer equipment is to be depreciated
over five years. The 'large' and 'small' categories reflect the institutionally-
defined threshold for size of equipment purchases to be subject to indirect
costs.  For currently funded efforts, equipment purchased for the last two grant
years (1997-1998) should be included in the depreciation figures.
Computer equipment is to be depreciated at three years or less; the depreciation
time should be indicated.
Indirect costs are those costs paid to the grantee institution as part of the
indirect cost agreement.
The total should be the total cost of each activity.

Cost Table

PRODUCTION
ACTIVITY                  #FTE'S     DIRECT     INDIRECT   TOTAL  %

Subclone Construction
--labor
--supplies

Template Preparation
--labor
--supplies

Sequencing Reaction
--labor
--supplies

Gel Electrophoresis
--labor
--supplies

ALLOCATED COSTS
Other
--labor
--supplies
--travel
--service contracts
--off-site training

Management and Admin.
--labor
--supplies

Informatics
--labor
--supplies

Information Management
--labor
--supplies

Process Development
--labor
--supplies

Equipment (non-computer)
--small
--large

Equipment (computer)

10.  This is an extra space to provide any other graphical material you feel
would be helpful.

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