PRIORITY SETTING FOR MOUSE GENOMICS AND GENETICS RESOURCES
Summary by
William Dove and David Cox, Co-Chairs
(Revised 6/11/98(1) )



BACKGROUND


The NIH Director, Harold Varmus, convened a distinguished group of national and international scientists for the purpose of defining and establishing priorities for the production of mouse genomics and genetics resources. Approximately 60 scientists met for three days in Bethesda, MD in March 1998 to discuss two major areas: structural genomics (mapping and sequencing resources) and functional genomics (specifically mutagenesis). The goal was to enable and facilitate research by the entire community of investigators who use the laboratory mouse as a tool for understanding mammalian biology. The recommendations for funding includes four components: (1) structural analysis of the mouse genome; (2) functional analysis of mouse biology; (3) resources; and (4) training. The recommendations are in the form of estimated direct costs for the first year and length of effort in years. Below is a summary of these recommendations.

 

I. STRUCTURAL ANALYSIS OF THE MOUSE GENOME:

TOTAL DIRECT COST FOR FIRST YEAR: $22.2 M (19.2 M new)


IA. PHYSICAL MAPPING RESOURCES

Three types of physical maps were identified that would be crucial for scientists interested in cloning genes. High resolution maps, those with thousands of mapped "sequence tagged sites" (STS) markers, were considered the most useful for the rapid isolation of genes. Approximately 100,000 markers will be needed. The combined U.S. and European effort have generated approximately 40,000 markers, therefore an approximately 60,000 additional markers will be needed. These new markers should be a combination of random and gene-based markers and can be generated from ESTs, BAC end sequences, YACs, and plasmids. The cost of generating the additional markers has been included in the cost of generating the BAC and RH maps.

i. Bacterial Artificial Chromosome (BAC) Libraries/Map.

Two BAC libraries of 10X coverage should be constructed using different restriction enzymes; the strains chosen should be those that have been designed as reference strains. Five to ten additional libraries of lower coverage should also be constructed from a variety of commonly used mouse strains.

A fingerprinted BAC map of 10X depth anchored with 20,000 markers of which half are gene/EST-based and the other half polymorphic and random markers should be generated.
DIRECT COST FOR FIRST YEAR: $3.0 M---DURATION: 3 YEARS

ii. High Resolution Radiation Hybrid (RH) Map

Radiation Hybrid Panel. A radiation hybrid panel of approximately 100 hybrid cell lines should be developed using a background other than hamster in order to minimize cross-hybridization.

The radiation hybrid map generated should have a minimum resolution of approximately 100 kilobases. DIRECT COST FOR FIRST YEAR: $5.0 M---DURATION: 3 YEARS

iii. Yeast Artificial Chromosome (YAC) Resource. A low resolution YAC map of the mouse genome currently exists. This resource can be use to develop additional markers for RH and BAC mapping and to fill gaps in BAC maps and genomic sequences.
DIRECT COST FOR FIRST YEAR: $0.2 M---DURATION: 5 YEARS

 

IB. GENETIC MAPPING RESOURCES

There are three resources that would further define genetic variation in the mouse so as to facilitate the study of complex or quantitative traits: (a) genotyping additional mouse strains; (b) low resolution (5cM0 single nucleotide polymorphism (SNP) map; and (c) consomic mouse strains.

i. Genotyping Additional Mouse Strains. A genetic map using simple sequence length polymporphisms (SSLP) as markers exists and is the basis for the current reference mouse genetic map. There are many existing inbred mouse strains that could provide a rich resource for the analysis of complex traits, but many are underutilized because they are not well characterized genetically. The value of these strains in understanding diseases would be increased tremendously if approximately 6,000 SSLP markers were typed on 50 additional strains.
DIRECT COST FOR FIRST YEAR: $1.0 M---DURATION: 1 YEAR

ii. Low Resolution (5 cM) Single Nucleotide Polymorphism (SNP) Map. A relatively new resource, SNPs, is becoming available to researchers interested in common diseases of humans. Whereas such a map has been shown to be of great value to researchers studying human diseases, its value in mouse biology has not been demonstrated. A low resolution mouse map with 1,500 to 2,000 SNP markers would be adequate to determine whether this would be a useful resource for mouse research. Before a SNP map can be generated, there are two resources or technologies which must be in place: discovery and detection of SNPs. Improving the technology to identify and score SNPs and at the same time developing a low resolution SNP map should be given a high priority.
DIRECT COST FOR FIRST YEAR: $1.0 M---DURATION: 2 YEARS

iii. Matched sets of mouse strains each carrying a different pair of chromosomes with defined patterns of variation from another mouse strain (Consomic Strains). One set of consomic strains is currently being developed. These strains have the potential to advance quantitative trait loci mapping and to readily map genes responsible for the many physiological, biochemical, immunological, neurological, developmental, and behavioral differences which have already been documented between two strains.
DIRECT COST FOR FIRST YEAR: $1.0M--DURATION: 2 YEARS

 

IC. POSITIONAL CLONING RESOURCES

There are several reasons to support the sequencing of mouse cDNAs at this time, particularly in light of the realization that the mouse genome will probably not be sequenced within the next five years. Sequencing of full-length cDNAs would enhance research about structure/function, facilitate gene mapping, and identify a significant number of the genes in the genome. Presently, the technology for generating full-length cDNA libraries does not exist. However, a large number of mouse cDNA libraries (less than full-length) are available. In addition, unlike the human cDNA libraries, mouse cDNA libraries can be generated for the various developmental stages of the mouse embryo. The use of these libraries for generating ESTs (gene tags) for mapping is a valuable resource for researchers interested in mouse and human biology.

i. 3'-end Sequencing of ESTs for Mapping. Over 100,000 mouse ESTs have been sequenced, but most of the information is from the 5'end. The value of ESTs is knowing their mapped positions on the genome; this requires information from the 3'end. Thus, sequencing of the 3'ends of mouse ESTS should be a high priority.
DIRECT COST FOR FIRST YEAR: $1.5M--DURATION: 3 YEARS

ii. Mapping of ESTs/cDNAs. The clones in the cDNA libraries gain enormous value if placed on a map. ESTs can be used as markers on BAC and radiation hybrid maps and are strong candidates for each gene that gains functional prominence due to an ENU-induced point mutation.

There is a small effort to develop a gene map of the mouse by mapping a limited number of ESTs onto radiation hybrids. Whereas this will be a useful initial resource, to be maximally useful to scientists interested in gene discovery, additional ESTs will need to be mapped.
DIRECT COST FOR FIRST YEAR: $1.0M--DURATION: 3 YEARS

iii. Specialized Libraries for Identifying Missing Genes. The generation of any new cDNA libraries should focus on obtaining most, if not all, transcripts. Investment in new technologies for normalization and/or obtaining low abundant transcripts should be encouraged.
DIRECT COST FOR FIRST YEAR: $0.5M--DURATION: 3 YEARS

iv. Full-Length cDNA Libraries. The technology for generating full-length cDNA clones is in the developmental stages and continues to represent a challenge to the scientific community. Research projects to significantly improve existing or generate new technology for isolating full-length cDNAs should be supported.
DIRECT COST FOR FIRST YEAR: $2.0M--DURATION: 3 YEARS


ID. SEQUENCING

In order to get a complete understanding of mouse biology, a comprehensive study of the genome is required. Although sequencing priority should be given to the human genome at least initially, it is important that mouse genomic sequence be given relatively high priority. Given the many uses and users of mouse genomic sequence, it was decided that there should be increased capacity to generate mouse genomic sequences at a high-throughput, highly accurate, and efficient manner. It was recommended that the support for increasing the sequencing capacity for the mouse begin soon. In the first year of that process, 12 Mb should be sequenced, ramping up to 400 Mb within 5 years, and that a reference mouse genomic sequence be completed by 2008.
DIRECT COST FOR FIRST YEAR: $6.0 M; DURATION: 10 YEARS


II. FUNCTIONAL ANALYSIS OF MOUSE BIOLOGY: TOTAL DIRECT COST FOR THE FIRST YEAR: $17.1 M

IIA. GENOME-WIDE MUTAGENESIS AND PHENOTYPING

As the Human Genome Project progresses and the sequence of more human and mouse genes is determined, the function of a large number of these genes will not be predictable by sequence and expression alone. Phenotype-driven mutagenesis screens provide an important approach to understanding the function of genes. In the mouse, ENU produces mutation rates sufficient to perform genome-wide mutagenesis screens. These mutagenesis screens are highly efficient and effective in isolating mutants systematically and comprehensively for available phenotypes. What is missing, however, are standardized protocols for mutagenesis and improved tools and a variety of assays for characterizing phenotypes. Therefore, the following is recommended:

i. Standardization of Mutagenesis Protocols. For the various mutagenesis screens currently in use, there is significant variation in the mutation rates, strains used, dosages, and breeding protocols employed. Ideally, to understand theses variations, an assessment at the molecular level would be appropriate. However, because of the expense involved, it was recommended that screening protocols for ENU be standardized for different strains of mice (used for different phenotypes), that the procedures for ENU mutagenesis be disseminated widely, and that training in ENU mutagenesis procedures be established.
TOTAL DIRECT COST FOR FIRST YEAR: $0.5M DURATION: 1 YEARS


ii. Centers for ENU Mutagenesis and Phenotyping. One way to ensure the systematic and comprehensive analyses of phenotypes is to establish ENU Mutagenesis and Phenotyping Centers. Such Centers might include a mutagenesis core, phenotypic screening core (and technology development to improve the procedure), mapping core; database core for dissemination of information, sperm cryopreservation and DNA bank of G1 mice, and mutant/sperm distribution core. These Centers might handle a steady-state annual population of 20,000 progeny of ENU-mutagenized mice, of which 2,000 would be first-generation progeny permitting the detection of strong dominant alleles. The Centers would also provide access for investigators outside the focal emphases of the Center to screen for mutant lines.
DIRECT COST FOR FIRST YEAR: $9.0M DURATION: 3 YEARS

 

IIB. DEVELOPMENT OF PHENOTYPING PROTOCOLS


i.Technology Development. Complete characterization of the phenotype of mutagenized mice is a major challenge in all mutagenesis studies. There is an urgent need for improved technologies for mouse physiology, pathology, antibody markers, reporter mice, expression arrays, behavior analysis, etc. These technologies should be developed within ENU Centers and by individual investigators.
DIRECT COST FOR FIRST YEAR: $6.0M DURATION: 5 YEARS

 

ii. Technology Transfer. Researchers working with the rat have developed phenotypic screens for rats that could be adapted for the mouse. Efforts should be made to transfer that technology to the mouse system taking into consideration the smaller size of the mouse.
DIRECT COST FOR FIRST YEAR: $1.0M DURATION: 5 YEARS

 

IIC. TARGETED MUTAGENESIS

Targeted mutagenesis is a well-established technology and widely used in the community. Standard approaches for generating null mutations are now being complemented by generation of allelic series of mutations and tissue-specific and induced mutations. Issues of standardization and resource availability, enhancement of emerging technologies and new tools for in depth phenotypic analysis to fully exploit the mutations being generated is needed. Improvements were suggested in the following two areas.

i. ES lines from different mouse strains need to be validated for specialized uses. A better understanding of the biology of ES cells could assist in such derivation.
DIRECT COST FOR FIRST YEAR: $0.1M DURATION: 5 YEARS

ii. There is a need to study mutations on different strain backgrounds, requiring backcrossing from mouse strain 129 to other strains. Molecular genotyping in conjunction with the construction of congenic strains (speed congenics) will assist this approach. The development of such a resource will be more to deliver a useful resource to the community.
DIRECT COST FOR FIRST YEAR: $0.5M DURATION: 3 YEARS


III. RESOURCES: TOTAL DIRECT COST FOR FIRST YEAR: $7.8 M

There are a variety of resources and needs that if addressed on a global scale would facilitate research and result in significant savings. Several such resources and needs were addressed and include the following:

 

IIIA. CRYOPRESERVATION

There are many more mouse mutants that exist than can be maintained as live stock because of the cost and the demand or lack thereof. Cryopreservation of sperm and ovary would facilitate future studies of these mutants and reduce the costs of maintaining live animals. There are two areas that need support.

i. Technology development projects to investigate the conditions that would make cryopreservation and recovery of sperm and ovary following cryopreservation very effective and efficient should be supported. An assessment of pathogen transfer should also be included in these studies.
DIRECT COST FOR FIRST YEAR: $2.0 M; DURATION: 2 YEARS

ii. Develop a storage facility for frozen gametes. The facility should have a visitor?s laboratory to allow access to cryopreservation technology and a recovery resource for scientists who do not have access to the technology.
DIRECT COST FOR FIRST YEAR: $1.5 M; DURATION: 5 YEARS

 

IIIB. REPOSITORY OF LIVE MOUSE STRAINS

The maintenance of live mouse strains is very expensive, especially for small laboratories. A repository that would maintain the most commonly used strains would facilitate research. A repository that would be capable of accommodating 250 new strains per year would be a valuable resource. Because of the varying and varied needs of the community, it would be essential to have a sub-committee of scientists to evaluate which strains to maintain as live stock and which strains to preserve as frozen germ plasma based on community needs. DIRECT COST FOR FIRST YEAR: $3.0 M; DURATION: 5 YEARS

 

IIIC. TRANSFER OF TARGETED ALLELES ONTO STANDARD BACKGROUND

Gene targeting experiments have been conducted on a variety of cell lines, thus limiting the uses of these resources by many scientists. It is recommended that the existing set of targeted alleles be transferred onto a chosen standard background, 129/Sv. The 129/SvEvTac may be the appropriate substrain, but this must be confirmed by the community of users. A complementary background strain (C57BL/6) should be employed in parallel, enabling the production of a uniform F1 hybrid background for each targeted allele, on which phenotyping is particularly robust.
DIRECT COST FOR FIRST YEAR: $0.5 M; DURATION: 2 YEARS

 

IIID. DATABASE RESOURCES

The significant amount of information that will be generated by the availability of genomic and genetic resources to facilitate research will result in a lot of data being generated. A variety of databases exists for collecting data. The usefulness of this data by others will depend upon the ease by which the generators of large data sets can submit their data to public databases and the ability of databases to communicate with each other. There are two areas needing attention:

i. Criteria to ensure that (a) large data sets can be easily deposited in a centralized public repository and (b) the centralized public repository captures information from or develop interfaces to a variety of databases and presents it to users in a manageable form.
DIRECT COST FOR FIRST YEAR: $0.3 M; DURATION: 1 YEARS

ii. Expand the animal models database to include disease states and phenotypes.
DIRECT COST FOR FIRST YEAR: $0.5 M; DURATION: 4 YEARS

IV. TRAINING: TOTAL DIRECT COST FOR FIRST YEAR: $2.2 M

i. Cryopreservation has the potential to save many dollars. The technology is still developing, but additional individuals need to be trained in this new technology. It is recommended that three training sessions be held each year to accommodate the need.
DIRECT COST FOR FIRST YEAR: $0.2 M; DURATION: 3 YEARS

ii. There are very few animal pathologists who are involved in mouse research. A training program to support veterinary fellows in a two year fellowship in mouse pathology should be implemented.
DIRECT COST FOR FIRST YEAR: $2.0 M; DURATION: 5 YEARS

 

V. OTHER ISSUES

During the course of the meeting, several issues were brought up that were not fully discussed. Below is a list of these topics that need further exploration and discussion.

1. Oversight Sub-Committees. The format for several types of oversight sub-committees was suggested that would: (a) identify reference mouse strains for genomic and cell line reagents; (b) determine which mouse genomic DNA regions should be sequenced first; and (c) discuss the best ways to establish and coordinate centralized databases

2. Mouse Husbandry Costs. The issue of costs in maintaining mice was discussed. Some participants thought that the high cost of maintaining these animals was due to federal regulations. Participants were encouraged to send their comments to the Director, NIH, who is looking into this matter.

 


FISCAL OVERVIEW
(Revised 6/22/98)2

I. STRUCTURAL ANALYSIS OF THE MOUSE GENOME
A. Physical Mapping Resources
  • BAC Libraries/Map
  • RH Map
  • YAC Resource


B. Genetic Mapping Resources

  • Genotyping Additional Mouse Strains
  • SNP Map at 5 cM Resolution
  • Additional Matched Sets of Consomic Strains


C. Positional Cloning Resources

  • 3'-end Sequencing of all ESTs for Mapping
  • Mapping ESTs/cDNAs
  • Specialized Libraries for Identifying Missing Genes
  • Full-length cDNA Libraries


D. Sequencing

II. FUNCTIONAL ANALYSIS OF MOUSE BIOLOGY
A. Genome-Wide Mutagenesis and Phenotyping

  • Standardization of Mutagenesis Protocols
  • Centers for ENU Mutagenesis and Phenotyping


B. Development of Phenotyping Protocols

  • Technology Development for Complete Characterization of Phenotypes of Mutagenized Mice
  • Technology Transfer of Phenotypic Screens from Rat to Mouse


C. Targeted Mutagenesis

  • Validate ES Lines from Different Strains for Specialized Uses
  • Study Mutations on Different Strain Backgrounds

III. RESOURCES
A. Cryopreservation

  • Technology Development to Make Cryopreservation More Effective and Efficient
  • Storage Facility for Frozen Gametes

B. Repository for 250 New Strains Per Year, with Continued Breeding
C. Transfer of Existing Set of Targeted Alleles onto Standard Background
D. Database Resources
  • Establish Criteria to Ensure Ease of Use
  • Expand Animal Models Database to Include Phenotypes and Disease States

IV. TRAINING

  • Courses in Cryopreservation ( 3 sessions per year)
  • Two-Year Fellowships in Mouse Pathobiology

TOTAL FOR MOUSE RESOURCES (FOR YEAR 01):

Genome structure
Functional analysis
Resources
Training

TOTAL

$22.2M
 

$3.0 M
$5.0 M
$0.2 M
 

 

$1.0 M
$1.0 M
$1.0 M
 

 

$1.5 M
$1.0 M
$0.5 M
$2.0 M
 

  $6.0 M

$17.1 M
 

  $0.5 M
$9.0 M
 

 

 
$6.0 M
$1.0 M
 

 

  $0.1 M
$0.5 M
 

  $7.8 M  

$2.0 M
$1.5 M


  $3.0 M
$0.5 M


  $0.3 M
$0.5 M

  $2.2 M

$0.2 M
$2.0 M

 

  $22.2 M
$17.1 M
$ 7.8 M
$ 2.2 M

$49.3 M

($19.2M NEW)
 

3 yrs
3 yrs
5 yrs
 

 

1 yr
2 yrs
2 yrs
 

 

3 yrs
3 yrs
3 yrs
3 yrs
 

  10 yrs
 

 

1 yr
3 yrs
 

 

 
5 yrs
5 yrs
 

 

  5 yrs
3 yrs
 

 

  2 yrs
5 yrs  


5 yrs
2 yrs
 

1 yr
4 yrs
 


3 yrs
5 yrs

3

BREAKOUT GROUP A: Physical Mapping

 

BAC Map

· Generate fingerprinted BAC map of 10X depth, anchored with 20,000 markers (approximately 80% coverage). Half the markers should be gene/EST-based, half should be a combination of polymorphic and random markers. Besides its immediate use for positional cloning, this resource could make a starting point for a future sequence-ready map. The resource should be developed using the 129 SVEV Tac strain.

· Generate additional BAC libraries to facilitate construction of map. Two libraries (using different restriction enzymes) of 10X coverage, in vectors that provide for ease of quality control, maximum adaptability for future purposes and multiple application. Five to ten additional libraries of 3X coverage constructed from different widely used mouse strains (males).

· Software development for fingerprint analysis, and for making the resource accessible to the community, especially smaller labs.


Cost estimate: $9 M Duration: 3 years


Radiation Hybrid (RH) Panel/Map

· Develop a new RH panel of 100 kb resolution using a background other than hamster to minimize cross-hybridization. This may require some lead time to construct, so should be a high priority.

· Generate ~60,000 new STS markers (from a mix of BAC end sequences, YACs, and plasmids) to add to the ~45,000 unigene markers now being developed. These markers can also be used for the fingerprinted BAC map.

· Place all ~100,000 markers on the new RH panel.

Cost estimate: $15 M Duration: 3 years


YAC Resource

· Make existing YAC resources more accessible for screening, for example by providing well-defined pools.

Cost estimate: $1 M Duration: 5 years


BREAKOUT GROUP B: cDNAs/ESTs

(Revised)

1. Sequencing Additional 3' ESTs to Facilitate Mapping and Gene Identification

A. New Library Generation

    ¨ Use Normalization/Subtraction

    ¨ Cost: $0.5 Million Duration: 2 Years

A. EST Sequencing

    ¨ 200,000 3' EST Sequences

    ¨ For Unique Clones - 5' EST Sequences

    ¨ Cost: $1.5 Million Duration: 3 Years

1. Full-Length cDNA Sequencing - Major Priority

A. Technology Development and Generation of Representative Full-Length cDNA Libraries

    ¨ Cost: $5 Million Duration: 3 Years

A. cDNA Sequencing

    ¨ 3% of Genome (estimated coding sequences)

    ¨ 90 Mb

    ¨ Cost: $45 Million @ $0.50/bp Duration: 3-5 Years

1. Prioritization of Strains/Tissues for Library Generation and Quality Control

    ¨ Community Steering Committee


Breakout Group C: Genetic Mapping

The breakout group concluded that the highest priority for the future of genetic mapping in the mouse was a SNP map. This would greatly simplify genotyping for several different purposes, e.g. positional cloning, identifying QTLs, analysis of LOH. It was also considered to be of very high priority for the SNPs to be in the public domain as quickly as possible, so that the academic community could have access to them. The group distinguished two aspects of the SNP question, SNP discovery and SNP deployment (scoring).

A specific recommendation was made with respect to SNP discovery. Initially, a relatively small number of SNPs, on the order of 1500-2000, should be generated. This would make it likely that in any particular pair of strains used in a cross, at least 300 - 400 SNPs would be informative, allowing a genome scan at about 5 cM resolution. In the first instance, SNPs should be chosen to give a uniform distribution across the genome, and to be useful for about 10 different diverse strains. It was estimated that a project of this magnitude would cost about $1-2M and it was recommended that two such projects be supported, in order to provide healthy competition for the SNP developers. It was thought that this could be done in two years, at which time the value of the SNP approach could be determined and, if warranted, a more dense collection could be developed. . It was considered important for the initial set of SNPs to be integrated with existing maps, but to leave the mechanism for doing to be determined by competition

With respect to deployment, it was felt that the development of the initial set of SNPs did not imply any specific technology for further use. Rather, the group recommended the support, chosen through a competition, of a variety of new approaches to scoring, that would lead to widespread use by a large number of small laboratories, as well as by the major users. It was also noted that technologies for scoring SNPs would also be applicable to the detection of induced point mutations.

As for the choice of strains, the group thought that it would be most appropriate for recommendations about specific strains to be left to a small committee of experts, that would include representatives from the NIH, from the Jackson Lab, and from Europe. It was felt that a list developed by this group should then be circulated to the wider community for a period comment and validation. Several factors were suggested for consideration in selecting the strains: genetic diversity, usefulness in studying a variety of phenotypes, usefulness in mutagenesis and knockout screens.

A second priority for genetic mapping resource was the development of additional sets of consomic strains. Currently, one such set is being developed, a set of A/J chromosomes onto a B6 background. The group thought that the recombinant consomic technology had the potential for major advances in QTL mapping, and that its usefulness would extend well beyond the traditional mouse genetics community in the sense that it would allow physiologists, developmental biologists, neurobiologists, etc. to rapidly and simply map genes that determine or modify phenotypes of interest. In this case, the recommendation was that initially NIH support the development of about 3-5 sets of particularly useful strains. Although the ultimate choice of strains should be made in a competition, it was felt a matched set of 129 and B6 consomic strains would be extremely useful. It was estimated that each set would cost about $500,000.

A third recommendation was to characterize more inbred strains by typing them with a large number of SSLP markers. It was thought that existing inbred strains provide a rich resource for the analysis of complex traits, but many are underutilized because they are not well genetically characterized. It was estimated that a one-time project typing about 6000 markers on 50 strains would cost about $1M and take about a year, and had the potential for opening up many more strains for the study of mutations, QTLs and modifiers.

Finally, a radiation hybrid panel that would allow markers to be ordered at higher resolution than the existing RH panel would be of value. Again, generating this resource would be a one-time effort, and was estimated to cost about $500,000.


BREAKOUT GROUP D: Genomic Sequencing

(Revised)

 

How will the mouse sequence be used?

This must be understood to address the questions below. Several different areas were identified:

1. positional cloning -- 1-2 BACs for 25-50 projects a year

2. region specific mutagenesis - 3-5 Mb

3. comparative sequences to define other elements, breakpoints etc.

4. reverse genetics -- small targeted regions

5. reference tool to interpret human sequence

For small projects directed at getting specific genes, the group concluded that means should be devised to enable small groups to obtain the needed sequence. This might, for example, involve skimming, followed by more accurate sequence for the gene of interest. This scale of sequencing should be brought within reach of most labs. The other projects however require more systematic sequencing on a larger scale and would provide a long term resource to the community. Comparative analysis of mouse and human sequence was the most compelling use in the eyes of the group.

What quality for the sequence?

This questions pits coverage versus completeness. There was considerable discussion of alternatives, including options such as 2x shotgun of BACs across the genome, or leaving a limited number of gaps to reduce costs. However, there was greater enthusiasm for a commitment to significant amounts of mouse sequence in the next few years and to get the whole mouse genome done in a reasonable time (vide infra). The group concluded that the temporary advantages of quicker, broader coverage were outweighed by the added costs incurred in achieving the ultimate goal of the complete reference mouse sequence. Accordingly, there was broad agreement that the mouse sequence standards should be the same as for human.

What is priority of completing the mouse relative to the human?

The greatest value would result from parallel efforts on human and mouse. However, practical limits of resources and capacity and the commitment to complete the human genome by 2005 will necessitate that priority be given to human sequencing. Nonetheless, the greatly added value that the mouse sequence will give to the human make it imperative that mouse sequencing not lag far behind human. It is important to begin a significant effort on mouse sequencing now, and expand that as rapidly as resources, capacity and the commitment to sequence the human allow. For example the group felt that it was more important to do more mouse sequence than finish the human early.

What priorities should be followed in the choice of mouse genomic regions to be sequenced?

If individual labs are enabled to do sufficient sequencing to support positional cloning efforts, they will establish their own priorities. For larger systematic efforts, it would make most sense to focus on regions of the mouse genome syntenic to those already sequenced in human. Larger regions of particular biological interest should also be considered. Selection of specific regions that match these broad guidelines is best left to individual labs in dialog with larger scale sequencing groups. A tool similar to the Human Genome Sequencing Index maintained by the NCBI should be constructed for the mouse genome and the syntenic regions of the human and mouse map should be linked. Such a tool will be useful to mouse researchers in determining what groups are mapping and sequencing the human genome in regions syntenic to their regions of interest and it will help to track and coordinate the mapping and sequencing of the mouse.

Is strain a consideration for generating a reference mapsequence?

Overall, the group felt there was little scientific reason for favoring one strain over the other. The one mandate was that the sequence be derived from a single well characterized strain, and not be a mosaic of different strains. The one practical consideration is that the BAC clones from 129 are already heavily used. Whatever strain is chosen, the selection should be made known, and the clones and other resources must be readily available.

What should be the priorities for resource generation in the sequencing area?

Highest priority should be given to the development of a sequence ready map. The estimated cost of building a BAC overlap clone map was estimated to be approximately $7M. Initial fingerprinting, contig building and chromosomal positioning could be done over three years. Efforts at closure would extend over two more years.

The next priority is to begin systematic sequencing of the mouse genome. Every effort should be made to increase available sequencing capacity to allow the amount of mouse sequence completed annually to grow from the 10-12 Mb in the next year to 400 Mb in 2005. The goal should be to obtain 1 Gb of mouse genomic sequence in this period. The remainder of the mouse genome should then be completed in the next three years. Thus by 2008 a complete reference mouse sequence should be available.

Finally means should be found to facilitate the sequencing of small regions (100-200 kb) by R01 funded labs. Equipment seems less of a problem than access to methods and informatics support to handle the relatively large data sets. Perhaps a resource similar to that in the UK could be established.


Breakout Group E: Targeted Mutagenesis

Targeted mutagenesis is a well-established technology and widespread in the community. Its value for analyzing gene function is undisputed. Standard approaches for generating null mutations are now being complemented by generation of allelic series of mutations and tissue-specific and induced mutations, which further enhance the utility of this approach. The group focussed on issues of standardization and resource availability across the community, enhancement of emerging technologies and the importance of new tools for in depth phenotypic analysis to fully exploit the mutations being generated.

A. Standardization of resources for gene targeting.

There was a strong consensus for use of a standard genetic background for gene targeting. Current use suggests that 129SvEvtac is the line of choice, for stability of lines and ease of maintaining inbred lines. Validated lines exist on this background.

- Support a mechanism for affordable, reliable distribution of validated 129SvEvtac (Hprt-)ES lines to the community.

Cost: $100k/yr, ongoing

It was also recognized that there is a need for validated ES lines from different strains for specialized uses. A better understanding of the biology of ES cells could assist in such derivation.

- Support establishment of validated ES cell lines from other strains and stable female cell lines.

Cost: $500k/yr for 3 years

There is a need to study mutations on different strain backgrounds, requiring backcrossing from 129 to other strains. Speed congenics assist in this approach, but are not easy for the average lab.

- Develop set of SSLPs for easy generation of speed congenics onto standard backgrounds (some may be available already)

Cost: $100k/yr for 2 years.

Issues of targeting technology were considered. The rate-limiting step in targeting is making the vector. The availability of BAC libraries in the 129SvEvtac strain is very important in this regard. One study suggests that it may be possible to use the BACs directly to make targeting vectors, which would then have very long regions of homology to enhance targeting efficiency.

- Test the feasibility of direct generation of targeting constructs in BACS and the possibility of targeting by zygote-injection.

- Cost: $300k/yr for 3yrs.

Possible strategies for generating genome- wide directed mutations were considered, such as sequence-tagged gene trap libraries or libraries of ENU-mutagenized sperm. The group did not support a new public-domain genome-wide gene trap effort and felt that the market place would determine the usefulness of Lexicon's current library. Any large-scale ENU screening center should be encouraged to archive sperm and DNA for possible sequence-based screening.

B. Conditional targeting strategies

The power of tissue-specific and inducible mutagenesis for dissection of the full roles of a gene is enormous. There was a strong feeling that the Cre-Lox system was working and that the main impediments to further use are the availability of fully characterized lines expressing Cre in a defined spatial and temporal manner. It was felt that many of the problems of mosaic Cre expression could be overcome by insertion of Cre into the genome so that it is controlled by endogenous regulatory elements. In addition, good ubiquitous lox-stop-lox reporter lines to validate Cre expression are needed. For inducible targeting, the nuclear receptor- Cre fusions show considerable promise and are being worked on extensively.

- Support effort to make versatile ubiquitous excision reporter lines and lines of mice expressing Cre in defined spatial and temporal patterns by knock-ins or enhancer trap approaches

Cost: $2M/Yr for 4 years

There is a clear case for a centralized facility to distribute the Cre lines and to create a database of the Cre lines. This should be costed under the resource facility for mutant distribution. There is still an outstanding patent issue with Dupont, which could inhibit distribution of this resource. The group considered the site-specific recombinase technology to be so important that, if this issue is not resolved soon, there must be an immediate switch to an alternate enzyme system to avoid wasting effort.

C. Phenotyping

This is a major challenge in all mutagenesis efforts. There is an urgent need for improved technologies for mouse physiology, pathology, antibody markers, reporter mice, expression arrays, behavior analysis, etc. It was felt that individual Institutes will need to invest in this to obtain the full value of the mutant resource for understanding mouse biology as it impacts on human disease.

- That the NIH convene a meeting this year to discuss enabling technologies for mouse phenotyping in different organ and tissue systems

D. Additional issues

1. Need for continued support for facilities to store and distribute mouse mutants.

2. Importance of cryopreservation for mutant stocks.

3. Need for mutation database, fully annotated with phenotypic information.

4. Need to address animal husbandry and whether current costly procedures are necessary for mouse welfare.



Breakout Group F: ENU Mutagenesis

Rationale: Phenotype-driven mutagenesis screens provide an important approach to understand the function of genes. As the genome project progresses and the sequence of more human and mouse genes are determined, the function of a large number of genes will not be predictable by sequence and expression alone. To understand the function of genes, mutations have provided a powerful approach to understand to this problem. In the mouse, the supermutagen, ENU, produces forward mutation rates (~1/650 per locus per gamete) sufficient to perform genome-wide mutagenesis screens at significant coverage so that, on average, mutations can be obtained in almost any gene. Phenotype-driven ENU mutagenesis screens provide a complimentary approach to gene targeting methods because both gain-of-function and loss-of-functions alleles can be obtained and importantly no pre-existing knowledge of the target genes is required. This forward genetic approach has been widely used and proven in model genetic organisms, however, in the mouse large-scale screens need to be performed in order to determine whether ENU mutagenesis can be applied broadly to understand gene function in the mouse. There was clear consensus from experience within the Breakout group and others that ENU screens are highly efficient and effective in isolating mutants for particular phenotypes. In order to apply this approach in a more systematic manner, the group recommends that a number of new initiatives should be launched (which are described below).

Ongoing large-scale ENU mutagenesis screens

Currently there are two large-scale ENU screens that have been initiated in Europe. Rudi Balling at the GSF is conducting an integrated screen of 40-50,000 mice for a number of dysmorphic and blood-assayable biochemical phenotypes. Steve Brown at Harwell is conducting a similar size screen of neurobehavioral phenotypes. In the first 6-12 months of the screens, significant numbers of mutants have already been obtained (about 150 mutants from 14,000 mice in a one generation dominant screen at GSF, and about 60 mutants out of 3000 mice screened at Harwell). Thus, the feasibility of large-scale "Center-based" integrated ENU screens appear feasible, efficient and productive.


Questions to the Breakout Group.

1. How can the efficiency of mutagenesis be monitered and improved?

In discussing the various screens, the group concluded that there is a significant variation in the mutations rates observed, strains used and breeding protocols employed. Experience at Oak Ridge (Monica Justice) and Madison, WI (Bill Dove and Alexandra Shedlovsky) suggests that strict quantitation of ENU doses is essential for achieving high mutagenesis rates (rates of 1/200 per locus per gamete). There is a need for protocol validation with different strains of mice (used for different phenotypes) and a need for dissemination and training of ENU mutagenesis procedures to make this approach more widely useful to the scientific community.

The group felt that adequate methods for assessing mutagenesis rates at the molecular level are not cost effective at this time. It would required scanning Megabase pair regions thoughout the genome to sample ENU-induced mutations adequately (the estimated molecular rate for ENU would be about 1 per 100,000 bp).

2. How can the cloning of point mutations fe facilitated?

The group strongly endorsed the recommendation of the structural genomics groups that a complete physical map of the mouse genome in BACs be made and that a high priority should be placed on full length cDNA cloning and sequencing (to high quality sequence standards).

3. What approaches are needed to improve the ability to identify recessive loss-of-function alleles?

The group endorsed ENU screens using targeted deletions in regions of the mouse genome that will have high priority for sequencing because of synteny with human, gene rich regions or regions of particular interest. In addition, large-scale recessive screens would be encouraged using the Centers of Excellence recommended below.

4. How can screening for phenotypes and validation of mutations be improved?

See recommendations below.

5. What the the priorities for chemical mutagenesis and what is the cost vs. the benefit?

Recommendations

I. The NIH should support systematic ENU screens in mice. Both Centers and individual investigators should be supported. A significant investment is required to test the feasibility of ENU screens as an approach to study the function of genes and pathways for broadly based phenotypes.

A. Establish Centers of Excellence for ENU screening that have a biological focus (with self-selected groups of investigators and consortia). These Centers would have:

¨ Mutagenesis core

¨ Phenotypic screening core (and technology development)

¨ Database core for dissemination of information

¨ Mapping core

¨ Sperm cryopreservation and DNA bank of G1 mice

¨ Mutant/sperm distribution provision

Establish at least 3 Centers of Excellence at $1-2M per year for 5 years.

A. Initiate an RFA to support individual investigators for other ENU screens that are not optimal for the Center format.

¨ Specialized phenotypes

¨ These R01's would have access to core facilities at Centers.

II. Initiate RFA to establish baseline characterization of a set of standard (consensus) phenotypes (behavior, neurological, motor, endocrine, biochemical, etc.) on a set of inbred strains of mice. This would provide a foundation of information for physiological parameters for strains of mice. The phenotypic characterization would be coordinated with the Centers and information would be disseminated by the database core facilities. In addition, the RFA should include development of technology for phenotypic screens in mice. For example, to transfer assays currently using the rat to the mouse. $1-3M per year for 5 years.

A systematic validation of ENU protocols on a standard set of mouse strains should be performed. ENU protocols and information should be disseminated.

$0.5M for 1 year.


BREAKOUT GROUP G:
Chromosomal Strategies, Insertions and Transgenes

1. What is needed to further the development of insertional mutagenesis?

An ideal insertional mutation system in the mouse should provide sequence-tagged Insertion of the germline on a genome wide scale. Such a system would facilitate functional genomics by providing a mutation at every locus, whose phenotype could be evaluated in the whole animal. Although efforts have been made to generate a P-element type transposon based in vivo insertional mutagen for the mouse, no such system is presently available. It is therefore recommended that high priority be assigned to obtaining an ES cell based resource that would provide a sequence-tag for each locus in the mouse genome. Such a resource would make it possible to scan the sequence-tag database for any gene of interest and to order the corresponding targeted ES cell line. This resource would permit the larger community of investigators to utilize genomic resources efficiently, and would be much more cost effective than the current effort to generate targeted knock-outs in individual laboratories, at an estimated cost of approximately $50,000 per knockout. Of course, this resource would only provide one null allele per locus, and would not obviate the need for ongoing targeted mutation of loci that are studied in depth. It would, however, be of enormous value to a large community of researchers. Making such a system available is of highest priority, and would be worth an investment of 10 M per year for several years. (Nearly this much is probably going into generating a few hundred knockout mice per year in small labs.)


2. What are the prospects for developing a collection of segmental deletions across the mouse genome?

Two ES cell based resources capable of generating deletions at marked sites throughout the genome are currently under development. The Merck Genome Initiative is supporting work in John Schimenti's lab to generate 500 ES cell lines with randomly inserted selectable TK inserts. The positions of the inserts will be determined by plasmid rescue of flanking DNA that can be mapped on a backcross panel. These ES cell lines will be described on a database and made freely available on request. Deletions from fixed insertion sites are also being generated by Alan Bradley at Baylor. Experience with these resources during the coming years will indicate whether additional resources will be needed in the future.

3. What is the value of analyzing polymorphic modifiers and QTLs, and how can their study be advanced?

Analysis of loci contributing to complex traits in the mouse was seen as an important future activity with broad biological applications. Many of the physical mapping resources discussed here will be important for QTL analysis. These include the generation of BAC libraries and maps, the development of SNPs, the generation of consomic lines of mice, the targeted ES cell library, and the development of expression arrays. All of these initiatives were strongly supported for their applications to QTL analysis.

4. What improvements in phenotyping are needed to facilitate functional genomics in the mouse?

A great deal of basic biological characterization of standard strains of mice will be required as background for assessment of phenotypic alterations in mutant mice. There is a serious shortage of expertise and manpower for sophisticated evaluation of mutant phenotypes. The following initiatives are proposed to address this problem:

a) A training program to support veterinary fellows in a 2 year fellowship in mouse pathology. With stipends in the range of $60,000 per year, it is recommended that 0.5 M per year be invested for the next 5 years.

b) Development of a Mouse Biology Database to provide access to phenotypic information. Data would be entered from the large published literature, and from current large scale programs. The goal would be a database that is organized on the model of the Mouse Genome Database; it was felt that a large effort would be required to initiate this new database, and initial funding at a level of 4 M per year was recommended.

c) Standardized phenotyping methods will be developed at large scale mutagenesis screening centers. It is recommended that supplemental funds be provided to such centers to enable external investigators to access these facilities for analysis of their mutant mice. An supplement of 5 to 10% of a center budget was recommended for this purpose.

d) Development and Distribution of validated arrays for studying gene expression. Gene expression arrays will provide an important new source of phenotypic information for characterizing new mutants. Significant support should be provided towards making these reagents available to the mouse genetics community.


BREAKOUT GROUP H: Mouse Resources

Cryopreservation

Move toward the broad scale use of cryopreservation for storage and dissemination of strains: Technology development. Investigate the pathogen transmission through sperm as well as the recovery of mice from frozen sperm following artificial insemination (AI), in vitro fertilization (IVF), and intracytoplasmic sperm injection (ICSI). Investigate the effects of strain variation and the effects of mutation(s) [ENU, transgenes, KOs] on recovery. Also, investigate the feasibility of ovary freezing for cryopreservation.

Cost estimate: $1M/lab Two years Two projects

Move to the broad scale use of cryopreservation for storage and dissemination of strains: Outreach. Enable cryopreservation technology to be widely disseminated to the general scientific community. Develop a hands on training course for cryopreservation technology. Also, develop a video/manual describing the details.

Cost estimate: $200K/year 3 training sessions/year/10 students per session

Resource: cryopreserved strains

Develop a storage facility for frozen gametes. Genotype (most/each) strains via gamete analysis. Do extensive quality control on a subset of strains. Develop a cryopreservation laboratory for use by scientists who do not have access to cryopreservation technology. Finally, develop a recovery resource(s) for scientists who do no have access to the technology.

Cost estimate: $1.5M/year 5 years

Resource: Live Strains

Develop a repository(ies) that can accommodate 250 new strains per year. Establish a committee of scientists to evaluate strains for importation. Costs for operating the facility should be paid for from the sale of mice.

Cost estimate: $3M/year 5 years

 

Database: Disease Models and Phenotypes

Develop a low pass mouse disease models and phenotypes database. Facilitate the expansion of an animal models database that includes not only cancer (already underway) but other disease states and phenotypes. Efforts to make databases interfaceable are imperative (i.e. disease models, molecules, sequences). The initial phase (phase I) should merely provide a "roadmap" or index to other databases containing information about spontaneous models, induced models, etc.

Cost estimate: $300K/year 3 years

Commercial Technology Interactions

For important enabling technologies NIH should explore the feasibility (early on) of establishing a mechanism acceptable to all parties for disseminating the technology(ies) to the general scientific community.


PRIORITY SETTING MEETING FOR MOUSE GENOMICS AND GENETICS RESOURCES

Natcher Building
National Institutes of Health
Bethesda, Md


March 19-21, 1998

INVITED PARTICIPANTS


CO-CHAIRS

David COX, M.D., Ph.D., Co Chair
Departments of Genetics and Pediatrics
Stanford University School of Medicine
300 Pasteur Drive, M-336
Stanford, CA 94305
TEL: (650) 725-8042
FAX: (650) 725-8058
E-MAIL: cox@shgc.stanford.edu
William DOVE, Ph.D., Co-Chair
McArdle Laboratory for Cancer Research
Madison Medical School
University of Wisconsin
1400 University Avenue
Madison, WI 53706-1599
TEL: (608) 262-4977
FAX: (608) 262-2824
E-MAIL: dove@oncology.wisc.edu

Mark ADAMS, Ph.D.
Department of Eukaryotic Genomics
The Institute for Genomic Research
9712 Medical Center Drive
Rockville, MD 20850
TEL: (301) 838-3507
FAX: (301) 838-0208
E-MAIL: mdadams@tigr.org

Kathryn ANDERSON, Ph.D.
Department of Molecular Biology
Sloan-Kettering Memorial Institute
1275 York Avenue
New York, NY 10021
TEL: (212) 639-6485
FAX: (212) 717-3623
E-MAIL: k-anderson@ski.mskcc.org

Philip AVNER, Ph.D.
Unite de Genetique Moleculaire Murine
Institut Pasteur
25 Rue du Docteur Roux
Paris Cedex 75015, France
TEL: 003-3-014-568-8625
FAX: 003-3-014-568-8656
E-MAIL: pavner@pasteur.fr

Rudi BALLING, Ph.D.
Institute of Mammalian Genetics
GSF Research Center for
Environment and Health
Ingolst.Landstr.1
85758 Neuherberg
Germany
TEL: 49-089-3187-4110
FAX: 49-089-3187-3099
E-MAIL: balling@gsf.de

Allan BALMAIN, Ph.D.
Onyx Pharmaceuticals
3031 Research Drive
Richmond, CA 94806
TEL: (510) 262-8780
FAX: (510) 758-3405
E-MAIL: allan@onyx-pharm.com

Gregory S. BARSH, M.D., Ph.D.
Departments of Pediatrics and Genetics
Beckman Center, Room B271
279 Campus Drive
Stanford University School of Medicine
Stanford, CA 94305-5323
TEL: (650) 723-5061
FAX: (650) 723-1399
E-MAIL: gbarsh@cmgm.stanford.edu


Mark S. BOGUSKI, M.D., Ph.D.
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health
Building 38A, Room 5S-514
8600 Rockville Pike
Bethesda, MD 20894
TEL: (301) 435-6015
FAX: (301) 480-9241
E-MAIL: boguski@castalia.nlm.nih.gov

Allan BRADLEY, Ph.D.
Plenary Session Speaker
Department of Molecular and Human Genetics
Baylor College of Medicine
Room T926
One Baylor Plaza
Houston, TX 77030
TEL: (713) 798-6671
FAX: (713) 798-8142
E-MAIL: abradley@bcm.tmc.edu

Stephen D.M. BROWN, Ph.D.
MRC Mammalian Genetics Unit and
MRC Mouse Genome Centre
Medical Research Council
Harwell
Oxon, OX11 ORD
United Kingdom
TEL: 44-0123-582-4541
FAX: 44-0123-582-4542
E-MAIL: s.brown@har.mrc.ac.uk

Maja BUCAN, Ph.D.
Department of Psychiatry
and Department of Genetics
University of Pennsylvania School of Medicine
Clinical Research Building, Room 115
415 Curie Boulevard
Philadelphia, PA 19104-6141
TEL: (215) 898-0020
FAX: (215) 573-2041
E-MAIL: bucan@pobox.upenn.edu


Neal COPELAND, Ph.D.
Chairperson, Session H: Mouse Resources
National Cancer Institute
Frederick Cancer Research
Building 539, PO Box B
Frederick, MD 21701
TEL: (301) 846-1260
FAX: (301) 663-1273
E-MAIL: nc20a@nih.gov


Pieter J. DE JONG, Ph.D.
Human Genetics Department
Roswell Park Cancer Institute
Elm and Carltons Streets
Buffalo, NY 14263
TEL: (716) 845-3168
FAX: (716) 845-8449
E-MAIL: pieter@dejong.med.buffalo.edu


Paul DENNY, Ph.D.
MRC Mammalian Genetics Unit and
MRC Mouse Genome Centre
Harwell
Oxon OX11ORD
United Kingdom
TEL: 44-0-123-582-4535
FAX: 44-0-123-582-4540
E-MAIL: paul@har.mrc.ac.uk

Geoff DUYK, M.D., Ph.D.
Exelixis Pharmaceuticals, Inc.
260 Littlefield Avenue
South San Francisco, CA 94080
TEL: (650) 825-2218
FAX: (650) 825-2290
E-MAIL: duyk@exelixis.com


Janan EPPIG
, Ph.D.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
TEL: (207) 288-6422
FAX: (207) 288-6053
E-MAIL: jte@jax.org


Wayne FRANKEL
, Ph.D.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
TEL: (207) 288-6354
FAX: (207) 288-6079
E-MAIL: wnf@jax.org


Richard GIBBS
, Ph.D.
Plenary Session Speaker
Department of Molecular and Human Genetics
Baylor College Of Medicine
One Baylor Plaza, BCMS-930
Houston, TX 77030
TEL: (713) 798-6539
FAX: (713) 798-5741
E-MAIL: agibbs@bcm.tmc.edu

Chris GOODNOW, BVSc., Ph.D.
Medical Genome Centre
Australian Cancer Research Foundation Genetics Laboratory
John Curtin School of Medical Research
The Australian National University
Mills Road, PO Box 334
Canberra, ACT
AUSTRALIA 2601
TEL: (612) 6249-3621
FAX: (612) 6279-8512
E-MAIL: chris.goodnow@anu.edu.au


Eric GREEN,
M.D., Ph.D.
Genome Technology Branch
National Human Genome Research Institute
National Institutes of Health
49 Convent Drive
Building 49, Room 2A08
Bethesda, MD 20892
TEL: (301) 402-0201
FAX: (301) 402-4725
E-MAIL: egreen@nhgri.nih.gov


Douglas HANAHAN,
Ph.D.
Department of Biochemistry and Biophysics
Room HSW-1090, Box 0534
513 Parnassus Avenue
University of California, San Francisco
San Francisco, CA 94143-0534
TEL: (415) 476-9209
FAX: (415) 731-3612
E-MAIL: doug_hanahan@biochem.ucsf.edu


Mary E. HATTEN
, Ph.D.
Laboratory of Developmental Neurobiology
Rockefeller University
1230 York Avenue
New York, NY 10021
TEL: (212) 327-7660
FAX: (212) 327-7140
E-MAIL: hatten@rockvax.rockefeller.edu


Karl HERRUP
, Ph.D.
Alzheimer Research Laboratory
Case Western Reserve Medical School
10900 Euclid Avenue
Cleveland, OH 44106
TEL: (216) 368-6100
FAX: (216) 368-3079
E-MAIL: kxh26@po.cwru.edu


Leroy HOOD
, M.D., Ph.D.
Department of Molecular Biotechnology
Room K357, Box 357730
University of Washington
Seattle, WA 98195-7730
TEL: (206) 616-5014
FAX: (206) 685-7301
E-MAIL: tawny@u.washington.edu


Brigid HOGAN
, Ph.D.
Chairperson, Session C: Genetic Mapping
Department of Cell Biology
Vanderbilt University Medical Center
Medical Center North, Room U-2219
1161 21st Avenue South
Nashville, TN 37232-2175
TEL: (615) 343-6418
FAX: (615) 343-2033
E-MAIL: brigid.hogan@mcmail.vanderbilt.edu


Tyler JACKS
, Ph.D.
Center for Cancer Research
Howard Hughes Medical Institute
Massachusetts Institute of Technology
77 Massachusetts Avenue, E17-517
Cambridge, MA 02139
TEL: (617) 253-0262
FAX: (617) 253-9863
E-MAIL: tjacks@mit.edu


Howard JACOB
, Ph.D.
Department of Physiology
Laboratory of Genetics Research
Medical College of Wisconsin
PO Box 26509
8701 Watertown Plank Road
Milwaukee, WI 53226-0509
TEL: (414) 456-4885
FAX: (414) 456-6516
E-MAIL: jacob@post.its.mcw.edu


Nancy JENKINS
, Ph.D.
Mammalian Genetics Laboratory
ABL-Basic Research Program
Building 539, PO Box B
Frederick, MD 21701
TEL: (301) 846-1260
FAX: (301) 663-1273
E-MAIL: nj8g@nih.gov


Alexandra JOYNER
, Ph.D.
Developmental Genetics Program
Skirball Institute
New York University Medical Center
540 First Avenue
New York, NY 10016
TEL: (212) 263-7290
FAX: (212) 263-7760
E-MAIL: joyner@saturn.med.nyu.edu


Monica JUSTICE
, Ph.D.
Life Sciences Division
Oak Ridge National Laboratory
Y-12 Bear Creek Road, Building 9211
Oak Ridge, TN 37831-8080
TEL: (615) 574-0700
FAX: (615) 574-1274
E-MAIL: justicem@bioax1.bio.ornl.gov


David Mark KINGSLEY
, Ph.D.
Co-Chair, Session F: ENU Mutagenesis
Department of Developmental Biology
Howard Hughes Medical Institute
Stanford University School of Medicine
279 Campus Drive, Beckman Center B300
Palo Alto, CA 94305-5329
TEL: (650) 725-5954
FAX: (650) 725-7739
E-MAIL: kingsley@cmgm.stanford.edu


Raju KUCHERLAPATI
, Ph.D.
Chairperson, Session A: Physical Mapping

Department of Molecular Genetics
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
TEL: (718) 430-2069
FAX: (718) 430-8776
E-MAIL: kucherla@aecom.yu.edu


Eric LANDER,
Ph.D.
Plenary Speaker
Center for Genome Research
Whitehead Institute
Massachusetts Institute of Technology
One Kendall Square, Building 300
Cambridge, MA 02139-1561
TEL: (617) 252-1906
FAX: (617) 252-1933
E-MAIL: lander@genome.wi.mit.edu


Marco MARRA
, Ph.D.
Genome Sequencing Center
Washington University School of Medicine
4444 Forest Park Avenue, Box 8501
St. Louis, MO 63108
TEL: (314) 286-1455
FAX: (314) 286-1810
E-MAIL: mmarra@watson.wustl.edu


John MCPHERSON,
Ph.D.
Department of Genetics
Genome Sequencing Center
Washington University School of Medicine
4444 Forest Park Avenue, Box 8501
St. Louis, MO 63108
TEL: (314) 286-1848
FAX: (314) 286-1810
E-MAIL: jmcphers@watson.wustl.edu


Miriam MEISLER,
Ph.D.
Chair, Session G: Chromosomal Strategies, Insertions and Transgenes
Department of Human Genetics
University of Michigan
4708 Medical Science Building
Ann Harbor, MI 48109-0618
TEL: (313) 763-5546
FAX: (313) 763-9691
E-MAIL: meislerm@umich.edu


Larry MOBRAATEN
, Ph.D.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
TEL: (207) 288-6373
FAX: (207) 288-6149
E-MAIL: lem@jax.org


Joe NADEAU,
Ph.D.
Department of Genetics
Case Western Reserve University
10900 Euclid Avenue, BRB 630
Cleveland, OH 44106-4955
TEL: (216) 368-0581
FAX: (216) 368-3432
E-MAIL: jhn4@po.cwru.edu


Jeffrey L. NOEBELS
, M.D., Ph.D.
Department of Neurology
Baylor College of Medicine
One Baylor Plaza
Houston, TX 77030
TEL: (713) 798-5860
FAX: (713) 798-7528
E-MAIL: jnoebels@bcm.tmc.edu


Kenneth PAIGEN,
Ph.D.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
TEL: (207) 288-6041
FAX: (207) 288-6044
E-MAIL: ken@jax.org


Peter RIGBY
, Ph.D.
Division of Eukaryotic and Molecular Genetics
National Institute for Medical Research
The Ridgeway, Mill Hill
London NW7 1AA
United Kingdom
TEL: 44-181-913-8533
FAX: 44-181-913-8527
E-MAIL: p-rigby@ns1.nimr.mrc.ac.uk


Janet ROSSANT
, Ph.D.
Plenary Session Speaker
Chair, Session E: Targeted Mutagenesis

Department of Molecular and Medical Genetics
University of Toronto
Samuel Lunenfeld Research Institute
Mount Sinai Hospital, Toronto
600 University Avenue
Toronto, Ontario M5G 1X5
CANADA
TEL: (416) 586-8267
FAX: (416) 586-8588
E-MAIL: rossant@mshri.on.ca


Eddy RUBIN
, M.D., Ph.D.
Genome Sciences
Lawrence Berkeley National Laboratory
University of California, Berkeley
MSC 74
Berkeley, CA 94720
TEL: (510) 486-7072
FAX: (510) 486-6746
E-MAIL: emrubin@lbl.gov


H. Earl RULEY
, Ph.D.
Department of Microbiology and Immunology
Vanderbilt University
116121 Avenue South, AA210MCN
Nashville, TN 37232
TEL: (615) 322-2087
FAX: (615) 343-7392
E-MAIL: earl.ruley@mcmail.vanderbilt.edu


Arthur T. SANDS, M.D., Ph.D.
Lexicon Genetics
4000 Research Forest Drive
The Wood Lands, TX 77381
TEL: (281) 364-0100
FAX: (281) 464-0155
E-MAIL: asands@lexgen.com


John SCHIMENTI
, Ph.D.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
TEL: (207) 288-6402
FAX: (207) 288-6053
E-MAIL: jcs@jax.org


Greg SCHULER
, Ph.D.
Plenary Session Speaker
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health
9000 Rockville Pike
Bethesda, MD 20894
TEL: (301) 496-4931
FAX: (301) 480-9241
E-MAIL: schuler@ncbi.nlm.nih.gov


Oliver SMITHIES,
Ph.D.
Plenary Session Speaker
Department of Pathology and
Laboratory Medicine
701 Brinkhous-Bullitt Building, CB 7525
University of North Carolina, Chapel Hill
Chapel Hill, NC 27599-7525
TEL: (919) 966-6913
FAX: (919) 966-8800
E-MAIL: jhlynch@med.unc.edu


M. Bento SOARES
, Ph.D.
Department of Pediatrics
The University of Iowa
451 EMRB
Iowa City, IA 52242
TEL: (319) 335-8250
FAX: (319) 335-7588
E-MAIL: bento-soares@uiowa.edu


Joseph S. TAKAHASHI
, Ph.D.
Plenary Session Speaker
Co-Chair, Session F: ENU Mutagenesis

Department of Neurobiology and Physiology
Howard Hughes Medical Institute
Northwestern University
2153 North Campus Drive
Evanston, IL 60208-3520
TEL: (847) 491-4598
FAX: (847) 491-4600
E-MAIL: j-takahashi@nwu.edu


Terry VAN DYKE
, Ph.D.
Department of Biochemistry
University of North Carolina, Chapel Hill
Campus Box 3280
Chapel Hill, NC 27599-3280
TEL: (919) 962-2145
FAX: (919) 962-4296
E-MAIL: tvdlab@med.unc.edu


Robert WATERSTON,
Ph.D.
Chair, Session D: Genomic Sequencing and Resequencing
Genome Sequencing Center
Washington University School of Medicine
4444 Forest Park Boulevard, Box 8501
St. Louis, MO 63108
TEL: (314) 362-2657
FAX: (314) 286-1810
E-MAIL: bwaterst@watson.wust1.edu


Barbara WOLD,
Ph.D.
Co-Chair, Session B: cDNA/ESTs
Division of Biology
California Institute of Technology
1201 East California Boulevard, 156-29
Pasadena, CA 91125
TEL: (626) 395-4923
FAX: (626) 449-0756
E-MAIL: woldb@starbase1.caltech.edu


Richard WOYCHIK
, Ph.D.
Department of Pediatrics
Case Western Reserve University
11100 Euclid Avenue
Cleveland, OH 44106
TEL: (216) 844-3842
FAX: (216) 844-3470
E-MAIL: rpw@po.cwru.edu


Huda ZOGHBI,
M.D.
Department of Pediatrics
Baylor College of Medicine
One Baylor Plaza
Houston, TX 77030-3411
TEL: (713) 798-6558
FAX: (713) 798-8728
E-MAIL: hzoghbi@bcm.tmc.edu


NIH ADVISORY COMMITTEE REPRESENTATIVES

NCI Pre-Clinical Models Group


Allan BRADLEY
(See Address Above)

Neal COPELAND
(See Address Above)

Wayne FRANKEL
(See Address Above)

Doug HANAHAN
(See Address Above)

Tyler JACKS
(See Address Above)

Ken PAIGEN
(See Address Above)

Janet Rossant
(See Address Above)

Terry VAN DYKE
(See Address Above)

Richard WOYCHIK
(See Address Above)


NHGRI Program Planning Subcommittee


Aravinda CHAKRAVARTI, Ph.D., Chair
Co-Chair, Session B: cDNA/ESTs
Department of Genetics
Case Western Reserve University
10900 Euclid Avenue, Room BRB 721
Cleveland, OH 44106
TEL: (216) 368-5847
FAX: (216) 368-5857
E-MAIL: axc39@po.cwru.edu

Charles H. LANGLEY, Ph.D.
Section of Evolution and Ecology
Center for Population Biology
University of California, Davis
Davis, CA 95616
TEL: (916) 752-4085
FAX: (916) 752-1449
E-MAIL: chlangley@ucdavis.edu


Alan R. WILLIAMSON, Ph.D.
760 Lawrence Avenue
Westfield, NJ 07090
TEL: (732) 232-7728
E-MAIL: alan-williamson@home.com


Barbara WOLD, Ph.D.
(See Address Above)


NICHD Advisory Council

Brigid HOGAN, Ph.D.
(See Address Above)


NIGMS Advisory Council

David A. CLAYTON, Ph.D.
Senior Scientific Officer
Howard Hughes Medical Institute
4000 Jones Bridge Road
Chevy Chase, MD 20815
TEL: (301) 215-807
FAX: (301) 215-8828
E-MAIL: claytond@hhmi.org


AGENCY REPRESENTATIVES

Howard Hughes Medical Institute

W. Maxwell COWAN, M.D., Ph.D.
Vice President and Chief Scientific Officer
Howard Hughes Medical Institute
4000 Jones Bridge Road
Chevy Chase, MD 20815
TEL: (301) 215-8803
FAX: (301) 215-8828
David A. CLAYTON, Ph.D.
(See Address Above)


Department of Energy

Ari PATRINOS, Ph.D.
Office of Biological and
Environmental Research
US Department of Energy
19901 Germantown Road, ER-70
Germantown, MD 20874-1290
TEL: (301) 903-3251
FAX: (301) 903-5051
E-MAIL: ari.patrinos@oer.doe.gov

Marvin FRAZIER,
Ph.D.
Health Effects and Life Sciences
Research Division
US Department of Energy
19901 Germantown Road, ER-72
Germantown, MD 20874-1290
TEL: (301) 903-5468
FAX: (301) 903-8521
E-MAIL: marvin.frazier@oer.doe.gov


NIH ORGANIZING COMMITTEE


Office of the Director

Harold VARMUS, M.D.
Vida BEAVEN, Ph.D.

National Cancer Institute

Richard KLAUSNER, M.D.
Grace SHEN, Ph.D.
Sue WALDROP


National Human Genome Research Institute

Francis COLLINS, M.D., Ph.D.
Bettie GRAHAM, Ph.D.
Mark GUYER, Ph.D.
Elke JORDAN, Ph.D.
Jane PETERSON, Ph.D.


National Institute of General Medical Sciences

Marvin CASSMAN, Ph.D.
Judith GREENBERG, Ph.D.
Paul WOLFE, Ph.D.

National Institute of Child Health and Human Development

Duane ALEXANDER, M.D.
A. Tyl HEWITT, Ph.D.
Steven KLEIN, Ph.D.
Richard TASCA, Ph.D.
Michael WHALIN, Ph.D.


NIH STAFF ASSISTANTS

Ms. Anita Allen
National Human Genome Research Institute

Ms. Stephanie Walker
National Human Genome Research Institute


REPORT FINALIZED JUNE 11, 1998

1 The original cost calculations for the structural analysis did not include the $6.0 million for sequencing.

2The original cost calculations did not take into consideration $6.0 million for sequencing. On 6/22 the table was revised to make it consistent with the meeting summary.

3All costs are direct costs.