WICGR Mouse Genomic Mapping Project, Data Release 12

[Donna Slonim]

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	  WHITEHEAD INSTITUTE/MIT CENTER FOR GENOME RESEARCH

		    MOUSE GENOMIC MAPPING PROJECT

		      Data Release October 1996

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GENETIC MAP

The July 1996 Data Release was the final release of the Mouse Genetic Map at
the Whitehead Institute/MIT Center for Genome Research. It reflects the data
represented in the 14 March, 1996 issue of Nature. Please see this paper,
and also Genetics 131:423-447 (1992) for descriptions of the materials and
methods used to construct the maps.

Dietrich, W.F., J. Miller, R. Steen, M.A. Merchant, D. Damron-Boles, Z.
Husain, R. Dredge, M.J. Daly, K.A. Ingalls, T.J. O'Conner, C.A. Evans, M.M.
DeAngelis, D.M. Levinson, L. Kruglyak, N. Goodman, N.G. Copeland, N.A.
Jenkins, T.L. Hawkins, L. Stein, D.C. Page, & E.S. Lander (1996) A
comprehensive genetic map of the mouse genome. Nature 380:149-152.
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MOUSE PHYSICAL MAPPING PROJECT

Since completing the genetic map, our goal is to construct a physical map of
the mouse, consisting of 10,000 markers screened against a mouse YAC
library. Many of the markers will be the SSLPs that are also on the genetic
map, but we will also be adding random STSs to the physical map to reach a
total of 10,000 markers.

In this release, we include data for 4,208 markers successfully screened
against the YAC library. 4,006 of these markers have been placed into
physcial map contigs. The table below shows the number of physically and
genetically-mapped markers on each chromosome. The right-most columns count
the number of markers shared by the two maps ("BOTH"), and the total number
of distinct markers mapped in any way ("TOTAL MARKERS").


Breakdown of Mapped Markers by Chromosome

 CHROMOSOME PHYSICAL  GENETIC  BOTH  TOTAL MARKERS
 chr1       371       511      323   559
 chr2       344       513      314   543
 chr3       188       342      166   364
 chr4       195       348      188   355
 chr5       237       401      226   412
 chr6       209       367      200   376
 chr7       209       356      207   358
 chr8       233       350      227   356
 chr9       205       336      193   348
 chr10      185       293      179   299
 chr11      253       350      248   355
 chr12      203       278      200   281
 chr13      248       302      241   309
 chr14      175       259      170   264
 chr15      202       264      195   271
 chr16      150       214      140   224
 chr17      75        254      74    255
 chr18      123       231      122   232
 chr19      83        134      83    134
 chrX       118       228      109   237
 TOTAL      4006      6331     3805  6532


YAC Library

The YAC library being used is described in an upcoming issue of Mammalian
Genome (Haldi, et al.). It consists of 40,000 YACs with an average insert
size of 820 kb. The entire library, or individual YAC clones, is available
through Research Genetics, Huntsville, Alabama (800-533-4363 phone,
800-336-9014 FAX) and Genome Systems, Inc. of St. Louis, Missouri, (phone
800-430-0030), and also through the Mouse Genome Centre, Oxfordshire,
England. We are currently using a subset of 24,000 clones in building the
physical map. These 24,000 clones are arrayed here at the Center in a
5-dimensional pooling scheme. The STSs are screened on these 5D pools, with
3 hits describing a single YAC address, and up to two extra hits confirming
that address.


STSs screened

Please note that this release of the physical map represents only a first
pass through the genome. It includes only those SSLPs that worked well on
the first try, and did not require any special attention. In later releases
we plan to include as many of the SSLPs as can be successfully screened, as
well as ESTs, random STSs and other markers.

The genetically-mapped SSLPs are screened on the 5-dimensional pools, using
the same pair of primers as were used when we placed them on the genetic
map. If the marker fails on the first try, it is run through the screening
process a second time. If it fails twice, we attempt to convert the SSLP
into an STS by picking two new primers and an internal oligo from one side
or the other side of the CA-repeat. Markers that fail this final step will
probably not be placed on the physical map. If you are working with an SSLP
that you want to know the precise placement of in relation to other SSLPs
nearby, you may wish to consult the European Collaborative Interpecific
Mouse Backcross. They are mapping our SSLPs in a high-resolution 1000-animal
backcross. Chromosomes 2, 11, 15, 16, and 17 are completed, chromosomes 3
and 4 are nearly done, and others are underway.

Many of the markers on both the genetic and physical map are available
through Research Genetics, at a reduced cost under a community discount
arrangement set up by the WICGR. (Note: WI/MIT CGR has placed the markers in
the public domain. The center and its personnel receive no financial benefit
from the sale of primers.)


Citing this data

Data releases occur on a quarterly basis or more frequently if the amount of
new data warrants it. At the end of each quarter, all genomic mapping data
are reviewed and prepared for distribution via CGR's electronic databases.
Data releases typically occur within two weeks of the close of the month.
Releases are announced by electronic messages posted to the following two
newsgroups: "bionet.genome.chromosomes" and "bionet.announce".

CGR's data release policy is among the most rapid, broad and regular of any
genome center. Its purpose is to ensure that scientific colleagues have
immediate access to information that may assist them in the search for
genes. Data releases do not constitute scientific publication of CGR's work,
but rather provide scientists with a regular look into our lab notebooks.
For projects aimed at the analysis of particular genes or subchromosomal
regions, permission is hereby granted to use our data without the need for a
formal collaboration, subject only to appropriate acknowledgment. For
projects aimed at large-scale mapping of entire chromosomes or entire
genomes, use of the data and markers should be on a collaborative basis.

References to this data in publications should be cited by listing each of
the following three sources:

1. Dietrich, W.F., J. Miller, R. Steen, M.A. Merchant, D. Damron-Boles, Z.
Husain, R. Dredge, M.J. Daly, K.A. Ingalls, T.J. O'Conner, C.A. Evans, M.M.
DeAngelis, D.M. Levinson, L. Kruglyak, N. Goodman, N.G. Copeland, N.A.
Jenkins, T.L. Hawkins, L. Stein, D.C. Page, & E.S. Lander (1996) A
comprehensive genetic map of the mouse genome. Nature 380:149-152.

2. Dietrich, W.F. et al. (1994) A genetic map of the mouse with 4,006 simple
sequence length polymorphisms. Nature Genetics 7:220-245.

3. Copeland, N.G., D.J. Gilbert, N.A. Jenkins, J.H. Nadeau, J.T. Eppig, L.J.
Maltais, J.C. Miller, W.F. Dietrich, R.G. Steen, S.E. Lincoln, A. Weaver,
D.C. Joyce, M. Merchant, M. Wessel, H. Katz, L.D. Stein, M.P. Reeve, M.J.
Daly, R.D. Dredge, A. Marquis, N. Goodman, E.S. Lander (1993) Genome Maps
IV. Science 262:67.

4. Supplemented by additional markers in: Whitehead Institute/MIT Center for
Genome Research, Genomic Map of the Mouse, Database Release 10, June 1996.

Additional publications with related information:

Dietrich, W., J. Miller, H. Katz, D. Joyce, R. Steen, S. Lincoln, M. Daly,
M.P. Reeve, A. Weaver, P. Anagnostopoulos, N. Goodman, N. Dracopoli, E.S.
Lander (1992) Genetic Maps. Stephen J. O'Brien, ed. Cold Spring Harbor
Laboratory Press.

Assay Conditions for the Genetic Map:

Assay conditions and other experimental details are given in:
Dietrich, W., et al., 1992. Genetics 131: 423-447.
Briefly, the PCR protocol used radiolabeled primers in a 25 cycle PCR (1 '94
degrees, 2' 55 degrees, 3' 72 degrees) on 20 ng of genomic DNA.


CONTENTS OF THIS DIRECTORY

 10-96.MarkerInfo.txt      PCR primer and product size
 10-96.GeneticMapInfo.txt  Genetic mapping information
 10-96.PhysicalMapInfo.txt Physical mapping information
 10-96.STS2Contig.txt      Contig information
 10-96.Contig2STS.txt      Contig information - inverted
 Sequences.txt             Raw source sequences for STSs
 pictures/                 Maps in postscript and Macintosh format


For further information contact:  Donna Slonim, slonim at genome.wi.mit.edu;
or Joyce Miller, jmiller at genome.wi.mit.edu

Last modified October 2, 1996