ANNOUNCEMENT: Whitehead/MIT Mouse Physical Map Data Release

Donna Slonim slonim at GENOME.WI.MIT.EDU
Mon Mar 10 16:01:36 EST 1997


                         ANNOUNCING:
      WHITEHEAD INSTITUTE/MIT CENTER FOR GENOME RESEARCH
               MOUSE GENOMIC MAPPING PROJECT 
                 DATA RELEASE 13 (MARCH 1997)

   (available at http://www-genome.wi.mit.edu/cgi-bin/mouse/index)
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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

Having completed the genetic map, we are now constructing a physical map of
the mouse consisting of 10,000 markers screened against a mouse YAC library.
Many of the markers are the SSLPs that are also on the genetic map, but are
also adding random STSs to the physical map to reach a total of 10,000
markers.

In this release, we include data for 6,018 markers successfully screened
against the YAC library. We have placed 4,917 of these markers into
singly-linked physical map contigs; 4,191 are in doubly-linked contigs.

The table below shows the number of physically and genetically-mapped
markers assigned to each chromosome. (Note that some markers that hit yacs
have not yet been mapped to a particular chromosome, so the total number of
physically-mapped markers in this table represents a subset of the total
number of markers in the release.) 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       431       559      403   655
 Chr2       399       553      388   656
 Chr3       250       382      229   458
 Chr4       261       367      240   430
 Chr5       288       433      268   511
 Chr6       294       383      252   482
 Chr7       272       356      260   423
 Chr8       263       361      262   404
 Chr9       256       371      235   444
 Chr10      243       317      223   389
 Chr11      324       356      280   470
 Chr12      241       289      222   335
 Chr13      281       317      266   376
 Chr14      216       271      202   327
 Chr15      238       274      215   346
 Chr16      202       215      172   267
 Chr17      127       255      107   312
 Chr18      192       236      155   306
 Chr19      125       134      113   169
 ChrX       179       230      153   287
 TOTAL      5082      6659     4645  8047

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 (phone, 800-533-4363; outside
US/Canada, 205-533-4363; FAX, 205-536-9016) and Genome Systems, Inc. of St.
Louis, Missouri, (phone 800-430-0030). 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 a work in
progress. It includes only those SSLPs that worked well on the first try and
that did not require any special attention. There are now 5,080 SSLPs on the
physical map, as well as 868 random STSs and 70 ESTs. In future releases, we
expect to add primarily ESTs and random 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 the release directory

 3-97.MarkerInfo.txt      PCR primer and product size
 3-97.GeneticMapInfo.txt  Genetic mapping information
 3-97.PhysicalMapInfo.txt Physical mapping information
 3-97.STS2Contig.txt      Contig information
 3-97.Contig2STS.txt      Contig information - inverted
 3-97.Sequences.txt       Raw source sequences for STSs
 pictures/                Maps in postscript and Macintosh format

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For further information contact: Victoria Wang victoria at genome.wi.mit.edu or
Donna Slonim slonim at genome.wi.mit.edu

Last modified March 10, 1997




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