Whitehead/MIT Mouse Physical Map Data Release 14

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.

Mouse Physical Mapping Project

Having completed the genetic map, construction is going on of 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.

Release information

In this release, data for 7,796 markers successfully screened against the YAC library are included. A number of  6,361 of these markers have been placed into singly-linked physical map contigs; 5,972 are in doubly-linked contigs. All the markers in doubly-linked contigs are linked to another marker in the contig by at least two YACs, while markers can be joined to a singly-linked contig by only one YAC. Thus, the doubly-linked contigs are generally smaller but more reliable.

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").

CHROMOSOME PHYSICAL GENETIC BOTH TOTAL MARKERS Chr1 Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 ChrX 565 326 472 329 395 286 327 299 190 271 169 579 363 390 390 395 390 344 371 261 559 317 356 289 317 271 274 215 255 236 134 553 382 367 433 383 356 361 371 230 403 223 280 222 266 202 215 172 107 173 114 388 229 240 268 252 260 262 235 165 789 472 618 423 490 397 435 364 375 367 212 836 571 559 613 583 541 485 559 357 TOTAL 7112 6659 4676 10046

The genetically-mapped SSLPs are screened on the 5-dimensional pools, using the same pair of primers as were used when they were placed 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, an attempt is made 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 Interspecific 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.

Availability

The Whitehead/MIT Mouse Physical Map Data can be downloaded as flat files from their anonymous ftp server, and can also be queried online.

Information provided by: Victoria Wang

Resources and further information

• Whitehead Institute for Biomedical Research/MIT Center for Genome Research
  http://www-genome.wi.mit.edu/
• Mouse Genetic and Physical Mapping Project
  http://www-genome.wi.mit.edu/cgi-bin/mouse/index
• Download Mouse database
  ftp://genome.wi.mit.edu/distribution/mouse_sslp_release s/may97/
• Human Genome Mapping Project Resource Centre (HGMP-RC)
  http://www.hgmp.mrc.ac.uk/
• European Collaborative Interspecific Mouse Backcross
  http://www.hgmp.mrc.ac.uk/MBx/MBxHomepage.html

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