International Mammalian Genome Society

The 13th International Mouse Genome Conference
October 31-November 3, 1999

Table of Contents * Structure * Bioinformatics * Sequence * Mapping * New Tools * Gene Discovery * Developmental * Mutagenesis * Functional Genomics

D7 An RH Map of the Mouse Genome

W. Van Etten, R. Steen, H. Nguyen, Melanie Muir, A. Castle, G. Farino, V. Frazzoni, Saulius Girnius, G. Schuler*, E. Lander and T. Hudson. Center for Genome Research, Whitehead Institute/MIT, and *National Center for Biotechnology Information

Radiation hybrid (RH) maps are a key tool for genome analysis, providing a direct method for localizing genes and anchoring physical maps and genomic sequence along chromosomes. We report a comprehensive RH reference map of the mouse genome. The map contains 2,486 loci screened 93 cell lines of the T31 RH panel. 2339 loci are simple sequence length polymorphisms (SSLPs) taken from the mouse genetic map, thereby providing direct integration between these two key maps.

The RH mapping of the SSLPs was performed by a new and efficient approach, in which traditional gel-based or hybridization-based assays were replaced by a homogeneous 5'-nuclease (TaqMan) assay involving a single common probe for all the genetic markers. The reference map provides essentially complete connectivity and coverage across the genome. It also provides good resolution for ordering loci, with an average of about 100 kilobases (kb) per centiRay (cR).

Toward the goal of generating a dense gene map, we have designed primers for 4,900 mouse Unigene clusters and pre-screened them by PCR against the pooled RH panel and mouse and hamster genomic DNA with 70% of the markers indicating suitability for RH mapping. We have streamlined RH mapping of ESTs using a modified single base extension (SBE) assay. We will report our progress toward the placement of 13,000 ESTs.

The RH map, together with an accompanying web server (, makes it possible for any investigator to rapidly localize sequences within the mouse genome.


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