Interspersed repetitive sequence (IRS)-PCR for typing of whole genome radiation hybrid panels

Abstract

The typing of a radiation hybrid (RH) panel is generally achieved using a unique primer pair for each marker. We here describe a complementing approach utilizing IRS-PCR. Advantages of this technology include the use of a single universal primer to specify any locus, the rapid typing of RH lines by hybridization, and the conservative use of hybrid DNA. The technology allows the mapping of a clone without the requirement for STS generation. To test the technique, we have mapped 48 BAC clones derived from mouse chromosome 12 which we mostly identified using complex probes. As mammalian genomes are repeat-rich, the technology can easily be adapted to species other than mouse.

Figure 1

Typing of the mouse whole genome RH panel by hybridization. Inter B1 repeat PCR was carried out on the 100 cell lines of the mouse T31 panel, and mouse and hamster controls. Individual samples were loaded onto a gel with three comb rows at 1.5 cm spacing and used to prepare a Southern blot. Top row, hybrid lines 1–32, 97, 98; middle row, lines 33–64, 99, 100; bottom row, lines 63–96, positive control 129aa (indicated with +), negative control hamster A23 (indicated with –). Hybridization probe is an IRS–PCR-fragment from mouse BAC clone mbac8h16.