VARIATION SCANNING WITH MISMATCH REPAIR DETECTION MRD)

DESCRIPTION (provided by applicant): One widely considered approach to identify susceptibility alleles is through linkage disequilibrium (LD) between these alleles and a universal set of relatively frequent SNPs distributed in all or most ethnic populations. This approach, however, may be unrealistic when variant alleles responsible for disease susceptibility are infrequent or are specific to a particular population. In such cases, identifying susceptibility alleles may require comprehensive sequence comparison between patients and controls. There is a paucity of techniques for high throughput scanning for unknown variations. Mismatch Repair Detection (MRD) has been described previously and it utilizes a bacterial mismatch repair system in vivo to detect sequence variants in human DNA samples. Mismatch Repair Detection (MRD)'s potential for high throughput scanning can be used to comprehensively compare sequences between patients and controls. MRD has been described previously and it utilizes a bacterial mismatch repair system in vivo to detect sequence variants in human DNA samples. Many fragments can be introduced into a specific bacterial strain Mutation Sorter (MS) that is engineered to sort these fragments to two pools: those carrying variations and those that do not. The problem of DNA variation detection is then reduced to the problem of identification of the fragment content of the two pools, and that can be done using a microarray hybridization. In phase I of this grant we aim to demonstrate the ability of MRD to scan for variations 500 exons simultaneously using a generic chip as the final readout.