Variation Scanning with Mismatch Repair Detection (MRD)

描述（由申请人提供）：一种被广泛考虑的鉴定易感等位基因的方法是通过这些等位基因之间的连锁不平衡（LD）和分布在所有或大多数种族人群中的一组普遍的相对频繁的snp。然而，当导致疾病易感性的变异等位基因不常见或仅针对特定人群时，这种方法可能是不现实的。在这种情况下，确定易感等位基因可能需要在患者和对照组之间进行全面的序列比较。对于未知变异的高通量扫描技术缺乏。错配修复检测（MRD）潜在的高通量扫描可用于全面比较患者和对照组之间的序列。MRD以前已经描述过，它利用细菌错配修复系统在体内检测人类DNA样本中的序列变异。许多片段可以被引入到一个特定的细菌菌株突变分选器（MS）中，该分选器被设计成将这些片段分为两个池：携带变异的和不携带变异的。然后，DNA变异检测的问题简化为鉴定两个池的片段含量的问题，这可以使用微阵列杂交来完成。在这项资助的第二阶段，我们的目标是应用MRD多重扫描能力，在数百名患者和对照中测试大约1000个候选外显子，以确定复杂性状的易感等位基因。从长远来看，我们希望在全基因组范围内应用MRD来扫描患者和对照组的所有外显子，以阐明复杂疾病的遗传基础。

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)'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 in 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 II of this grant we aim to apply MRD multiplex scanning ability to test about 1,000 candidate exons in hundreds of patients and controls to identify susceptibility alleles of a complex trait. In the long term, we see applying MRD on a whole genomic scale to scan all the exons of patients and controls to elucidate the genetic basis of complex disease.