Using a MALDI-TOF System for SNP Analysis

描述（由申请人提供）：全基因组关联研究（GWAS）是一种非常强大的方法，用于复杂性状的遗传分析，以及遗传易感性和环境之间的相互作用。在对大队列的高密度全基因组关联研究进行统计分析后，研究人员通常进行两个阶段的随访基因分型。第一种是在一个更大的个体队列中对最高度相关的SNP（<384个SNP）进行立即的中等密度基因分型，试图复制并确认最初鉴定的SNP的显著关联。第二种分析包括对所谓的顶部信号（约1500个SNP）进行中到高密度基因分型，这些信号在其他生物信息学分析（例如途径分析工具）的指导下更有选择性地选择。西北大学遗传医学中心（CGM）的基因组学核心具有用于主要GWAS研究的适当仪器（能够运行高达1 M SNP的Affyphase和Illumina系统），以及第二阶段顶部信号的中等至高密度基因分型（Illumina）。然而，Genomics Core目前缺乏合适的系统用于第一即时阶段分析，以快速和成本有效地表征少于384个SNP。本提案中要求的Sequenom MassARRAY系统是一种灵活的序列分析系统，其使用基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF MS）对高通量方法鉴定的区域进行中通量和低通量基因分型。在基因组学核心的Sequenom基因分型系统的可用性将以具有竞争力的价格为西北大学及其附属机构的研究人员提供使用该技术的机会。具体地，Sequenom MassARRAY系统将允许几个西北大学的研究者a）鉴定解释胎儿生长和母体代谢的遗传基础的基因以及这些基因与环境在确定其表型中的相互作用，B）鉴定早产的易感基因座，c）验证DNA甲基化在多发性骨髓瘤发病机制中的作用，d）研究TGF-β信号传导轴中的遗传多态性在硬皮病/系统性硬化症的发病机制中的作用，f）快速基因分型Y-染色体和常染色体SNP，以评估北坡史前和现代居民之间进化关系的性质，g）调查少数民族哮喘差异的遗传基础，h）研究糖尿病和肥胖与绝经后乳腺癌风险之间的联系。 公共卫生相关性：目前在核心设施处可用的基因分型平台不理想地适合于对中等数量的单核苷酸多态性（SNP）进行基因分型，使用昂贵，并且不进行低密度甲基化分析。从Sequenom获得MassARRAY系统是必要的，以填补这一空白，并允许有效和及时地完成NIH和NSF资助的项目，重点是广泛的疾病，如心力衰竭，高血糖症和不良妊娠结局，早产，多发性骨髓瘤，哮喘和硬皮病/硬化症在我们的机构及其附属机构。

DESCRIPTION (provided by applicant): Whole Genome Association Studies (GWAS) is a very powerful approach for the genetic analysis of complex traits, and interaction(s) between genetic predisposition and environment. Following the statistical analysis of high-density genome-wide association studies in large cohorts, investigators generally pursue two phases of follow-up genotyping. The first is an immediate, medium-density genotyping of the most highly associated SNPs (<384 SNPs) in a much larger cohort of individuals with an attempt to replicate and confirm the significant association of the initially identified SNPs. The second analysis consists of medium- to high-density genotyping of so called top signals (~1500 SNPs) that are more selectively chosen with the guidance of additional bioinformatics analyses, e.g. pathway analysis tools. The Genomics Core of the Center of Genetic Medicine (CGM) at Northwestern University has the appropriate instrumentation for primary GWAS studies (Affymetrix and Illumina systems with the capacity to run up to 1 M SNPs), and second phase medium- to high-density genotyping of the top signals (Illumina). However, the Genomics Core currently lacks a suitable system for the first immediate phase analysis for the rapid and cost- efficient characterization of less than 384 SNPs. The Sequenom MassARRAY system, requested in this proposal, is a flexible sequence analysis system which uses Matrix-Assisted Laser Desorption/Ionization Time- of-Flight Mass Spectrometry (MALDI-TOF MS) to perform medium- and low-throughput genotyping of regions identified with high-throughput approaches. Availability of a Sequenom genotyping system at the Genomics Core will provide access to this technology to the investigators at Northwestern University and affiliated institutions at a competitive price. Specifically, a Sequenom MassARRAY system will permit several Northwestern university investigators to a) identify genes that account for the genetic underpinnings of fetal growth and maternal metabolism and the interaction of those genes with the environment in determination of their phenotype, b)identify susceptibility loci of Preterm Birth, c) validate the effect of DNA methylation in pathogenesis of Multiple Myeloma, d) Investigate the role of genetic polymorphisms in the TGF-ss signaling axis in the pathogenesis of Scleroderma/Systemic Sclerosis, e) investigate the genetic and structural determinants of heart failure and left ventricular hypertrophy, f)rapidly genotype the Y-chromosome and autosomal SNPs to assess the nature of the evolutionary relationships between prehistoric and modern inhabitants of the North Slope, g) investigate genetic basis for asthma disparities in minorities, h) study the link between diabetes and obesity to postmenopausal breast cancer risk. PUBLIC HEALTH RELEVANCE: Currently available genotyping platforms at the core facility are not ideally suited for genotyping intermediate number of Single Nucleotide Polymorphisms (SNPs), are expensive to use, and do not perform low-density methylation analyses. Acquiring the MassARRAY system from Sequenom is necessary to fill this gap and to permit the efficient and timely completion of NIH- and NSF-funded projects focusing on a broad spectrum of diseases such as heart failure, hyperglycemia and adverse pregnancy outcomes, preterm birth, multiple myeloma, asthma, and scleroderma/ sclerosis at our institution and its affiliates.