Using a MALDI-TOF System for SNP Analysis

描述(申请人提供)：全基因组关联研究是一个非常强大的方法，用于复杂性状的遗传分析，以及遗传易感性和环境之间的交互作用(S)。在对大规模队列中的高密度全基因组相关性研究进行统计分析之后，研究人员通常会进行两个阶段的后续基因分型。第一种方法是在更大的人群中对高度关联的SNPs(&lt；384个SNPs)立即进行中等密度的基因分型，试图复制和确认最初发现的SNPs的显著关联。第二个分析包括对所谓的TOP信号(~1500个SNP)进行中密度到高密度的基因分型，在其他生物信息学分析的指导下更有选择性地选择这些信号，例如路径分析工具。西北大学遗传医学中心(CGM)的基因组学核心拥有适当的仪器，用于Gwas的初步研究(Affymetrix和Illumina系统，最多可运行1M个SNPs)，以及顶端信号的第二阶段中到高密度基因分型(Illumina)。然而，基因组学核心目前缺乏一个合适的系统来进行第一个即时阶段的分析，以快速和经济高效地表征不到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，它使用基质辅助激光解吸/电离飞行时间质谱仪(MALDI-TOF MS)对用高通量方法确定的区域进行中低通量的基因分型。基因组学核心中心的Sequenom基因分型系统的供应将使西北大学及其附属机构的研究人员以具有竞争力的价格获得这项技术。具体地说，Sequenom Massarray系统将允许西北大学的几名研究人员a)在确定其表型时确定胎儿生长和母体新陈代谢的遗传基础以及这些基因与环境的相互作用，b)确定早产的易感基因，c)验证DNA甲基化在多发性骨髓瘤发病机制中的作用，d)调查转化生长因子-ss信号轴的基因多态在硬皮病/系统性硬化症发病机制中的作用，e)调查心力衰竭和左心室肥厚的遗传和结构决定因素，F)对Y染色体和常染色体SNPs进行快速分型，以评估北坡史前居民和现代居民之间进化关系的性质；g)调查少数群体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。 与公共卫生相关：目前核心设施的现有基因分型平台不太适合对中等数量的单核苷酸多态(SNPs)进行基因分型，使用成本高昂，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，并允许高效和及时地完成由NIH和NSF资助的项目，重点关注我们机构及其附属机构的一系列疾病，如心力衰竭、高血糖和不良妊娠结局、早产、多发性骨髓瘤、哮喘和硬皮病/硬化症。

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.