GENOTYPING CORE

基因分型核心

• 批准号: 7707387
• 负责人: JAMES E. HIXSON
• 金额: $ 14.25万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-05-01 至 2010-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7707387
• 关键词: Address; African American; Agreement; Alleles; Biological; Biological Assay; Birth; Cartilage; Cells; Chondrocytes; Collagen; Data; Engineering; Ensure; Environment; Epidemiologic Studies; Extracellular Matrix; Extracellular Matrix Degradation; Genes; Genetic; Genetic Polymorphism; Genotype; Glycosaminoglycans; Goals; Growth Factor; Hand; Hispanics; Human; Human Genetics; Insulin-Like Growth Factor I; Integrins; Investigation; Kinetics; Knowledge; Laws; Lead; Length; Mass Spectrum Analysis; Mechanics; Modeling; Molecular; National Institute of Child Health and Human Development; Numbers; Population; Pregnancy; Premature Birth; Property; Published Comment; Range; Rate; Reaction; Reliability of Results; Research; Risk; Sampling; Score; Signal Transduction; Skeletal system; Staging; Surveys; System; Technology; Texas; Time; Universities; Work; articular cartilage; base; blind; cytokine; fetal; gene environment interaction; instrument; programs; racial and ethnic; receptor; soft tissue; transmission process

This is a revision of Program Project proposal 1 PO1 HD-047609 "Gene-Environment Interactions in Human Parturition" that was submitted in October 2003, reviewed by an NICHD Special Emphasis Panel, and received a priority score of 199 (30th percentile). In this research program we proposed to identify the genetic and environmental determinants of the length of human gestation/ timing of onset of spontaneous parturition, and to model the gene, environment, and maternal-fetal interactions that may underlie the risk of premature birth among three racial/ ethnic populations: African-Americans, Hispanics and nonHispanic Whites. The previous review commented very favorably on all aspects of the Genotyping Core as proposed, and noted that the expertise of the Core Director (Hixson) and track record of gene sequencing efforts at the University of Texas Human Genetics Center would ensure the goals will be realized and the reliability of the results will be at the highest possible level. The review did not raise any concerns. The Core received a priority score of 110. One issue that was brought up in the review of Project III relates to the accuracy of the MALDI-TOF platform for SNP assay in a high throughput environment. Since this issue is pertinent to the Genotyping Core, it is addressed here in the present revision with the following data about assay reliability that was generated by the Core. "Mefhodo/ogy for re-sequencing and SNP typing are not fully established in Core C and Project 1 on which Project 3 depends - accuracy of the allele calls with the MALDI-TOF platform of SNP assay is still not fully documented in a high throughput environment." Many different automated platforms have been developed for high-throughput genotyping based on a wide array of current molecular technologies. The Brucker Biflex III MALDI-TOF system (Sequenom, Inc.) is a proven and wellestablished genotyping platform that is based on distinguishing allele-specific mini-sequencing reactions using mass spectrometry analysis. In our hands, we have found that the Sequenom platform produces accurate and consistent allele calls in a high-throughput environment. We have used this instrument for several large epidemiological studies that included comprehensive blind duplicate programs to assess genotyping error rates. The numbers of blind duplicates in these studies range from 5% to 10% of the samples. Table 1 presents results from a monthly survey of blind duplicate data for an on-going study. This analysis of seven different polymorphisms (A-G) yielded 98-100% agreement for blind duplicate allele calls. This information is now included in the revised description of the Core (p.304).

这是计划项目提案1 PO 1 HD-047609“基因-环境相互作用， 2003年10月提交的《人类分娩》，经国家人道主义排雷中心特别重点小组审查， 优先级得分为199（第30百分位数）。在这项研究计划中，我们提出要确定 人类妊娠期长短的遗传和环境决定因素/自发性妊娠发作的时间 分娩，并模拟基因，环境和母胎相互作用，可能是风险的基础。 三个种族/民族人群中的早产：非洲裔美国人、西班牙裔和非西班牙裔 白人 先前的综述对所提出的基因分型核心的各个方面都给予了非常有利的评价， 并指出，核心主任（希克森）的专业知识和基因测序工作的记录， 得克萨斯大学人类遗传学中心将确保目标的实现和可靠性， 结果将是尽可能高的水平。审查没有提出任何关切。核心收到了一份 优先级110 在项目III的审查中提出的一个问题涉及MALDI-TOF的准确性 用于高通量环境中SNP测定的平台。由于这个问题与基因分型核心有关， 在本修订版中，使用以下生成的有关检测试剂盒可靠性的数据对其进行了说明 的核心。 “用于重新测序和SNP分型的Mefhodo/ogy在核心C和项目1中尚未完全建立， 项目3所依赖的-SNP测定的MALDI-TOF平台的等位基因调用的准确性仍然不是 在高吞吐量环境中完全记录。" 已经开发了许多不同的自动化平台，用于基于基因分型的高通量基因分型。 一系列的现代分子技术。布鲁克酒店 Biflex III MALDI-TOF系统（Sequenom，Inc.）是一个被证明和完善的 基因分型平台是基于区分 使用质谱法的等位基因特异性微型测序反应 分析.在我们手中，我们发现Sequenom平台 以高通量产生准确和一致的等位基因调用， 环境我们已经用这种仪器进行了几次大规模的测试。 流行病学研究，包括全面的盲 重复程序以评估基因分型错误率。的数量 这些研究中的盲法重复范围为5%至10%， 样品表1列出了盲人每月调查的结果。 正在进行的研究的重复数据。分析了七种不同的 多态性（A-G）产生了98-100%的一致性，盲法重复 等位基因调用。这一信息现已列入修订后的说明中 核心（p.304）