GENOTYPING CORE

这是对计划项目建议书1PO1HD-047609《基因与环境的相互作用》的修订 2003年10月提交的《人类分娩》，由日内瓦国际排雷中心的一个特别强调小组审查，以及 获得199(第30个百分位数)的优先级分数。在这项研究计划中，我们建议确定 人类孕期长短/自然发病时间的遗传和环境决定因素 分娩，并对基因、环境和母胎相互作用进行建模，这些因素可能是导致糖尿病风险的基础 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 白色的。 前一次审查对所提议的基因分型核心的所有方面都给予了非常有利的评价， 并注意到核心主任(希克森)的专业知识和基因测序工作的记录 德克萨斯大学人类遗传学中心将确保这些目标的实现和可靠性 结果将达到可能的最高水平。这项审查没有引起任何担忧。核心收到了一份 优先级分数为110。 在审查项目三时提出的一个问题涉及MALDI-TOF的准确性 高通量环境中的SNP分析平台。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分析可靠性的数据对其进行处理 被核心。 “关于重新测序和SNP分型的Mefhodo/ogy在核心C和项目1中没有完全建立。 哪个项目3依赖于SNP分析的MALDI-TOF平台的等位基因调用的准确性仍然不是 在高吞吐量环境中进行了全面的记录。 已经开发了许多不同的自动化平台用于高通量的基于 关于一系列当前的分子技术。布鲁克人 Biflex III MALDI-TOF系统(Sequenom公司)是一个经过验证和完善的 一种基于区分的基因分型平台 利用质谱仪进行等位基因特异的微型测序反应 分析。在我们手中，我们发现Sequenom平台 在高吞吐量中生成准确且一致的等位基因调用 环境。这台仪器我们已经用了好几次了 包括全面失明在内的流行病学研究 评估基因分型错误率的重复程序。的数量 这些研究中的盲复本在5%到10%的范围内 样本。表1显示了每月盲人调查的结果。 正在进行的研究的重复数据。这七个不同的分析 多态(A-G)对盲复本的符合率为98%-100% 等位基因呼叫。该信息现已包含在修订后的说明中 核心(第304页)。

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).