POPULATION SCALE HLA TYPING FOR HOMELAND DEFENSE

描述（由申请人提供）：目前的HLA分型技术不具有快速现场反应能力，因为它太昂贵，太复杂，无法在人口规模的紧急情况下实施。该提案的最终目标是开发一种简单、准确、低成本的方法，通过开发一种“HLA芯片”来进行复杂的HLA分型，该芯片将能够对大量最重要的HLA等位基因进行群体规模的分析。美国基因组学公司（GUSA）开发了一种独特的“自组装”微阵列技术和生物信息学，使中密度微阵列的大规模生产成本非常低。在该SBIR的I期中，实现了以下主要目标：1）发现了原始自组装GUSA微阵列平台的使能变体，其允许相对于原始申请中描述的技术的高序列特异性和杂交信号的10倍增加。观察到的这一重大改进的结果是直接的、生物化学辅助的SNP检测，具有低成本、群体规模HLA分型所需的简单性、准确性和再现性。2)开发生物信息学工具以产生大量SNP选择性杂交探针，其与探针“自组装”附着到微阵列表面所施加的物理要求一致，以及已经证明，口腔拭子是用于在HLA芯片上进行小型化HLA分型的极好的DNA来源，并且是在现场收集口腔拭子并将其储存用于集中检测的简单方法。在干燥状态下的HLA处理也被开发。在该SBIR的第二阶段，HLA芯片开发过程将扩展到整个HLA基因座，并作为β现场测试进行验证，以记录每个便携式实验室每天1000人的准确HLA基因分型。β测试将通过简单的外推法证明，仅使用10个低成本便携式现场实验室就能够对大量接触人群（每周10万人）进行HLA分型。这样的HLA数据然后可以在“真实的时间”中用于在HLA水平上预测生物武器感染的个体风险或对针对相同传染因子的疫苗接种的个性化应答。这种低成本、便携式HLA芯片技术的变体可以被“剥离”用于各种其他应用：灾难中的平民身份识别或个性化医疗，特别是用于自身免疫性疾病。这些其他应用程序在技术上类似，但将独立探索和资助。该项目的重点是开发一种低成本的人群规模的HLA芯片技术，该技术可以在快速反应环境中实施，允许对大量暴露人群（每周10万人）进行快速HLA分型，以识别高风险个体并在个体水平上预测他们对疫苗接种的个性化反应。

DESCRIPTION (provided by applicant): Current technology for HLA typing does not have rapid field response capability because it too expensive and is too complicated to be implemented in the context of a population-scale emergency. The ultimate goal of this proposal is to develop a simple, accurate, low cost method to perform complex HLA typing through development of an "HLA Chip" which will enable population-scale analysis of a large set of the most important HLA alleles. Genomics USA (GUSA) has developed a unique "self-assembling" microarray technology and bioinformatics to enable the mass production of medium density microarrays at very low cost. In Phase I of this SBIR, the following major objectives were accomplished: 1) An enabling variant of the original self-assembling GUSA microarray platform was discovered which allows high sequence specificity and a 10-fold increase in hybridization signal relative to the technology described in the original application. The observed result of this major improvement is direct, biochemically-unaided SNP detection with the simplicity, accuracy and reproducibility required for low cost, population scale HLA typing. 2) Bioinformatics tools were developed to create large sets of SNP- selective hybridization probes that are consistent with the physical requirements imposed by "self- assembling" attachment of probes to the microarray surface and 3) It was demonstrated that a buccal swab is an excellent source of DNA for miniaturized HLA typing on the HLA Chip and a simple approach to collect buccal swabs in the field and to store them for centralized HLA processing in the dry state was also developed. In Phase II of this SBIR, the HLA Chip development process will be extended to the entire HLA locus and validated as a beta field test to document accurate HLA genotyping at a rate of 1000 individuals per day per portable laboratory site. The beta test will demonstrate, via, simple extrapolation, the ability to HLA type a large exposed population (100,000 individuals per week) using as few as 10 low cost, portable field laboratories. Such HLA data could then be used in "real time" to anticipate, at the HLA level, individual risk of infection by a biological weapon or personalized response to vaccination against the same infectious agent. Variants of this low cost, portable HLA Chip technology could be "spun off" for a variety of other applications: civilian ID in a disaster or personalized medicine, especially for autoimmune diseases. Those other applications are technically similar, but will be explored and funded independently. The project focus is the development of a low-cost population-scale HLA Chip technology that can be implemented in a rapid-response environment that would allow rapid HLA typing of a large exposed population (100,000 individuals per week) in order to identify high risk individuals and to predict, on an individual level, their personalized response to vaccination.