Array informatics to understand ploidy concordance

说明（由申请人提供）：在每个试管婴儿周期中，必须决定选择哪些胚胎进行移植。这一决定对体外受精周期的结果，即胚胎是否会发育成健康的孩子，有着深远的影响。据估计，至少50%的人类胚胎受到染色体异常的影响，如非整倍体，植入这种胚胎可能导致不希望的结果，如植入失败、自然流产或生出三体后代。生殖专家越来越多地转向胚胎植入前遗传学诊断（PGD），以努力确定最有可能发育成健康儿童的胚胎。然而，目前的技术既昂贵又不可靠，而且通常只能检测一小部分染色体。GSN开发了一种称为亲代支持tm （parents SupportTM， PS）的创新技术，其输出是在数千个位点上对胚胎DNA进行计算机重建，置信度超过99%。这项技术将首次允许试管婴儿医生筛查胚胎的染色体异常，包括所有23对染色体的非整倍体、易位和缺失，错误率低于0.1%。该应用程序的第一阶段目标是将我们的PS技术与一个新的，高度并行的定制的基于infinium的基因分型平台集成在一起，以显着降低成本，从而使GSN能够提供具有卓越准确性，范围和成本的PGD服务，相当于目前不太可靠的FISH方法。然后，新的定制平台将应用于II期，我们建议在第5天评估新的滋养外胚层活检技术，第3天传统卵裂球活检技术与实际儿童之间的一致性。这些研究的结果将使我们能够评估新的活检技术的价值，评估在第3天到第5天之间胚胎自我纠正的大部分未被研究的现象，并为试管婴儿医生提供关于每个胚胎发育潜力的强大而深远的知识。公共卫生相关性：随着疾病表型如何与基因型相关知识的积累，出现了如何应用这些知识来改善生活质量和健康的问题。染色体疾病，如非整倍体，是儿童发病和死亡的重要原因，受影响儿童的生活质量将因涉及哪条染色体而异。在体外受精（IVF）的背景下，据估计，至少50%的人类胚胎受到非整倍体和其他染色体异常的影响。这些胚胎的植入会导致普遍不希望的医疗结果，如胚胎植入失败、自然流产或三体婴儿的出生。因此，生殖专家越来越多地转向胚胎植入前遗传学诊断（PGD）测试，以努力确定最有可能发育成健康儿童的胚胎，这并不奇怪。有了这笔资金，基因安全网络（GSN）将开发一个新的定制技术平台，将GSN的专有生物信息学技术与illumina的基因分型技术集成在一起。这个定制的平台将使试管婴儿医生能够以前所未有的准确性和范围筛选胚胎中的所有染色体的非整倍体，缺失，插入和易位，并且与其他方法相比成本相似。这项技术被称为亲代支持tm (PS)，是建立在减数分裂和人类基因组计划数据的基本原理之上的。与其他现有的PGD方法相比，GSN的新定制平台使：i)非整倍体的测定错误率降低了大约两个数量级；Ii)所有染色体的非整倍性测定；iii)非整倍体与常见染色体缺失、插入和易位同时测定。GSN正在开发增强的报告系统、统计方法和湿实验室基础设施，为美国六家领先的试管婴儿中心提供这项服务（所有这些中心都已签署了购买该服务的意向书），并随后向全球试管婴儿社区提供这项服务。2006年，在美国和国际上进行了大约152,000和653,000次试管婴儿周期，PGD继续以每年约33%的速度增长。总之，这项研究的资金将使GSN能够设计和开发一个定制的技术平台，用于同时检测非整倍体、易位、缺失和插入；验证新技术的性能；并将该技术应用于研究新兴胚胎活检技术的实用性。GSN的技术将把胚胎着床前诊断领域带入可靠的诊断领域，可以作为体外受精过程中护理标准的一部分进行调节和使用。

DESCRIPTION (provided by applicant): In each IVF cycle, a decision must be made as to which embryo(s) will be selected for transfer. This decision has a far reaching impact on the outcome of an IVF cycle, namely whether the embryo will develop into a healthy child. It is estimated that at least 50% of human embryos are affected by chromosomal abnormalities such as aneuploidy, and implantation of such embryos can lead to undesired outcomes such as failed implantation, spontaneous abortion, or birth of a trisomic offspring. Reproductive specialists have been increasingly turning to pre-implantation genetic diagnosis (PGD) in efforts to identify embryos with the best chance of developing into healthy children. However, current techniques are expensive, unreliable and typically test only a small selection of chromosomes. GSN has developed an innovative technology termed Parental SupportTM (PS) whose output is an in silico reconstruction of the embryonic DNA at thousands of loci with confidence exceeding 99%. This technology will, for the first time, allow IVF physicians to screen embryos for chromosomal abnormalities including aneuploidy, translocations and deletions across all 23 pairs of chromosomes with an error rate below 0.1%. The Phase I objective of this application is to integrate our PS technology with a new, highly parallelized custom Infinium-based genotyping platform to dramatically reduce costs that will, in turn, enable GSN to offer PGD service with superior accuracy, scope and at a cost equivalent to current, less reliable FISH methods. The new customized platform will then be applied in Phase II where we propose to evaluate the concordance between a new trophectoderm biopsy technique on day 5, traditional blastomere biopsy on day 3, and the actual child. The results from these studies will allow us to assess the value of the new biopsy technique, evaluate the largely unstudied phenomenon of embryo self-correction between day 3 and day 5, and provide IVF physicians with powerful and far-reaching knowledge about the developmental potential of each embryo. PUBLIC HEALTH RELEVANCE: With the accumulating knowledge of how disease phenotypes are associated with genotypes, the question arises how this knowledge can be applied to improve the quality of life and health. Chromosomal disorders such as aneuploidy have been important causes of childhood morbidity and mortality, and the quality of life of the affected children will vary depending on which chromosome(s) is involved. In the context of in vitro fertilization (IVF), it is estimated that at least 50% of human embryos are affected by aneuploidy and other chromosomal abnormalities. Implantation of these embryos can lead to universally undesired medical outcomes such as failed embryo implantation, spontaneous abortion, or birth of a trisomic child. It is, therefore, not surprising that reproductive specialists are increasingly turning to preimplantation genetic diagnosis (PGD) testing in efforts to identify embryos with the best chance of development into healthy children. With this grant, Gene Security Network (GSN) will develop a new customized technology platform that integrates GSN's proprietary bioinformatics technology with Illumina-based genotyping technology. This customized platform will enable IVF physicians to screen embryos for aneuploidy, deletions, insertions and translocations across all chromosomes with unprecedented accuracy and scope, and at a similar cost compared to other methods. This technology, termed Parental SupportTM (PS), is built on the fundamental principles of meiosis and Human Genome Project data. In comparison to other existing PGD methods, GSN's new customized platform enables: i) determination of aneuploidy with roughly two orders of magnitude lower error rates; ii) determination of aneuploidy across all chromosomes; and iii) determination of aneuploidy simultaneously with common chromosomal deletions, insertions and translocations. GSN is developing the enhanced reporting system, statistical methods, and wet- lab infrastructure to offer this service to six of the leading IVF centers in the US (all of which have already signed letters of intent to purchase the service) and subsequently to the worldwide IVF community. Roughly 152,000 and 653,000 IVF cycles were performed in 2006 in the US and internationally, and PGD continues to grow at roughly 33% annually. In summary, funding for this study will enable GSN to design and develop a custom technology platform for simultaneous detection of aneuploidy, translocations, deletions, and insertions; validate the performance of the new technology; and apply the technology to investigate the utility of an emerging embryo biopsy technique. GSN's technology will bring the domain of embryo pre-implantation diagnosis into the realm of reliable diagnostics which can be regulated and used as part of the standard of care during in-vitro fertilization.