Array informatics to understand ploidy concordance

描述(申请人提供)：在每个试管受精周期中，必须决定选择哪个胚胎(S)进行移植。这一决定对试管受精周期的结果有着深远的影响，即胚胎是否会发育成一个健康的孩子。据估计，至少有50%的人类胚胎受到非整倍体等染色体异常的影响，这种胚胎的植入可能会导致不希望看到的结果，如着床失败、自然流产或出生三体后代。生殖专家越来越多地转向植入前遗传诊断(PGD)，以努力识别最有可能发育成健康儿童的胚胎。然而，目前的技术昂贵、不可靠，通常只测试一小部分染色体。GSN开发了一项名为Parental SupportTM(PS)的创新技术，其成果是以电子方式重建数千个基因座的胚胎DNA，置信度超过99%。这项技术将首次允许试管受精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技术与新的高度并行的基于Infinium的定制基因分型平台相集成，以大幅降低成本，从而使GSN能够以与当前可靠性较低的FISH方法相当的成本提供精度、范围和成本都更高的PGD服务。然后，新的定制平台将应用于第二阶段，在该阶段，我们建议评估新的滋养外胚层活检技术在第5天与传统的卵裂球活检在第3天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组织检查技术的价值，评估在第3天到第5天之间胚胎自我纠正这一基本上未被研究的现象，并为试管受精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：随着关于疾病表型如何与基因相关的知识的积累，问题产生了如何将这些知识应用于改善生活和健康的质量。染色体疾病，如非整倍体，一直是儿童发病率和死亡率的重要原因，受影响儿童的生活质量将根据涉及的染色体而有所不同(S)。在体外受精(IVF)的背景下，估计至少有50%的人类胚胎受到非整倍体和其他染色体异常的影响。这些胚胎的植入可能会导致普遍不受欢迎的医疗后果，如胚胎植入失败、自然流产或出生三体儿童。因此，生殖专家越来越多地转向植入前基因诊断(PGD)测试，以努力识别最有可能发育成健康儿童的胚胎也就不足为奇了。有了这笔赠款，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基于Illumina的基因分型技术相结合。这个定制的平台将使试管受精医生能够以前所未有的准确性和范围，以与其他方法类似的成本，在所有染色体上筛查胚胎的非整倍体、缺失、插入和易位。这项技术被称为父母支持TM(PS)，建立在减数分裂的基本原理和人类基因组计划数据的基础上。与其他现有的PGD方法相比，GSN的新定制平台能够：i)以大约低两个数量级的错误率检测非整倍体；ii)检测所有染色体的非整倍体；以及iii)同时检测常见的染色体删除、插入和易位。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，以便向美国六家领先的试管受精中心(所有这些中心都已签署购买该服务的意向书)以及随后向全球试管受精社区提供这项服务。2006年，美国和国际上进行了大约152,000个和653,000个试管受精周期，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；并应用该技术来研究新兴的胚胎活检技术的实用性。GSN的技术将把胚胎植入前诊断领域带入可靠诊断领域，这种诊断可以进行调整，并作为体外受精过程中护理标准的一部分。

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.