Novel Informatics for Highly Reliable Multi-Locus Allele Calling for Embryo Scree

用于胚胎筛选的高度可靠的多位点等位基因调用的新颖信息学

• 批准号: 7686149
• 负责人: Matthew Rabinowitz
• 金额: $ 65.87万
• 依托单位: NATERA, INC.
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-04-15 至 2010-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7686149
• 关键词: Alleles; Aneuploidy; Applaud; Area; Biopsy; Blood; Blood Cells; Blood specimen; Boston; Cell model; Cells; Child; Chromosomes; Clinical; Clinical Research; Clinical Trials; Collaborations; Communities; Complex; Computer Simulation; Congresses; Consent Forms; Couples; Cystic Fibrosis; DNA; Data; Diagnosis; Diagnostic; Diagnostic Procedure; Diagnostic Services; Diagnostic tests; Disease; Dropout; Embryo; Enrollment; Ensure; Fathers; Female; Fertility; Fertilization; Fertilization in Vitro; Fluorescent in Situ Hybridization; Funding; Genes; Genetic; Genetic Markers; Genetic screening method; Genome; Genotype; Germ Cells; Goals; Grant; Growth; Guidelines; Harvest; Health; Healthcare; Hour; Human Genome; Human Genome Project; Huntington Disease; Implant; Individual; Informatics; Information Technology; Informed Consent; Knowledge; Laboratories; Laws; Letters; Link; Live Birth; Marketing; Measurement; Measures; Meiosis; Modeling; Monosomy; Mothers; Multi-Institutional Clinical Trial; Outcome; Outcome Study; Parents; Patients; Performance; Phase; Phase I Clinical Trials; Predisposition; Prevalence; Process; Protocols documentation; Quality of life; Regulation; Reporting; Research Ethics Committees; Research Infrastructure; Running; Sampling; Screening procedure; Security; Services; Simulate; Staging; Statistical Methods; Statutes and Laws; System; Techniques; Technology; Test Result; Testing; Triad Acrylic Resin; Trisomy; United States; United States Food and Drug Administration; United States National Institutes of Health; Validity and Reliability; Work; X Chromosome; base; blind; cost; disease phenotype; embryo stage 2; genome wide association study; implantation; improved; innovation; male; new technology; novel; preimplantation; public health relevance; reproductive; satisfaction; sperm cell; standard of care

DESCRIPTION (provided by applicant): In 2006, across the globe, more than 800,000 in-vitro fertilization (IVF) cycles were run. Of 150,000 cycles run in the US, roughly 10,000 involved pre-implantation genetic diagnosis (PGD). Current PGD techniques are unregulated, expensive and highly unreliable: error rates for screening disease-linked loci or aneuploidy are on the order of 10%; each screening test costs more than $5,000; and a couple is forced to choose between testing aneuploidy, which afflicts roughly 40% of IVF embryos, or screening for disease-linked loci on the single cell. There is a great need for an affordable technology that can reliably determine genetic data from the single cell in order to screen in parallel for aneuploidy, monogenic diseases such as Cystic Fibrosis, and susceptibility to complex disease phenotypes for which the multiple genetic markers are known through whole-genome association (WGA) studies. The process of PGD during IVF involves extracting a single cell from the roughly 8 cells of an early-stage embryo for analysis. Since only a single copy of the DNA is available from one cell, direct measurements of the DNA are highly error-prone, or noisy. Gene Security Network (GSN) has developed a novel technology, termed Parental SupportTM (PS), for determining the embryonic DNA at hundreds of loci together with copy numbers for 23 chromosomes, with error rates below 0.1%, from a single cell. The proprietary technique makes use of genetic data of the mother and the father, together with the knowledge of the mechanism of meiosis and noisy measurements of the embryonic DNA, in order to determine which segments of parent chromosomes contributed to the gametes that fertilized and hence to reconstruct in silico the embryonic DNA with confidence exceeding 99%. Based on the results of our phase I study, GSN has executed letters of intent with the 5 leading IVF centers in the United States to use the GSN diagnostic service. In aim 1 of this proposal, we will demonstrate the ability of the PS technology to reliably reconstruct genetic data using the measured genetic data from isolated single cells from a born child, and parental genetic data. In aim 2 we will demonstrate the ability of the PS technology to detect aneuploidy at all 23 chromosomes, also using isolated single cell genetic data, by means of an innovative single cell model for aneuploidy that does not require direct work on embryos. In Aim 3 we will perform a clinical trial in conjunction with Stanford IVF Center, Boston IVF and Huntington Reproductive Center that applies the techniques from aims 1 and 2 to real blastomeres in the IVF context and compare our predictions with truth measured on the child when born. One goal of the study is to generate data that will be used to obtain approval of this diagnostic technique by the Food and Drug Administration. The PS technology of Gene Security Network will bring the domain of PGD into the realm of reliable diagnostics which can be regulated and used with confidence in clinical decisions. The selection of the embryos to implant is a clinical decision that has direct and absolute impact on outcomes. Narrative and Relevance to Healthcare PUBLIC HEALTH RELEVANCE: As data associating disease phenotypes with genotype continues to grow, the question arises: how can this knowledge be used to improve the quality of life and health? With this grant, Gene Security Network will thoroughly validate a technology for screening embryos during in-vitro fertilization for a multiplicity of disease linked genes and TM aneuploidy. This technology, termed Parental Support (PS) which is built on the fundamental principles of meiosis and data that has recently become available through the human genome project. Compared to existing technologies, PS enables: i) determination of disease linked loci with roughly two orders of magnitude lower error rates; ii) determination of multiple disease-linked loci in parallel; iii) determination of aneuploidy with roughly two orders of magnitude lower error rates; and iv) determination of aneuploidy across all chromosomes together with multiple disease-linked loci all from a single cell. GSN is developing the enhanced reporting system, statistical methods, and wet-lab infrastructure to offer this service to the leading IVF centers who have signed letters of intent to purchase the service, and then to the worldwide IVF community. Funding for this study will enable us to validate the performance of the diagnostic with known truth models on single cells, and to validate predictions made from a single blastomere by comparing those predictions with genetic data measured when a child is born. Roughly 152,000 and 653,000 IVF cycles were performed in 2006 in the US and internationally. The rate of growth of PGD is roughly 33% annually. Funding for this study will enable us to validate the performance of the diagnostic with known truth models on single cells, and to validate predictions made from a single blastomere by comparing those predictions with genetic data measured when a child is born. GSN's PS technology of will bring the domain of PGD into the realm of reliable diagnostics which can be regulated and used as part of the standard of care during in-vitro fertilization.

描述（由申请人提供）：2006年，在全球范围内，运行了超过800,000个体外受精（IVF）周期。在美国运行的15万个周期中，大约有10,000个涉及植入前遗传诊断（PGD）。当前的PGD技术不受监管，昂贵且高度不可靠：筛查疾病连接基因座或非整倍性的错误率在10％的阶段；每个筛选测试的成本超过5,000美元；一对夫妇被迫在测试非整倍性之间进行选择，该测试折磨了大约40％的IVF胚胎，或筛选单个细胞上的疾病连接基因座。非常需要一种可靠的技术，该技术可以可靠地确定单个细胞的遗传数据，以便对非整倍性，单基因疾病（例如囊性纤维化）以及对复杂疾病表型的敏感性并行进行筛查。 IVF期间的PGD过程涉及从早期胚胎的大约8个细胞中提取单个细胞进行分析。由于只有一个单元格可用DNA的单个副本，因此DNA的直接测量值高于错误或嘈杂。 Gene Security网络（GSN）开发了一种新型技术，称为父母支持TM（PS），用于确定数百个基因座的胚胎DNA以及23个染色体的拷贝数，单个细胞的错误率低于0.1％。专有技术利用了母亲和父亲的遗传数据，以及对胚胎DNA的减数分裂机理和嘈杂的测量机理的了解，以确定父母染色体的哪些片段有助于施肥的配子，从而在富含信心的胚胎DNA中施加了施肥的配子，并具有超过99％的99％。根据我们阶段研究的结果，GSN已与美国5个领先的IVF中心执行了意向书，用于使用GSN诊断服务。在该提案的目标1中，我们将使用来自诞生儿童的孤立单个细胞和父母遗传数据的测量遗传数据可靠地重建遗传数据的PS技术的能力。在AIM 2中，我们将通过在所有23种染色体上检测PS技术在所有23种染色体上检测到非整倍性的能力，该染色体也使用孤立的单细胞遗传学数据，通过用于非整倍性的创新单细胞模型，该模型不需要直接在胚胎上进行工作。在AIM 3中，我们将与斯坦福大学IVF中心，波士顿IVF和亨廷顿生殖中心一起进行临床试验，该中心将目标1和2的技术应用于IVF环境中的真实胚胎，并将我们的预测与我们的预测与诞生后对儿童进行的真理进行比较。该研究的目标之一是生成用于获得食品药物管理局批准这种诊断技术的数据。基因安全网络的PS技术将使PGD领域进入可靠的诊断领域，可以在临床决策中充满信心地调节和使用。植入物的胚胎选择是对结果有直接和绝对影响的临床决定。与医疗保健公共卫生相关性的叙述和相关性：随着与基因型有关的数据关联的疾病表型不断增长，问题出现了：如何使用这些知识来改善生活质量和健康的质量？借助这项赠款，基因安全网络将彻底验证一种在体外受精期间筛查胚胎的技术，以实现多种疾病联系的基因和TM非整倍性。这项技术称为父母支持（PS），它建立在最近通过人类基因组项目获得的减数分裂和数据的基本原理。与现有技术相比，PS启用：i）确定疾病连接的基因座，错误率较低两个数量级； ii）并行确定多个疾病连接的基因座； iii）确定非整倍性，大约两个数量级误差率；和iv）在所有染色体上测定各染色体的非整倍性，以及来自单个细胞的多个疾病连接的基因座。 GSN正在开发增强的报告系统，统计方法和湿lab基础架构，以向已签署了购买该服务的意向书，然后向全球IVF社区提供此服务。这项研究的资金将使我们能够通过单个细胞上的已知真理模型来验证诊断的性能，并通过将这些预测与儿童出生时测得的遗传数据进行比较来验证由单个胚泡做出的预测。 2006年在美国和国际上进行了大约152,000和653,000 IVF周期。 PGD​​的增长率每年约为33％。这项研究的资金将使我们能够通过单个细胞上的已知真理模型来验证诊断的性能，并通过将这些预测与儿童出生时测得的遗传数据进行比较来验证由单个胚泡做出的预测。 GSN的PS技术将将PGD领域带入可靠的诊断领域，可以在体外受精过程中调节并将其用作护理标准的一部分。

项目成果

Preclinical validation of a microarray method for full molecular karyotyping of blastomeres in a 24-h protocol.

• DOI: 10.1093/humrep/dep452
• 发表时间: 2010-04
• 期刊: Human reproduction (Oxford, England)
• 作者: Johnson DS;Gemelos G;Baner J;Ryan A;Cinnioglu C;Banjevic M;Ross R;Alper M;Barrett B;Frederick J;Potter D;Behr B;Rabinowitz M
• 通讯作者: Rabinowitz M