Non-Invasive Detection of Fetal Aneuploidy by Next-Generation DNA Sequencing

通过下一代 DNA 测序无创检测胎儿非整倍体

基本信息

批准号：
8604720
负责人：
David Gerard Peters
金额：
$ 46.74万
依托单位：
MAGEE-WOMEN'S RES INST AND FOUNDATION
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-05-15 至 2016-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8604720
关键词：
Alleles Amniocentesis Aneuploidy Anxiety Apoptotic Biological Assay Blood Circulation Cells Chorionic Villi Sampling Chorionic villi Chromosomes, Human, Pair 13 Collaborations Communities Computer software DNA DNA Sequence Data Data Analyses Detection Development Diagnosis Diagnostic Procedure Diagnostics Research Discipline of obstetrics Down Syndrome Economics Fetal Diseases Fetus First Pregnancy Trimester Genomics Genotype Goals Hereditary Disease High-Throughput DNA Sequencing Inherited Karyotype Laboratory Technicians Methods Morbidity - disease rate Mothers Non-Invasive Cancer Detection Nucleic Acids Plasma Positioning Attribute Pregnancy Pregnant Women Prenatal Diagnosis Procedures Publishing RNA Research Risk Sampling Sensitivity and Specificity Serum Serum Proteins Shotguns Spontaneous abortion Technology Testing Translations Ultrasonography Work analytical method analytical tool clinical Diagnosis clinical care clinical practice cohort computer science cost cost effective fetal graphical user interface high throughput analysis improved minimally invasive mortality next generation next generation sequencing novel open source prenatal prevent public health relevance research study screening statistics tool

项目摘要

DESCRIPTION (provided by applicant): Prenatal diagnosis of fetal genetic disease has evolved to reach a prominent position in obstetric clinical care. Established screening methods targeted towards serum proteins are used routinely alongside ultrasonography to identify potentially abnormal pregnancies. Definitive diagnosis is then undertaken using interventional procedures such as amniocentesis and chorionic villus sampling (CVS) that obtain fetal or placental cells, respectively, for karyotype analysis. However, these invasive procedures involve a risk of associated miscarriage. This is significant because, for trisomy 21, current non-invasive first trimester screening methods have detection rates of 82 to 87% and false positive rates of approximately 5%. Therefore, up to 18% of true positives are missed and one expectant mother in every twenty who are screened will undergo an unnecessary invasive diagnostic procedure that could result in the avoidable miscarriage of her baby. In addition to the risk of mortality and morbidity, invasive procedures invoke considerable parental anxiety. Our goal is to dramatically reduce these avoidable miscarriages and other associated risks by developing a diagnostic method that significantly improves the sensitivity and specificity of non-invasive prenatal detection of aneuploidy in the first trimester. To achieve this goal we will expand on our recently published work to test the hypothesis that shotgun next generation sequencing of first trimester maternal plasma DNA provides improved sensitivity and specificity over existing combinations of serum screening and ultrasound. Significantly, earlier economic and logistical barriers preventing the translation of this approach to clinical practice have very recently been overcome by the emergence of methods for high-throughput DNA sequencing that are cost-effective for clinical diagnosis. Specifically, in Aim 1, we will carry out shotgun next generation sequencing on samples of maternal plasma DNA obtained in the first trimester of pregnancy from large cohorts of confirmed aneuploidy and control pregnancies (combined n = 70). We will then undertake a formal statistical analysis to determine the sensitivity and specificity of next-generation DNA sequencing for the detection of aneuploidy on chromosomes 13, 18, 21 and X and compare these results to sensitivity and specificity data obtained using existing first trimester screening methods in the same cohort (Aim 2). Finally we will develop a software package with graphical user interface that can be utilized by non-specialist end users for the rapid analysis of next generation sequencing data and the detection of aneuploidy (Aim 3). We anticipate that this new first trimester test will increase the detection rate of fetal aneuploidy to 95% and reduce the false positive rate to 1%, resulting in an 80% reduction in unnecessary miscarriages associated with invasive prenatal diagnosis after first trimester screening.

描述（由申请人提供）：胎儿遗传疾病的产前诊断已经发展为在产科临床护理中的重要地位。靶向血清蛋白的已建立筛查方法常规与超声检查一起使用，以鉴定潜在的异常妊娠。然后，使用诸如羊膜穿刺术和绒毛膜绒毛采样（CV）等介入程序进行明确的诊断，分别获得胎儿或胎盘细胞进行核型分析。但是，这些侵入性程序涉及相关流产的风险。这很重要，因为对于第21三体，当前的非侵入性头三个月筛查方法的检测率为82至87％，假阳性率约为5％。因此，多达18％的真实积极因素被错过，每二十名被筛选的一位准母亲将接受不必要的侵入性诊断程序，这可能导致她的婴儿可避免的流产。除了死亡率和发病率的风险外，侵入性程序还引起了父母的焦虑。我们的目标是通过开发一种诊断方法来大大减少这些可避免的流产和其他相关风险，从而显着提高头三个月非侵入性产前检测的敏感性和特异性。为了实现这一目标，我们将扩展我们最近发表的工作，以检验以下假设：shot弹枪的下一代孕妇血浆DNA的下一代测序可提高灵敏度和特异性，比血清筛查和超声的现有组合。值得注意的是，最近，通过出现高通量DNA测序的方法来克服了这种临床实践方法的早期经济和后勤障碍，这些方法在临床诊断方面具有成本效益。具体而言，在AIM 1中，我们将对从大量确认的衰老和对照妊娠的妊娠中期获得的母体血浆DNA样品进行shot弹枪测序（合并n = 70）。然后，我们将进行形式的统计分析，以确定下一代DNA测序的灵敏度和特异性，以检测染色体上的非整倍性13、18、21和X，并将这些结果与使用同一同一队列中的现有第一培养剂筛选方法获得的敏感性和特异性数据（AIM 2）。最后，我们将开发一个具有图形用户界面的软件包，该软件包可以由非专家最终用户可以使用，以快速分析下一代测序数据和检测Aneuploidy（AIM 3）。我们预计，这项新的孕期新测试将使胎儿非整倍性的检测率提高到95％，并将假阳性率降低到1％，从而导致与首次妊娠筛查后与侵入性产前诊断相关的不必要的流产降低了80％。