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：
8447109
负责人：
David Gerard Peters
金额：
$ 44.7万
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/8447109
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 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）：胎儿遗传病的产前诊断已发展到产科临床护理中的重要地位。针对血清蛋白的既定筛查方法通常与超声检查一起使用，以识别潜在的异常妊娠。然后通过羊膜穿刺术和绒毛膜绒毛取样（CVS）等介入手术分别获取胎儿或胎盘细胞进行核型分析，进行最终诊断。然而，这些侵入性手术存在相关流产的风险。这一点意义重大，因为对于 21 三体，目前的非侵入性早孕期筛查方法的检出率为 82% 至 87%，假阳性率约为 5%。因此，高达 18% 的真阳性被遗漏，每 20 名接受筛查的准妈妈中就有 1 名将接受不必要的侵入性诊断程序，这可能会导致本可以避免的婴儿流产。除了死亡和发病的风险外，侵入性手术还会引起父母的极大焦虑。我们的目标是通过开发一种诊断方法，显着提高妊娠早期非整倍体非侵入性产前检测的敏感性和特异性，从而显着减少这些可避免的流产和其他相关风险。为了实现这一目标，我们将扩展我们最近发表的工作，以测试以下假设：与现有的血清筛查和超声组合相比，对妊娠早期母体血浆 DNA 进行鸟枪式下一代测序可提供更高的灵敏度和特异性。值得注意的是，早期阻碍这种方法转化为临床实践的经济和后勤障碍最近已经被高通量 DNA 测序方法的出现所克服，这些方法对于临床诊断来说具有成本效益。具体来说，在目标 1 中，我们将对妊娠前三个月从大量已确认的非整倍体和对照妊娠（组合 n = 70）中获得的母体血浆 DNA 样本进行鸟枪式下一代测序。然后，我们将进行正式的统计分析，以确定下一代 DNA 测序用于检测 13、18、21 和 X 号染色体非整倍性的敏感性和特异性，并将这些结果与使用现有的妊娠早期筛查方法获得的敏感性和特异性数据进行比较在同一队列中（目标 2）。最后，我们将开发一个具有图形用户界面的软件包，可供非专业最终用户用于快速分析下一代测序数据和检测非整倍体（目标 3）。我们预计，这项新的妊娠早期检测将把胎儿非整倍体的检出率提高到 95%，并将假阳性率降低到 1%，从而使妊娠早期筛查后与侵入性产前诊断相关的不必要流产减少 80%。