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

• 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
• 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

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到在产科临床护理中占据突出地位。针对血清蛋白的既定筛查方法通常与超声检查一起用于识别潜在的异常妊娠。然后使用介入程序进行明确诊断，如羊膜穿刺术和绒毛膜绒毛取样（CVS），分别获得胎儿或胎盘细胞进行核型分析。然而，这些侵入性手术涉及相关流产的风险。这一点很重要，因为对于21三体，目前的非侵入性妊娠早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%的真阳性漏检，每20名接受筛查的孕妇中就有1名将接受不必要的侵入性诊断程序，这可能导致本可避免的婴儿流产。除了死亡率和发病率的风险，侵入性手术引起相当大的父母焦虑。我们的目标是通过开发一种诊断方法，显著提高孕期前三个月非整倍体非侵入性产前检测的敏感性和特异性，从而显著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，以测试假设，即早期妊娠孕妇血浆DNA的霰弹枪下一代测序比现有的血清筛查和超声组合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，这种方法对临床诊断具有成本效益。具体而言，在Aim 1中，我们将对妊娠前三个月从确认非整倍体和对照妊娠（合计n = 70）的大队列中获得的母体血浆DNA样本进行霰弹枪下一代测序。然后，我们将进行正式的统计分析，以确定下一代DNA测序检测染色体13、18、21和X上的非整倍体的敏感性和特异性，并将这些结果与在同一队列中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（目的2）。最后，我们将开发一个具有图形用户界面的软件包，非专业最终用户可以使用该软件包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，这种新的妊娠早期检测将使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侵入性产前诊断相关的不必要流产减少80%。