Clinical Diagnostic Sequencing of Structural Variation

摘要 新兴的基因组医学计划将影响产前和儿科诊断，包括 评估胎儿结构异常（FSA）从子宫穿刺术和快速采用非侵入性 产前筛查（NIPS）。事实上，全基因组测序（WGS）成本的快速下降和 分析基因组学方法的改进的复杂性已经将产前筛查带到了一个关键的转折点。 正在进行的研究发现WGS和全外显子组测序（WES）的诊断产率提高， 常规核型和微阵列（CMA）;然而，技术，分析和解释的挑战 由结构变体（SV）呈现的突变继续混淆基于序列的诊断。该领域缺乏 标准化的方法来解释来自WGS和WES的SV，但这些变异是WGS和WES的重要组成部分的基础。 产前诊断，特别是对于具有多种先天性异常（MCA）的高危胎儿。我们的临床SV 该计划最初是为了培养技术和算法开发方面的专业知识， 解释，母胎医学和大规模参考文献，以探讨高分辨率SV的影响 产前诊断中的检测。这一重新提交建立在方法，资源，和发现， 这些研究旨在建立统一的方法，以联合发现和解释SV，最初来自穿刺术 最终使用非侵入性方法。我们将重点关注作为基因组诊断范例的MCAs， 严重的临床转诊。我们最初资助期间的发现共同表明了几个关键的 这些进步可以改变产前筛查和遗传诊断，我们直接解决三个主要问题， 在这种更新中，这些进展的障碍：（1）在FSA中，WES的诊断率变化很大， 不一致的方法和捕获SV的有限灵敏度。目标1将基准诊断收益率从 MCA案例中的WGS使用我们的标准化开源管道。(2)这些基因导致了 人类严重的胎儿畸形在很大程度上仍然未知，因为对MCA的研究大多局限于 小队列和低分辨率CMA方法。目标2将汇总这些严重的胎儿异常， 对来自WES的短变体和SV进行统一变体检测和联合关联分析， WGS在FSA三重奏在多个财团，我们将比较人口规模的聚合控制。（三） NIPS是超低分辨率的，并且无法捕获MCAs下的大多数因果变体类。目标3将 对一种创新方法进行基准测试，以检测来自cffDNA的编码突变和SV， 目前的NIPS和腹腔穿刺术作为护理标准。因此，我们的团队将利用互补的专业知识， 新方法和独特的患者资源，以推进产前诊断中的常规基因组筛查。

ABSTRACT Emerging genomic medicine initiatives are poised to impact prenatal and pediatric diagnostics, including assessment of fetal structural anomalies (FSAs) from amniocentesis and the rapid adoption of non-invasive prenatal screening (NIPS). Indeed, the rapid decrease in whole-genome sequencing (WGS) costs and the improved sophistication of analytic genomics methods has brought prenatal screening to a critical inflection point. Ongoing studies find improved diagnostic yields from WGS and whole exome sequencing (WES) over conventional karyotype and microarray (CMA); however, the technical, analytical, and interpretative challenges presented by structural variants (SVs) continue to confound sequence-based diagnostics. The field lacks standardized methods to interpret SVs from WGS and WES, yet these variants underlie a significant fraction of prenatal diagnoses, particularly for high risk fetuses with multiple congenital anomalies (MCAs). Our clinical SV program was initially formed to nucleate expertise in technology and algorithm development, variant interpretation, maternal-fetal medicine, and large-scale references to explore the impact of high-resolution SV detection in prenatal diagnostics. This resubmission builds upon the methods, resources, and discoveries from those studies to establish uniform approaches to jointly discover and interpret SVs, initially from amniocentesis and ultimately using non-invasive methods. We will focus on MCAs as exemplars of genomic diagnostics in severe clinical referrals. The discoveries from our initial funding period collectively suggest several critical advances could transform prenatal screening and genetic diagnostics, and we directly address three major barriers to these advances in this renewal: (1) Diagnostic yields from WES in FSAs are highly variable due to inconsistent methods and limited sensitivity to capture SVs. Aim 1 will benchmark diagnostic yields from WGS in MCA cases using our standardized open-source pipelines. (2) The genes contributing to the most severe fetal anomalies in humans remain largely unknown, as studies of MCAs have mostly been restricted to small cohorts and low-resolution CMA methods. Aim 2 will aggregate these severe fetal anomalies and perform uniform variant detection and joint association analyses of short variants and SVs from WES and WGS in FSA trios across multiple consortia, which we will compare to population-scale aggregated controls. (3) NIPS is ultra-low resolution and fails to capture most causal variant classes underlying MCAs. Aim 3 will benchmark an innovative approach to detect coding mutations and SVs from cffDNA, comparing yields to current NIPS and amniocentesis as the standard-of-care. Our team will thus leverage complementary expertise, novel methods, and unique patient resources to advance routine genomic screening in prenatal diagnostics.