Clinical Diagnostic Sequencing of Structural Variation

摘要 新兴的基因组医学倡议将对产前和儿科诊断产生影响，包括 羊膜穿刺术中胎儿结构异常的评估及无创性检查的快速应用 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和整个外显子组测序(WES)的诊断效率高于 常规核型和微阵列(CMA)；然而，技术、分析和解释方面的挑战 结构变异(SVS)的提出继续混淆了基于序列的诊断学。这块地缺少 解释来自WGS和WES的SVS的标准化方法，然而这些变体构成了很大一部分 产前诊断，特别是对患有多发性先天性畸形(MCAS)的高危胎儿。我们的临床服务 最初形成的计划是为了形成技术和算法开发方面的专业知识，变体 解释，母胎医学，和大规模参考，以探索高分辨率SV的影响 产前诊断中的检测。此重新提交建立在方法、资源和发现的基础上 这些研究旨在建立统一的方法来联合发现和解释SVS，最初是从羊膜穿刺术 并最终使用非侵入性方法。我们将重点关注MCAS作为基因组诊断的样本 严重的临床转诊。我们最初资助期的发现共同表明了几个关键的 进步可以改变产前筛查和基因诊断，我们直接解决三个主要问题 这一更新中这些进展的障碍：(1)FSA中WES的诊断收益非常不稳定，原因是 捕获SVS的方法不一致，灵敏度有限。AIM 1将对诊断收益率进行基准测试 WGS在MCA案例中使用我们的标准化开源管道。(2)贡献最大的基因 人类严重的胎儿异常在很大程度上仍然未知，因为对MCAS的研究大多局限于 小队列和低分辨率的CMA方法。目标2将汇集这些严重的胎儿畸形和 对WES和SVS中的短变异和SVS进行统一的变异检测和联合关联分析 FSA中的WG三人组跨越多个财团，我们将其与人口规模的聚合控制进行比较。(3) NIPS是超低分辨率的，无法捕获MCAS下的大多数因果变体类。目标3将 对一种从cffDNA中检测编码突变和SVS的创新方法进行基准测试，将产量与 目前的NIPS和羊水穿刺术是护理的标准。因此，我们的团队将利用互补的专业知识， 新的方法和独特的患者资源，以促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.