Clinical impact of a targeted next-generation sequencing gene panel for autoinflammation and vasculitis.
Clinical impact of a targeted next-generation sequencing gene panel for autoinflammation and vasculitis.
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DOI：
10.1371/journal.pone.0181874
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Brogan PA
中科院分区：
文献类型：
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作者：
Omoyinmi E;Standing A;Keylock A;Price-Kuehne F;Melo Gomes S;Rowczenio D;Nanthapisal S;Cullup T;Nyanhete R;Ashton E;Murphy C;Clarke M;Ahlfors H;Jenkins L;Gilmour K;Eleftheriou D;Lachmann HJ;Hawkins PN;Klein N;Brogan PA
单基因自身炎性疾病（AID）是一组迅速扩大的遗传多样性，但表型重叠的系统性炎症性疾病与先天免疫失调。它们造成严重的发病率、死亡率和经济负担。在这里，我们的目的是开发和评估NGS靶向基因面板，“血管炎和炎症面板”（VIP）的AID和血管炎的临床影响。使用Agilent SureDesign工具设计2个版本的VIP; VIP 1靶向113个基因，以及更高版本的VIP 2靶向166个基因。为72名患者制备的捕获和索引文库（QXT靶富集系统）在Illumina MiSeq测序仪上以150 bp配对末端模式作为16个样品的多重测序。该队列包括22个阳性对照DNA样本，来自先前在各种基因中验证过突变的患者;以及50个来自先前基于桑格的遗传筛查未被诊断的疑似AID患者的前瞻性样本。VIP在检测22个阳性对照中所有不同类型的已知突变时是敏感和特异的，包括基因缺失、小INDELS和等位基因分数低至3%的体细胞嵌合。6/50例未分类的AID患者（12%）至少有一种5类（明确致病）变异; 11/50例（22%）至少有一种可能致病的变异（4类）。总体而言，VIP检测在16/50例患者（32%）中得到了明确或强烈怀疑的分子诊断。这种全面的靶向基因组的高诊断率和准确性验证了对疑似AID患者使用广泛的基于NGS的检测。
Monogenic autoinflammatory diseases (AID) are a rapidly expanding group of genetically diverse but phenotypically overlapping systemic inflammatory disorders associated with dysregulated innate immunity. They cause significant morbidity, mortality and economic burden. Here, we aimed to develop and evaluate the clinical impact of a NGS targeted gene panel, the “Vasculitis and Inflammation Panel” (VIP) for AID and vasculitis. The Agilent SureDesign tool was used to design 2 versions of VIP; VIP1 targeting 113 genes, and a later version, VIP2, targeting 166 genes. Captured and indexed libraries (QXT Target Enrichment System) prepared for 72 patients were sequenced as a multiplex of 16 samples on an Illumina MiSeq sequencer in 150bp paired-end mode. The cohort comprised 22 positive control DNA samples from patients with previously validated mutations in a variety of the genes; and 50 prospective samples from patients with suspected AID in whom previous Sanger based genetic screening had been non-diagnostic. VIP was sensitive and specific at detecting all the different types of known mutations in 22 positive controls, including gene deletion, small INDELS, and somatic mosaicism with allele fraction as low as 3%. Six/50 patients (12%) with unclassified AID had at least one class 5 (clearly pathogenic) variant; and 11/50 (22%) had at least one likely pathogenic variant (class 4). Overall, testing with VIP resulted in a firm or strongly suspected molecular diagnosis in 16/50 patients (32%). The high diagnostic yield and accuracy of this comprehensive targeted gene panel validate the use of broad NGS-based testing for patients with suspected AID.