DataSheet_3_Pharmacogenomics of intravenous immunoglobulin response in Kawasaki disease.pdf

IntroductionKawasaki disease (KD) is a diffuse vasculitis in children. Response to high dose intravenous gamma globulin (IVIG), the primary treatment, varies according to genetic background. We sought to identify genetic loci, which associate with treatment response using whole genome sequencing (WGS).
MethodWe performed WGS in 472 KD patients with 305 IVIG responders and 167 non-responders defined by AHA clinical criteria. We conducted logistic regression models to test additive genetic effect in the entire cohort and in four subgroups defined by ancestry information markers (Whites, African Americans, Asians, and Hispanics). We performed functional mapping and annotation using FUMA to examine genetic variants that are potentially involved IVIG non-response. Further, we conducted SNP-set [Sequence] Kernel Association Test (SKAT) for all rare and common variants.
ResultsOf the 43,288,336 SNPs (23,660,970 in intergenic regions, 16,764,594 in introns and 556,814 in the exons) identified, the top ten hits associated with IVIG non-response were in FANK1, MAP2K3:KCNJ12, CA10, FRG1DP, CWH43 regions. When analyzed separately in ancestry-based racial subgroups, SNPs in several novel genes were associated. A total of 23 possible causal genes were pinpointed by positional and chromatin mapping. SKAT analysis demonstrated association in the entire MANIA2, EDN1, SFMBT2, and PPP2R5E genes and segments of CSMD2, LINC01317, HIVEPI, HSP90AB1, and TTLL11 genes
ConclusionsThis WGS study identified multiple predominantly novel understudied genes associated with IVIG response. These data can serve to inform regarding pathogenesis of KD, as well as lay ground work for developing treatment response predictors.

引言
川崎病（Kawasaki disease, KD）是一种儿童弥漫性血管炎。作为一线治疗方案的大剂量静脉注射丙种球蛋白（intravenous gamma globulin, IVIG）的治疗反应存在遗传背景差异。本研究旨在通过全基因组测序（whole genome sequencing, WGS）鉴定与治疗反应相关的遗传位点。

方法
本研究对472例川崎病患者开展全基因组测序，其中305例为IVIG应答者，167例为符合美国心脏协会（American Heart Association, AHA）临床标准定义的IVIG无应答者。我们在全研究队列以及基于祖先信息标记划分的4个亚组（白人、非裔美国人、亚洲人及西班牙裔人群）中构建logistic回归模型，以检验加性遗传效应。采用FUMA工具开展功能映射与注释分析，以探究可能与IVIG无应答相关的遗传变异。此外，我们针对所有常见及罕见变异开展了SNP集序列核关联测试（SNP-set Sequence Kernel Association Test, SKAT）。

结果
本研究共鉴定出43,288,336个单核苷酸多态性（single nucleotide polymorphism, SNPs），其中基因间区23,660,970个、内含子区16,764,594个、外显子区556,814个。与IVIG无应答关联最显著的前10个遗传位点分别位于FANK1、MAP2K3:KCNJ12、CA10、FRG1DP、CWH43基因区域。在基于血统信息的种族亚组单独分析中，多个新发现基因内的单核苷酸多态性呈现显著关联。通过位置映射与染色质定位分析，我们精准定位了23个潜在致病基因。SKAT分析显示，MANIA2、EDN1、SFMBT2及PPP2R5E全基因，以及CSMD2、LINC01317、HIVEPI、HSP90AB1、TTLL11基因的部分区域存在显著关联。

结论
本项全基因组测序研究鉴定出多个此前未被充分研究的新型基因，这些基因与IVIG治疗反应相关。本研究结果可为阐明川崎病的发病机制提供理论支撑，同时为开发治疗反应预测工具奠定研究基础。