Manshaei Roozbeh, Merico Daniele, Reuter Miriam S, Engchuan Worrawat, Mojarad Bahareh A, Chaturvedi Rajiv, Heung Tracy, Pellecchia Giovanna, Zarrei Mehdi, Nalpathamkalam Thomas, Khan Reem, Okello John B A, Liston Eriskay, Curtis Meredith, Yuen Ryan K C, Marshall Christian R, Jobling Rebekah K, Oechslin Erwin, Wald Rachel M, Silversides Candice K, Scherer Stephen W, Kim Raymond H, Bassett Anne S
Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Deep Genomics Inc., Toronto, ON, Canada.
Front Genet. 2020 Sep 15;11:957. doi: 10.3389/fgene.2020.00957. eCollection 2020.
Recent genome-wide studies of rare genetic variants have begun to implicate novel mechanisms for tetralogy of Fallot (TOF), a severe congenital heart defect (CHD). To provide statistical support for case-only data without parental genomes, we re-analyzed genome sequences of 231 individuals with TOF ( = 175) or related CHD. We adapted a burden test originally developed for variants to assess ultra-rare variant burden in individual genes, and in gene-sets corresponding to functional pathways and mouse phenotypes, accounting for highly correlated gene-sets and for multiple testing. For truncating variants, the gene burden test confirmed significant burden in (Bonferroni corrected -value < 0.01). For missense variants, burden in achieved genome-wide significance only when restricted to constrained genes (i.e., under negative selection, Bonferroni corrected -value = 0.004), and showed enrichment for variants affecting the extracellular domain, especially those disrupting cysteine residues forming disulfide bonds (OR = 39.8 vs. gnomAD). Individuals with ultra-rare missense variants, all with TOF, were enriched for positive family history of CHD. Other genes not previously implicated in CHD had more modest statistical support in gene burden tests. Gene-set burden tests for truncating variants identified a cluster of pathways corresponding to VEGF signaling ( = 0%), and of mouse phenotypes corresponding to abnormal vasculature ( = 0.8%); these suggested additional candidate genes not previously identified (e.g., and ). Results for the most promising genes were driven by the TOF subset of the cohort. The findings support the importance of ultra-rare variants disrupting genes involved in VEGF and NOTCH signaling in the genetic architecture of TOF, accounting for 11-14% of individuals in the TOF cohort. These proof-of-principle data indicate that this statistical methodology could assist in analyzing case-only sequencing data in which ultra-rare variants, whether or inherited, contribute to the genetic etiopathogenesis of a complex disorder.
近期针对罕见基因变异的全基因组研究已开始揭示法洛四联症（TOF）这一严重先天性心脏病（CHD）的新机制。为在无亲本基因组的情况下为仅病例数据提供统计支持，我们重新分析了231例TOF患者（ = 175）或相关CHD患者的基因组序列。我们采用了最初为 变异体开发的负担检验，以评估单个基因以及与功能途径和小鼠表型相对应的基因集中的超罕见变异体负担，同时考虑了高度相关的基因集和多重检验。对于截短变异体，基因负担检验证实 中存在显著负担（Bonferroni校正 -值 < 0.01）。对于错义变异体，只有在限于受约束基因时（即在负选择下，Bonferroni校正 -值 = 0.004）， 中的负担才达到全基因组显著性，并且显示出影响细胞外结构域的变异体富集，尤其是那些破坏形成二硫键的半胱氨酸残基的变异体（OR = 39.8 对比gnomAD）。具有 超罕见错义变异体的个体均患有TOF，且CHD阳性家族史富集。其他先前未涉及CHD的基因在基因负担检验中的统计支持较为适度。针对截短变异体的基因集负担检验确定了一组与VEGF信号传导相对应的途径（ = 0%），以及一组与异常脉管系统相对应的小鼠表型（ = 0.8%）；这些提示了先前未鉴定的额外候选基因（例如 和 ）。最有前景基因的结果由队列中的TOF亚组驱动。这些发现支持了超罕见变异体破坏参与VEGF和NOTCH信号传导的基因在TOF遗传结构中的重要性，占TOF队列中个体的11 - 14%。这些原理验证数据表明，这种统计方法可有助于分析仅病例测序数据，其中超罕见变异体，无论是 还是遗传的，都对复杂疾病的遗传病因学有贡献。
