More than 90% of genetic variants are rare in most modern sequencing studies, such as the Alzheimer's Disease Sequencing Project (ADSP) whole-exome sequencing (WES) data. Furthermore, 54% of the rare variants in ADSP WES are singletons. However, both single variant and unit-based tests are limited in their statistical power to detect an association between rare variants and phenotypes. To best use missense rare variants and investigate their biological effect, we examine their association with phenotypes in the context of protein structures. We developed a protein structure–based approach, protein optimized kernel evaluation of missense nucleotides (POKEMON), which evaluates rare missense variants based on their spatial distribution within a protein rather than their allele frequency. The hypothesis behind this test is that the three-dimensional spatial distribution of variants within a protein structure provides functional context to power an association test. POKEMON identified three candidate genes (TREM2, SORL1, and EXOC3L4) and another suggestive gene from the ADSP WES data. For TREM2 and SORL1, two known Alzheimer's disease (AD) genes, the signal from the spatial cluster is stable even if we exclude known AD risk variants, indicating the presence of additional low-frequency risk variants within these genes. EXOC3L4 is a novel AD risk gene that has a cluster of variants primarily shared by case subjects around the Sec6 domain. This cluster is also validated in an independent replication data set and a validation data set with a larger sample size.

中文翻译：

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蛋白质结构内罕见错义变异空间分布的关联测试确定了阿尔茨海默病相关模式

在大多数现代测序研究中，超过 90% 的遗传变异是罕见的，例如阿尔茨海默病测序计划 (ADSP) 的全外显子组测序 (WES) 数据。此外，ADSP WES 中 54% 的稀有变体是单例。然而，单一变异和基于单元的测试在检测罕见变异和表型之间关联的统计能力方面都受到限制。为了最好地使用错义稀有变异并研究它们的生物学效应，我们在蛋白质结构的背景下检查它们与表型的关联。我们开发了一种基于蛋白质结构的方法，即错义核苷酸的蛋白质优化核评估 (POKEMON)，它根据蛋白质内的空间分布而不是等位基因频率来评估罕见的错义变异。该测试背后的假设是蛋白质结构内变体的三维空间分布为关联测试提供了功能背景。POKEMON确定了三个候选基因（TREM2、SORL1和EXOC3L4）以及来自 ADSP WES 数据的另一个提示性基因。对于TREM2和SORL1这两个已知的阿尔茨海默氏病 (AD) 基因，即使我们排除已知的 AD 风险变异，来自空间簇的信号也是稳定的，表明这些基因中存在额外的低频风险变异。EXOC3L4是一种新型 AD 风险基因，具有一组主要由 Sec6 域周围的病例受试者共享的变体。该集群也在一个独立的复制数据集和一个更大样本量的验证数据集中进行了验证。