Genome-wide association studies (GWAS) have identified more than 75 genetic risk loci for Alzheimer’s Disease (AD), however for a substantial portion of these loci the genetic variants or genes directly involved in AD risk remain to be found. A GWAS locus defined by the index SNP rs1476679 in ZCWPW1 is one of the largest AD loci as the association signal spans 56 potential risk genes. The three most compelling candidate genes in this locus are ZCWPW1, PILRA and PILRB, based on genetic, transcriptomic, and proteomic evidence. We performed amplicon-based target enrichment and next-generation sequencing of the exons, exon-intron boundaries, and UTRs of ZCWPW1, PILRA and PILRB on an Illumina MiSeq platform in 1048 Flanders-Belgian late-onset AD patients and 1037 matched healthy controls. Along with the single-marker association testing, the combined effect of Sanger-validated rare variants was evaluated in SKAT-O. No common variants (n = 40) were associated with AD. We identified 20 validated deleterious rare variants (MAF < 1%, CADD score ≥ 20), 14 of which in ZCWPW1. This included 4 predicted loss-of-function (LoF) mutations that were exclusively found in patients (P = 0.011). Haplotype sharing analysis revealed distant common ancestors for two LoF mutations. Single-molecule long-read Nanopore sequencing analysis unveiled that all LoF mutations are phased with the risk haplotype in the locus. Our results support the recent report for the role of ultra-rare LoF ZCWPW1 variants in AD and suggest a potential risk mechanism for AD through ZCWPW1 haploinsufficiency.

中文翻译：

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ZCWPW1 阿尔茨海默病中的功能丧失变异

全基因组关联研究 (GWAS) 已经确定了超过 75 个阿尔茨海默病 (AD) 的遗传风险位点，但是对于这些位点中的很大一部分，仍有待发现直接与 AD 风险相关的遗传变异或基因。通过在索引SNP rs1476679所述的GWAS轨迹ZCWPW1是最大AD基因座关联信号跨度56个潜在风险基因中的一个。基于遗传、转录组学和蛋白质组学证据，该基因座中三个最引人注目的候选基因是ZCWPW1、PILRA和PILRB。我们对ZCWPW1、PILRA和PILRB的外显子、外显子-内含子边界和 UTR 进行了基于扩增子的目标富集和下一代测序在 Illumina MiSeq 平台上，1048 名法兰德斯-比利时迟发性 AD 患者和 1037 名匹配的健康对照。与单标记关联测试一起，在 SKAT-O 中评估了 Sanger 验证的罕见变异的综合效果。没有常见的变异 ( n = 40) 与 AD 相关。我们确定了 20 个经过验证的有害罕见变异（MAF < 1%，CADD 评分 ≥ 20），其中 14 个在ZCWPW1 中。这包括仅在患者中发现的 4 个预测的功能丧失 (LoF) 突变（P= 0.011）。单倍型共享分析揭示了两个 LoF 突变的远距离共同祖先。单分子长读长纳米孔测序分析表明，所有 LoF 突变都与基因座中的风险单倍型分相。我们的结果支持最近关于超罕见 LoF ZCWPW1变体在 AD 中的作用的报告，并通过ZCWPW1 单倍剂量不足提出了 AD 的潜在风险机制。