Department of Genomics, Arkana Laboratories, 10810 Executive Center Drive, Suite 100, Little Rock, AR, 72211, USA.
Immunogenetics. 2018 Jun;70(6):347-353. doi: 10.1007/s00251-017-1044-0. Epub 2017 Nov 16.
Objective Assimilation of SNPs Interacting in Synchrony (OASIS) is a locus-based clustering algorithm recently described that can potentially address false positives and negatives in genome-wide association studies (GWAS) of complex disorders. Diabetic nephropathy (DN) is incompletely understood due to a paucity of genes identified despite several GWAS. OASIS was applied to three DN dbGAP GWAS datasets (4725 subjects; 1.06 million SNPs). OASIS identified 19 DN genes which were verified using single variant replication in a standard association study and gene-based analysis using GATES. CARS and FRMD3 were confirmed as DN genes, and five known diabetes-associated genes, viz. NLRP3, INPPL1, PIK3C2G, NRXN3, and TBC1D4, not previously identified using these datasets were discovered. Furthermore, three additional novel DN genes were found which replicated in two sets of analysis, viz. NTN1, EBF2, and DNAH11. Hence, composite analysis with OASIS, gene-based, and single variant association testing can be universally applied to existing GWAS datasets for the identification of new genes.
同步作用 SNP 的特征同化（OASIS）是最近描述的一种基于基因座的聚类算法，它可以解决复杂疾病全基因组关联研究（GWAS）中的假阳性和假阴性问题。由于尽管进行了几次 GWAS，但只鉴定出少数几个基因，因此糖尿病肾病（DN）的发病机制仍不完全清楚。OASIS 应用于三个 DN dbGAP GWAS 数据集（4725 个对象；106 万个 SNP）。OASIS 鉴定出 19 个 DN 基因，这些基因通过在标准关联研究中对单一变异进行复制以及使用 GATES 进行基于基因的分析进行了验证。CARS 和 FRMD3 被确认为 DN 基因，并且发现了五个以前未使用这些数据集鉴定出的已知与糖尿病相关的基因，即 NLRP3、INPPL1、PIK3C2G、NRXN3 和 TBC1D4。此外，还发现了另外三个新的 DN 基因，它们在两组分析中得到了复制，即 NTN1、EBF2 和 DNAH11。因此，OASIS、基于基因和单一变异关联测试的综合分析可以普遍应用于现有的 GWAS 数据集，以鉴定新的基因。
