DNA Laboratory, Department of Paediatric Neurology, Charles University and University Hospital Motol, Prague, Czech Republic.
Genet Test Mol Biomarkers. 2020 May;24(5):264-273. doi: 10.1089/gtmb.2019.0232. Epub 2020 Apr 7.
Genomic studies play a major role in variant observations between and within populations and in identifying causal relationships between genotypes and phenotypes. Analyses using databases such as gnomAD can provide insight into the frequencies of alleles in large populations. There have been reports that detail such frequencies for several countries and ethnic groups, but as yet, there are no such datasets for the Czech population. Whole-exome sequencing (WES) data from 222 individuals from the Czech Republic were analyzed by The Genome Analysis Toolkit best practices pipeline. These data were annotated with the ANNOVAR tool, and the allele frequencies were computed. We developed a database that contains 300,111 variants in 17,512 genes. It is accessible through a simple web query available at prot2hg.com/variantbrowser. Gene-based analyses identified those genes that are most tolerant to variants in our population. Second, allele frequencies in our population were compared to the gnomAD database and groups of variants frequent in our population, but ultra-rare in gnomAD as a whole were identified. This tool should be useful for detecting local variants in the Czech population of patients with neurogenetic diseases.
基因组研究在人群之间和人群内部的变异观察以及确定基因型和表型之间的因果关系方面发挥着重要作用。使用 gnomAD 等数据库进行的分析可以深入了解大人群中等位基因的频率。已经有报道详细说明了几个国家和种族群体的这种频率，但迄今为止，还没有捷克人群的此类数据集。 通过 The Genome Analysis Toolkit 最佳实践管道分析了来自捷克共和国的 222 个人的全外显子组测序 (WES) 数据。这些数据使用 ANNOVAR 工具进行注释，并计算了等位基因频率。 我们开发了一个数据库，其中包含 17,512 个基因中的 300,111 个变体。它可以通过 prot2hg.com/variantbrowser 上提供的简单网络查询访问。基于基因的分析确定了我们人群中最能耐受变异的那些基因。其次，将我们人群中的等位基因频率与 gnomAD 数据库进行了比较，并确定了我们人群中常见但在 gnomAD 中整体极为罕见的变异组。 该工具应该有助于检测捷克神经遗传疾病患者人群中的本地变异。
