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首页> 外文期刊>BMC Genomics >mGAP: the macaque genotype and phenotype resource, a framework for accessing and interpreting macaque variant data, and identifying new models of human disease
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mGAP: the macaque genotype and phenotype resource, a framework for accessing and interpreting macaque variant data, and identifying new models of human disease

机译：mGAP：猕猴基因型和表型资源，用于访问和解释猕猴变异数据并识别人类疾病新模型的框架

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Non-human primates (NHPs), particularly macaques, serve as critical and highly relevant pre-clinical models of human disease. The similarity in human and macaque natural disease susceptibility, along with parallel genetic risk alleles, underscores the value of macaques in the development of effective treatment strategies. Nonetheless, there are limited genomic resources available to support the exploration and discovery of macaque models of inherited disease. Notably, there are few public databases tailored to searching NHP sequence variants, and no other database making use of centralized variant calling, or providing genotype-level data and predicted pathogenic effects for each variant. The macaque Genotype And Phenotype (mGAP) resource is the first public website providing searchable, annotated macaque variant data. The mGAP resource includes a catalog of high confidence variants, derived from whole genome sequence (WGS). The current mGAP release at time of publication (1.7) contains 17,087,212 variants based on the sequence analysis of 293 rhesus macaques. A custom pipeline was developed to enable annotation of the macaque variants, leveraging human data sources that include regulatory elements (ENCODE, RegulomeDB), known disease- or phenotype-associated variants (GRASP), predicted impact (SIFT, PolyPhen2), and sequence conservation (Phylop, PhastCons). Currently mGAP includes 2767 variants that are identical to alleles listed in the human ClinVar database, of which 276 variants, spanning 258 genes, are identified as pathogenic. An additional 12,472 variants are predicted as high impact (SnpEff) and 13,129 are predicted as damaging (PolyPhen2). In total, these variants are predicted to be associated with more than 2000 human disease or phenotype entries reported in OMIM (Online Mendelian Inheritance in Man). Importantly, mGAP also provides genotype-level data for all subjects, allowing identification of specific individuals harboring alleles of interest. The mGAP resource provides variant and genotype data from hundreds of rhesus macaques, processed in a consistent manner across all subjects ( https://mgap.ohsu.edu ). Together with the extensive variant annotations, mGAP presents unprecedented opportunity to investigate potential genetic associations with currently characterized disease models, and to uncover new macaque models based on parallels with human risk alleles.
机译：非人类灵长类动物（NHP），尤其是猕猴，是人类疾病的关键且高度相关的临床前模型。人类和猕猴自然疾病易感性的相似之处，以及平行的遗传风险等位基因，突显了猕猴在制定有效治疗策略中的价值。尽管如此，可用于支持探索和发现猕猴遗传病模型的基因组资源有限。值得注意的是，很少有专门用于搜索NHP序列变体的公共数据库，没有其他数据库使用集中变体调用或提供每个变体的基因型水平数据和预测的致病作用。猕猴基因型和表型（mGAP）资源是第一个提供可搜索，带注释的猕猴变体数据的公共网站。 mGAP资源包括源自全基因组序列（WGS）的高可信度变体目录。根据293恒河猴的序列分析，当前的mGAP发行时（1.7）包含1,087,212个变体。开发了一个自定义管道来启用猕猴变体的注释，从而利用人类数据源，其中包括调节元件（ENCODE，RegulomeDB），已知的疾病或表型相关变体（GRASP），预期影响（SIFT，PolyPhen2）和序列保守（Pylop，PhastCons）。目前，mGAP包含与人类ClinVar数据库中列出的等位基因相同的2767个变异体，其中276个变异体跨越258个基因，被确定为致病性。预计有12,472个变体具有高影响力（SnpEff），有13,129个变体具有破坏性（PolyPhen2）。总体而言，这些变异预计与OMIM（人类在线孟德尔遗传）中报告的2000多种人类疾病或表型条目相关。重要的是，mGAP还可以为所有受试者提供基因型水平的数据，从而可以鉴定出具有相关等位基因的特定个体。 mGAP资源提供了数百个恒河猴的变体和基因型数据，并在所有受试者中以一致的方式进行了处理（https://mgap.ohsu.edu）。与广泛的变体注释一起，mGAP提供了前所未有的机会来研究与当前表征的疾病模型的潜在遗传关联，并发现与人类风险等位基因相似的新猕猴模型。

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