Recent genomic heritage in Scotland
Recent genomic heritage in Scotland
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DOI：
10.1186/s12864-015-1605-2
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发表时间：
2015-06-06
期刊：
影响因子：
4.4
通讯作者：
Haley, Chris S.
中科院分区：
文献类型：
--
作者：
Amador, Carmen;Huffman, Jennifer;Haley, Chris S.
背景资料：苏格兰一代苏格兰家庭健康研究（GS：SFHS）包括来自苏格兰各地的23，960名参与者，他们记录了许多与健康相关的特征和环境协变量。目前可用于10，000名参与者的基因型与700 K SNP相似。该队列被设计为遗传和健康相关研究以及复杂性状研究的资源。在这项研究中，我们开发了一套分析，以解开GS：SFHS个人的基因组分化，以描述和优化的样品和方法，为未来的analysis.Results：我们结合了GS：SFHS的基因型信息与1092个人从1000个基因组项目，并估计他们的基因组关系。然后，我们进行了主成分分析的结果关系，以调查不同群体的基因组起源。我们描述了两组个体的特征：基因组中有一些稀疏的罕见标记的个体，以及有几个大的罕见单倍型的个体，这些单倍型可能代表相对较近的外源性祖先。我们确定了一些可能具有意大利血统的个体和一个具有一些潜在的非洲/亚洲血统的群体。在GS：SFHS样本中的纯合性分析显示了与其他欧洲人群非常相似的模式。我们还确定了一个携带1号染色体单亲二体性的个体。我们发现的证据表明，当地的地理分层的人口内有影响的基因组structure.Conclusions：这些研究结果照亮了苏格兰人口的历史，并有影响，如研究的贡献，常见和罕见的变异性状遗传和疾病的基因组和表型预测的评估进一步分析。
Background: The Generation Scotland Scottish Family Health Study (GS:SFHS) includes 23,960 participants from across Scotland with records for many health-related traits and environmental covariates. Genotypes at similar to 700 K SNPs are currently available for 10,000 participants. The cohort was designed as a resource for genetic and health related research and the study of complex traits. In this study we developed a suite of analyses to disentangle the genomic differentiation within GS: SFHS individuals to describe and optimise the sample and methods for future analyses.Results: We combined the genotypic information of GS: SFHS with 1092 individuals from the 1000 Genomes project and estimated their genomic relationships. Then, we performed Principal Component Analyses of the resulting relationships to investigate the genomic origin of different groups. We characterised two groups of individuals: those with a few sparse rare markers in the genome, and those with several large rare haplotypes which might represent relatively recent exogenous ancestors. We identified some individuals with likely Italian ancestry and a group with some potential African/Asian ancestry. An analysis of homozygosity in the GS: SFHS sample revealed a very similar pattern to other European populations. We also identified an individual carrying a chromosome 1 uniparental disomy. We found evidence of local geographic stratification within the population having impact on the genomic structure.Conclusions: These findings illuminate the history of the Scottish population and have implications for further analyses such as the study of the contributions of common and rare variants to trait heritabilities and the evaluation of genomic and phenotypic prediction of disease.