A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them
A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them
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DOI：
10.1111/1755-0998.12502
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发表时间：
2016-07-01
影响因子：
7.7
通讯作者：
Hoffman, J. I.
中科院分区：
文献类型：
--
作者：
Humble, E.;Martinez-Barrio, A.;Hoffman, J. I.
定制基因分型阵列提供了一种灵活和准确的方法，对基本上任何生物体的大量个体中的单核苷酸多态性（SNP）进行基因分型。然而，验证率（定义为在群体中被验证为多态性的推定SNP的比例）通常非常低。已经确定了许多检测失败的潜在原因，但没有一个进行了系统的探索。特别是，由于SNP通常是从转录组中开发的，因此很少考虑与基因组背景相关的参数。在这里，我们组装了一个南极软毛海豹（Arctocephalus gazella）基因组草案（组装大小：2.41 Gb;支架/重叠群N-50：3.1 Mb/27.5 kb）。然后，我们使用这个资源映射探针序列的144个假定的SNPs基因分型在480个人。探针到基因组映射的数量和比对长度一起解释了验证成功率的近三分之一的变化，表明序列的独特性和与内含子-外显子边界的接近性起着重要作用。在将探针序列映射到海象和威德尔海豹基因组后发现了相同的模式，这表明物种的基因组差异高达2300万年，可以保存与SNP验证结果相关的信息。此外，对先前七项研究的基因分型数据的重新分析发现，相同的两个变量与各种分类群的SNP验证成功显著相关。最后，我们的研究揭示了验证率有待提高的相当大的范围，无论是通过简单地过滤其侧翼序列与参考基因组唯一且完全对齐的SNP，还是通过预测建模。
Custom genotyping arrays provide a flexible and accurate means of genotyping single nucleotide polymorphisms (SNPs) in a large number of individuals of essentially any organism. However, validation rates, defined as the proportion of putative SNPs that are verified to be polymorphic in a population, are often very low. A number of potential causes of assay failure have been identified, but none have been explored systematically. In particular, as SNPs are often developed from transcriptomes, parameters relating to the genomic context are rarely taken into account. Here, we assembled a draft Antarctic fur seal (Arctocephalus gazella) genome (assembly size: 2.41 Gb; scaffold/contig N-50: 3.1 Mb/27.5 kb). We then used this resource to map the probe sequences of 144 putative SNPs genotyped in 480 individuals. The number of probe-to-genome mappings and alignment length together explained almost a third of the variation in validation success, indicating that sequence uniqueness and proximity to intron-exon boundaries play an important role. The same pattern was found after mapping the probe sequences to the Walrus and Weddell seal genomes, suggesting that the genomes of species divergent by as much as 23 million years can hold information relevant to SNP validation outcomes. Additionally, reanalysis of genotyping data from seven previous studies found the same two variables to be significantly associated with SNP validation success across a variety of taxa. Finally, our study reveals considerable scope for validation rates to be improved, either by simply filtering for SNPs whose flanking sequences align uniquely and completely to a reference genome, or through predictive modelling.