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首页> 外文期刊>Journal of genetics >Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium
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Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium

机译：将在1000个基因组计划中检测到的遗传变异与国际HapMap联盟确定的SNP进行比较

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摘要

Single-nucleotide polymorphisms (SNPs) determined based on SNP arrays from the international HapMap consortium (HapMap) and the genetic variants detected in the 1000 genomes project (1KGP) can serve as two references for genomewide association studies (GWAS). We conducted comparative analyses to provide a means for assessing concerns regarding SNP array-based GWAS findings as well as for realistically bounding expectations for next generation sequencing (NGS)-based GWAS. We calculated and compared base composition, transitions to transversions ratio, minor allele frequency and heterozygous rate for SNPs from HapMap and 1KGP for the 622 common individuals. We analysed the genotype discordance between HapMap and 1KGP to assess consistency in the SNPs from the two references. In 1KGP, 90.58% of 36,817,799 SNPs detected were not measured in HapMap. More SNPs with minor allele frequencies less than 0.01 were found in 1KGP than HapMap. The two references have low discordance (generally smaller than 0.02) in genotypes of common SNPs, with most discordance from heterozygous SNPs. Our study demonstrated that SNP array-based GWAS findings were reliable and useful, although only a small portion of genetic variances were explained. NGS can detect not only common but also rare variants, supporting the expectation that NGS-based GWAS will be able to incorporate a much larger portion of genetic variance than SNP arrays-based GWAS.
机译：基于国际HapMap联盟（HapMap）的SNP阵列确定的单核苷酸多态性（SNP）和在1000个基因组计划（1KGP）中检测到的遗传变异可以作为全基因组关联研究（GWAS）的两个参考。我们进行了比较分析，以提供一种评估对基于SNP阵列的GWAS发现的担忧以及对基于下一代测序（NGS）的GWAS的现实期望的方法。我们计算并比较了622个常见个体的HapMap和1KGP的SNP的碱基组成，转变转化率，次要等位基因频率和杂合率。我们分析了HapMap和1KGP之间的基因型不一致，以评估两个参考文献中SNP的一致性。在1KGP中，在HapMap中未检测到36,817,799个SNP中的90.58％。在1KGP中发现的等位基因频率小于0.01的SNP比HapMap多。这两个参考文献在常见SNP的基因型中具有较低的不一致（通常小于0.02），与杂合性SNP的不一致最多。我们的研究表明，尽管仅解释了遗传变异的一小部分，但基于SNP阵列的GWAS结果是可靠且有用的。 NGS不仅可以检测到常见变异，而且还可以检测到罕见变异，这支持了基于NGS的GWAS能够比基于SNP阵列的GWAS整合更大比例的遗传变异的期望。

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