Evaluation of coverage variation of SNP chips for genome-wide association studies
Evaluation of coverage variation of SNP chips for genome-wide association studies
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DOI：
10.1038/sj.ejhg.5202007
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发表时间：
2008-05-01
影响因子：
5.2
通讯作者：
Guan, Weihua
中科院分区：
文献类型：
--
作者：
Li, Mingyao;Li, Chun;Guan, Weihua
针对复杂人类疾病的全基因组关联（GWA）研究现在已经可行。许多GWA研究依赖于商业SNP芯片，其共同的评价标准是基因组的全球覆盖度。虽然提供了对 SNP 芯片的整体评估，但全局覆盖率并没有告诉我们覆盖率在整个基因组中如何变化，这是一个应该考虑的重要特征，因为覆盖率变化通常会导致功效变化，并在后续关联分析中可能导致搜索出现偏差。为了更全面地了解 SNP 芯片覆盖度，我们对覆盖度进行了详细评估，包括 (1) 局部覆盖度图 - 在小的连续基因组区域上计算；以及 (2) 基因覆盖度 - 对基因组中每个已知基因计算。这些评估可以揭示每个SNP芯片覆盖基因组的变异程度，并可以促进SNP芯片在更精细范围内的比较。
Genome-wide association ( GWA) studies for complex human diseases are now feasible. Many GWA studies rely on commercial SNP chips, for which a common evaluation criterion is global coverage of the genome. Although providing an overall evaluation of an SNP chip, the global coverage does not tell us how the coverage varies across the genome, an important feature that should be taken into consideration, as coverage variation often results in power variation and potentially biased search in subsequent association analysis. To achieve a fuller understanding of SNP chip coverage, we conducted detailed evaluation of coverage, including ( 1) a map of local coverage-calculated over small consecutive genomic regions and ( 2) gene coverage-calculated for each known gene in the genome. These evaluations can reveal the degree of variation of each SNP chip in covering the genome and can facilitate SNP chip comparisons at a finer scale.