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首页> 外文会议>Pacific symposium on biocomputing >ON THE POWER TO DETECT SNP/PHENOTYPE ASSOCIATION IN CANDIDATE QUANTITATIVE TRAIT LOCI GENOMIC REGIONS: A SIMULATION STUDY
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ON THE POWER TO DETECT SNP/PHENOTYPE ASSOCIATION IN CANDIDATE QUANTITATIVE TRAIT LOCI GENOMIC REGIONS: A SIMULATION STUDY

机译：关于候选定量特征在候选定量性状基因组区域中SNP /表型关联的能力：模拟研究

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We use coalescent methods to investigate the ability of linked neutral 'markers" to reveal in simulated population samples the presence of one or more single nucleotide polymorphisms that is contributing to a trait having a complex genetic basis (QTN: quantitative trait nucleotide). Realistic mutation and recombination rates in our simulations allow us to generate SNP data appropriate for analyzing human variation across short chromosomal intervals corresponding to approximately 100 kilobases. We investigate the performance of both single marker and multiple-marker (haplotype) data for several ad hoc procedures. Our results with single SNP markers indicate that (1) the density of SNP markers need not be much higher than 10% in order to achieve near-maximal detection of a QTN; (2) a higher density of markers does not improve much on the ability to localize a QTN within an interval unless the recombination rate is high. Haplotype-based tests were investigated for the case in which more than one QTN is present in the studied interval. Larger sample sizes improve both the probability of detecting the haplotype with the largest number of QTNs, as well as the ability to infer correct haplotypes from genotypic data. Testing a series of short haplotypes across a longer interval can also be beneficial. The rate of false positives (i.e., when the most significant haplotype does not contain the greatest number of QTNs in the sample) can be very high when the contribution of individual QTNs to a trait is small. The elimination of low-frequency haplotypes does not substantially reduce the probability of detecting the haplotype with the largest number of QTNs but it can reduce the rate of false positives.
机译：我们使用结段方法来研究链接中性'标志物在模拟人群中揭示的能力样本存在一种或多种单一核苷酸多态性的存在，这些单一核苷酸多态性有助于具有复杂遗传基础的性状（QTN：定量性状核苷酸）。现实突变我们的模拟中的重组率允许我们产生适合于分析对应于约100千碱基的短染色体间隔的人类变异的SNP数据。我们研究了单个标记和多标记（单倍型）数据的若干临时程序的性能。我们的单个SNP标记的结果表明（1）SNP标记的密度不需要高于10％，以便实现QTN的近乎最大地检测;（2）更高的标记密度不会提高能力很大在间隔内定位QTN，除非重组率高。对案件的情况研究了基于单倍型的测试汉一个QTN存在于学习间隔中。较大的样本尺寸可以提高检测单倍型的概率，以QTN的最大数量，以及从基因型数据中推断正确的单倍型的能力。在较长间隔中测试一系列短单倍型也可能是有益的。当个体QTN与特征的贡献很小时，误报（即，当最重要的单倍型不含最大数量的QTN时，最重要的单倍型不含最大的QTN）的速率就会非常高。消除低频单倍型不会显着降低具有最大数量的QTN的单倍型的概率，但它可以降低误报的速率。

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