Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors
Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors
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DOI：
10.1002/gepi.20066
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发表时间：
2005-05-01
影响因子：
2.1
通讯作者：
Zhang, SL
中科院分区：
文献类型：
--
作者：
Sha, QY;Dong, JP;Zhang, SL
本研究引入了新的单倍型共享传播/不平衡测试（hs - tdt），允许随机基因分型错误。我们在各种场景下评估了新提议测试的I型错误率和功率，并在提议测试、HS-TDT和单标记TDT之间进行了功率比较。结果表明，当剔除孟德尔不一致三元组或将孟德尔不一致标记作为缺失基因型处理时，HS-TDT显示I型误差显著增加，并且I型误差的幅度随着样本量的增加和基因分型错误率的增加而增加。结果还表明，一个简单的策略，即将每个罕见单倍型合并到一个最相似的常见单倍型，可以控制I型错误膨胀在很大范围内的基因分型错误率，并且在合并罕见单倍型后，测试的能力与没有合并罕见单倍型的测试非常相似。因此，我们得出结论，一个简单的策略可能使HS-TDT对基因分型错误具有鲁棒性。我们的模拟结果还表明，该策略也可能适用于其他基于单倍型的tdt。(c) 2005 Wiley-Liss, Inc。
The present study introduces new Haplotype Sharing Transmission/Disequilibrium Tests (HS-TDTs) that allow for random genotyping errors. We evaluate the type I error rate and power of the new proposed tests under a variety of scenarios and perform a power comparison among the proposed tests, the HS-TDT and the single-marker TDT. The results indicate that the HS-TDT shows a significant increase in type I error when applied to data in which either Mendelian inconsistent trios are removed or Mendelian inconsistent markers are treated as missing genotypes, and the magnitude of the type I error increases both with an increase in sample size and with an increase in genotyping error rate. The results also show that a simple strategy, that is, merging each rare haplotype to a most similar common haplotype, can control the type I error inflation for a wide range of genotyping error rates, and after merging rare haplotypes, the power of the test is very similar to that without merging the rare haplotypes. Therefore, we conclude that a simple strategy may make the HS-TDT robust to genotyping errors. Our simulation results also show that this strategy may also be applicable to other haplotype-based TDTs. (c) 2005 Wiley-Liss, Inc.