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Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors.

Qiuying Sha·Jianping Dong·Renfang Jiang·Huann-Sheng Chen·Shuanglin Zhang
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Abstract

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.

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AlgorithmsComputer SimulationGenetic MarkersGenotypeHaplotypesHumansInheritance PatternsLinkage DisequilibriumModels, GeneticJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, U.S. Gov't, P.H.S.

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Qiuying Sha, Jianping Dong, Renfang Jiang, Huann-Sheng Chen, Shuanglin Zhang. 2005. Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors.. https://doi.org/10.1002/gepi.20066

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