Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors
✍ Scribed by Qiuying Sha; Jianping Dong; Renfang Jiang; Huann-Sheng Chen; Shuanglin Zhang
- Publisher
- John Wiley and Sons
- Year
- 2005
- Tongue
- English
- Weight
- 156 KB
- Volume
- 28
- Category
- Article
- ISSN
- 0741-0395
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✦ Synopsis
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. Genet. Epidemiol. © 2005 Wiley‐Liss, Inc.