Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors
Document Type
Article
Publication Date
5-2005
Department
Department of Mathematical Sciences
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
Publication Title
Genetic Epidemiology
Recommended Citation
Sha, Q.,
Dong, J.,
Jiang, R.,
Chen, H.,
&
Zhang, S.
(2005).
Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors.
Genetic Epidemiology,
28(4), 341-351.
http://doi.org/10.1002/gepi.20066
Retrieved from: https://digitalcommons.mtu.edu/michigantech-p/3634