Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors.
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.
Sha
Qiuying
Q
Department of Mathematical Sciences, Michigan Technological University, Houghton 49931, USA.
Dong
Jianping
J
Jiang
Renfang
R
Chen
Huann-Sheng
HS
Zhang
Shuanglin
S
D000465:Algorithms; D003198:Computer Simulation; D005819:Genetic Markers; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D040582:Inheritance Patterns / Q000235:genetics; D015810:Linkage Disequilibrium; D008957:Models, Genetic
D005819:Genetic Markers