Premium
Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors
Author(s) -
Sha Qiuying,
Dong Jianping,
Jiang Renfang,
Chen HuannSheng,
Zhang Shuanglin
Publication year - 2005
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.20066
Subject(s) - genotyping , haplotype , type i and type ii errors , biology , statistics , genetics , disequilibrium , linkage disequilibrium , allele , genotype , mathematics , medicine , gene , ophthalmology
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.