Reply to Knapp and Becker

To the Editor:Knapp and Becker (2004xImpact of genotyping error on type I error rate of the haplotype-sharing transmission /disequilibrium test (HS-TDT). Knapp, M and Becker, T. Am J Hum Genet. 2004; 74: 589–591Abstract | Full Text | Full Text PDF | PubMed | Scopus (25)See all References2004 [in this issue]) have argued that genotyping errors may lead to an inflated type I error rate for the haplotype-sharing transmission/disequilibrium test (HS-TDT) that we proposed (Zhang et al.2003xTransmission/disequilibrium test based on haplotype sharing for tightly linked markers. Zhang, S, Sha, Q, Chen, HS, Dong, J, and Jiang, R. Am J Hum Genet. 2003; 73: 566–579Abstract | Full Text | Full Text PDF | PubMed | Scopus (61)See all References2003). The reason is that transmitted haplotypes are partially checked for genotyping errors by Mendelian inconsistency (MI), whereas there is no such checking at all for nontransmitted haplotypes. As a result of the unbalanced checking for genotyping errors, nontransmitted haplotypes appear less similar than transmitted haplotypes, which may lead to an inflated type I error rate for the HS-TDT. This is especially true for cases in which there is only one child per nuclear family. As noted by Gordon et al. (2001xA transmission/disequilibrium test that allows for genotyping errors in the analysis of single-nucleotide polymorphism data. Gordon, D, Heath, SC, Liu, X, and Ott, J. Am J Hum Genet. 2001; 69: 371–380Abstract | Full Text | Full Text PDF | PubMed | Scopus (121)See all References2001), the original TDT also has this problem. The HS-TDT that we proposed is applicable to any size of nuclear family and to different traits. To quantify the magnitude of type I error inflation of HS-TDT, Knapp and Becker (2004xImpact of genotyping error on type I error rate of the haplotype-sharing transmission /disequilibrium test (HS-TDT). Knapp, M and Becker, T. Am J Hum Genet. 2004; 74: 589–591Abstract | Full Text | Full Text PDF | PubMed | Scopus (25)See all References2004) performed a simulation study of nuclear families with one child. In fact, the magnitude of the type I error inflation caused by the unbalanced checking of the genotyping errors depends on the genotyping error rate as well as the following factors: 1.The number of children. If there is more than one child in the nuclear family, the genotyping errors in the haplotypes that do not transmit to the first child may be still detectable because these haplotypes may transmit to the other children. So, the inclusion of families with more than one child can reduce the type I error inflation.2.The allele frequencies. A smaller minor allele frequency will lead to a larger probability of homozygous genotypes and, therefore, a larger probability of detectable genotyping errors (MI). Consequently, it will lead to larger type I error inflation (see table 3 of Gordon et al. 2001xA transmission/disequilibrium test that allows for genotyping errors in the analysis of single-nucleotide polymorphism data. Gordon, D, Heath, SC, Liu, X, and Ott, J. Am J Hum Genet. 2001; 69: 371–380Abstract | Full Text | Full Text PDF | PubMed | Scopus (121)See all References2001). For HS-TDT, a marker with a small minor allele frequency in the middle part of the haplotype has a bigger effect than a marker with a small minor allele frequency in the edge part of the haplotype.3.The haplotype similarity measure.We believe that the reasons for the high type I error rate of HS-TDT in Knapp and Becker’s simulation studies are the following: (1) only families with one child were used; (2) the minor allele frequencies are small for the markers in the middle part of the haplotypes (for the total 19 markers, the minor allele frequencies from marker 7 to marker 16 are 0.16, 0.125, 0.143, 0.143, 0.11, 0.268, 0.089, 0.143, 0.143, and 0.036, respectively); and (3) the haplotype similarity measure that we proposed in Zhang et al. 2003xTransmission/disequilibrium test based on haplotype sharing for tightly linked markers. Zhang, S, Sha, Q, Chen, HS, Dong, J, and Jiang, R. Am J Hum Genet. 2003; 73: 566–579Abstract | Full Text | Full Text PDF | PubMed | Scopus (61)See all References2003 is not robust to genotyping errors. To compare the different haplotype similarity measures, we propose another measure (called “new similarity measure”) as follows. For two haplotypes, H and h, let Hi (hi) denote the allele of the haplotype H (h) at marker i. To find the similarity measure of the two haplotypes around marker i, we compare alleles of the two haplotypes in the right-hand markers, beginning with marker i+1, until marker i+r satisfies Hi+r≠hi+r and either Hi+r+1≠hi+r+1 or Hi+r+2≠hi+r+2. Then, similarly, we compare alleles of the two haplotypes in the left-hand markers, beginning with marker i-1, until marker i-l satisfies Hi-l≠hi-l and either Hi-l-1≠hi-l-1 or Hi-l-2≠hi-l-2. The new similarity measure is defined as the distance between marker i-l and marker i+r. Note that a genotyping error that occurs at one marker but does not occur at the nearby markers will not affect the new similarity measure. The probability that genotyping errors will occur in several consecutive markers is very small. To compare the effect of the number of children and different haplotype similarity measures, we performed simulation studies in which we used the data and the error options EO2 and EO3 given by Knapp and Becker (2003). We did not use EO1 because our program automatically deletes the families with MI genotyping errors. The simulation results are summarized in table 1table 1. This table reveals that, if there are three children in each of the nuclear families, a good agreement between the nominal and estimated type I error rate is evident for all the simulated samples. In the case of one child per family, the inflation of the type I error rate is greatly reduced by using the new similarity measure. We currently are investigating methods that are more robust to genotyping errors.Table 1Parameters and Results of Simulation Study of Type I Error Rate of HS-TDT in the Presence of Genotyping ErrorType I Error Rate forParametersEO2EO3Similarity MeasureNo. of Children/ FamilyNo. of Nuclear Families/ SampleTyping Error Rate (e)α=.05aaα=.01aaα=.05aaα=.01aaOriginal:1100.01.457.227.364.1471100.005.228.08.193.0751200.005.364.147.315.1203100.01.053.012.06.0163100.005.056.013.046.0113200.005.044.008.053.006New:1100.01.117.037.092.0191100.005.079.016.073.0141200.005.081.016.101.0293100.01.059.016.042.0063100.005.059.015.043.0093200.005.047.010.045.003Note.—The “original similarity measure” refers to the one used by Zhang et al. (2003xTransmission/disequilibrium test based on haplotype sharing for tightly linked markers. Zhang, S, Sha, Q, Chen, HS, Dong, J, and Jiang, R. Am J Hum Genet. 2003; 73: 566–579Abstract | Full Text | Full Text PDF | PubMed | Scopus (61)See all References2003). Simulation studies were based on 1,000 replicated samples.aα = nominal type I error rate.