Reply to: ZNF804A and schizophrenia: An open peer commentary

We read the comment by Dr. Sand on our recent article [Li et al., 2012], in which we confirmed a risk SNP rs359895 in the promoter region of ZNF804A for schizophrenia in Chinese population. Dr. Sand has raised some issues about the sample information, statistical test and others, but unfortunately all issues raised are purely subjective and speculative. We have presented the frequencies of the listed alleles in schizophrenia patients and controls in Table S2. An allele is simply defined as aminor allele if its frequency is lower than 0.5. Therefore, it is easy to tell the status of the listed alleles without needing extra information. In Table S2, the SNPs were called from the forward or reverse strand, which may lead to some misunderstanding. However, as long as the meta-analysis employed the allele calling from the same strand (which was indeed the case), this would not generate any bias for the association analyses. Similarly, previous studies on rs1344706 have also used allele callings from different DNA strand (A/C or G/T) [Hill and Bray, 2011;Walter et al., 2011]. For the speculated striking frequency differences from references for rs7557843 and rs17584522, it was totally a misunderstanding. For rs7557843, the T allele frequency is 0.4638 in Yuxi control sample, 0.4689 in Kunming control sample, 0.4644 in Beijing control sample, 0.4728 in Singapore control sample, and 0.5103 in Chinese according to data from the 1000-Human-Genome Project; also for rs17584522, the G allele frequency is 0.2173 in Yuxi control sample, and0.2473 inChinese from the 1000-HumanGenome Project. We did not observe any so-called ‘‘striking’’ differences. For the results of rs359895 in the combined Chinese samples, Dr. Sand calculated the P-values using allele counts directly, which is not a sound statistical analysis. It is well known that combined analysis using different samples should consider the site specific factors, and that is why we calculated the P-value using Cochran –Mantel–Haenszel test as already described in the Materials and Methods Section, and we are confident that the calculated P-value of rs359895 was correct. Due to the limited space for publication, the primer sequences, reference sequence specifications, and genotype raw data are all available upon request, which is a common practice for genetic association studies. Additionally, although we used different genotyping methods in different samples, we did not see obvious population stratification in our samples based on the presented analysis. We have stated in the paper that the genotyping success rate for the tested SNPs in all samples was over 96%. For the genotyping of rs359895 inour samples, this SNPhas been previously tested in the Kunming (404 cases and 607 controls) sample [Li et al., 2011], and the Kunming sample for rs359895 in Table II were based on the published data. In this study, we have collected extra samples from Kunming. This is why the Kunming sample inTable II is different from theKunming sample inTable S1. For the Beijing sample, 954 cases and 979 controls were genotyped for rs12693384 and rs7557843, and we also genotyped rs359895 in some additional Beijing samples besides the 954 cases and 979 controls. To avoid the misunderstanding, we showed the results of rs359895 in Table II, and the other SNPs in Table S2 separately. For the expression analysis of ZNF804A in schizophrenia patients and controls, we have stated in the paper that all the included subjects have no significant structural brain pathology, history of central nervous system disease, or drug abuse. For the schizophrenia patients, medication was stopped for 3 months and then the blood samples were collected, excluding the potential confounding effects caused by medication. Comparisons of differences in ZNF804A mRNA expression between SCZ patients and controls were analyzed by the Student’s t-test (two-tailed) with SPSS16.0 for Windows, we re-examined our data and there is no